I: pbuilder: network access will be disabled during build I: Current time: Fri May 31 23:04:08 +14 2024 I: pbuilder-time-stamp: 1717146248 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_2.7.11b+dfsg-1.dsc] I: copying [./rna-star_2.7.11b+dfsg.orig.tar.xz] I: copying [./rna-star_2.7.11b+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Feb 9 16:25:56 2024 gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rna-star_2.7.11b+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting rna-star in rna-star-2.7.11b+dfsg dpkg-source: info: unpacking rna-star_2.7.11b+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.11b+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying mathRoutinesNotInScope.patch dpkg-source: info: applying do-not-enforce-avx2.patch dpkg-source: info: applying gcc-12.patch dpkg-source: info: applying packaged_simde dpkg-source: info: applying fix_typos.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/354062/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 31 09:04 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/354062/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/354062/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=4e464bfb0e76426fa3d99140cc40c995 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=354062 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HTDRYzvN/pbuilderrc_Thvf --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HTDRYzvN/b2 --logfile b2/build.log rna-star_2.7.11b+dfsg-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 28 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/354062/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libhts-dev, xxd, zlib1g-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on xxd; however: Package xxd is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} xxd{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 25.7 MB of archives. After unpacking 101 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.1-2 [94.2 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 35 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.8.0-1 [434 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.8.0-1 [540 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 xxd amd64 2:9.1.0377-1 [94.8 kB] Fetched 25.7 MB in 1s (50.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.1-2_amd64.deb ... Unpacking bsdextrautils (2.40.1-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../29-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../30-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../31-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../32-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../33-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../34-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../35-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../36-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../37-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../38-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../39-libnghttp2-14_1.61.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../40-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../41-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../42-libssh2-1t64_1.11.0-5_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-5) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../43-libcurl3t64-gnutls_8.8.0-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.8.0-1) ... 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Unpacking liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../50-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../51-libhts-dev_1.19+ds-1.1+b1_amd64.deb ... Unpacking libhts-dev:amd64 (1.19+ds-1.1+b1) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../52-libsimde-dev_0.8.2-1_all.deb ... Unpacking libsimde-dev (0.8.2-1) ... Selecting previously unselected package xxd. Preparing to unpack .../53-xxd_2%3a9.1.0377-1_amd64.deb ... Unpacking xxd (2:9.1.0377-1) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libsimde-dev (0.8.2-1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-2) ... 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Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.8.0-1) ... Setting up libcurl4-gnutls-dev:amd64 (8.8.0-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libhts-dev:amd64 (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-11) ... 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: user script /srv/workspace/pbuilder/354062/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/354062/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/rna-star-2.7.11b+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rna-star_2.7.11b+dfsg-1_source.changes dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.11b+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=source dh_auto_clean -O--sourcedirectory=source cd source && make -j20 clean make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 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-2.7.11b+dfsg' mkdir --parents /build/reproducible-path/rna-star-2.7.11b+dfsg/debian/rna-star/usr/lib/rna-star/bin dh_auto_clean ; dh_auto_build -- SFX=-avx2 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 && dh_auto_clean ; dh_auto_build -- SFX=-avx CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx && dh_auto_clean ; dh_auto_build -- SFX=-sse4.1 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 && dh_auto_clean ; dh_auto_build -- SFX=-ssse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 && dh_auto_clean ; dh_auto_build -- SFX=-sse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 && true cd source && make -j20 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 "INSTALL=install --strip-program=true" SFX=-avx2 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funPrimaryAlignMark.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeOutLoad.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Chain.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:225:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bam_cat.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamRemoveDuplicates.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortUnmapped.cpp bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:78:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ 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 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx2 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 "INSTALL=install --strip-program=true" SFX=-avx "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funPrimaryAlignMark.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeOutLoad.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Stats.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_generateCigarP.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:225:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bam_cat.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' serviceFuns.cpp bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortUnmapped.cpp BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:78:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ 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()); | ~~~~~~^~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedFlush()': BAMoutput.cpp:72:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR-avx -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mavx systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 "INSTALL=install --strip-program=true" SFX=-sse4.1 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funPrimaryAlignMark.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_classifyAlign.cpp opal.cpp: In static member function 'static __mxxxi SimdSW::add(const __mxxxi&, const __mxxxi&)': opal.cpp:103:67: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 103 | static inline __mxxxi add(const __mxxxi& a, const __mxxxi& b) { return _mmxxx_adds_epi8(a, b); } | ^ In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function 'simde__m256i simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_transformGenome.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_alignScore.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_generateCigarP.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:225:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bam_cat.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMfunctions.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortUnmapped.cpp BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedFlush()': BAMoutput.cpp:72:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:78:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR-sse4.1 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse4.1 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse4.1 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 "INSTALL=install --strip-program=true" SFX=-ssse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funPrimaryAlignMark.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_classifyAlign.cpp opal.cpp: In static member function 'static __mxxxi SimdSW::add(const __mxxxi&, const __mxxxi&)': opal.cpp:103:67: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 103 | static inline __mxxxi add(const __mxxxi& a, const __mxxxi& b) { return _mmxxx_adds_epi8(a, b); } | ^ In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function 'simde__m256i simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_findSuperTr.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_alignScore.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ STAR.cpp: In function 'int main(int, char**)': STAR.cpp:225:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bam_cat.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' serviceFuns.cpp bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortUnmapped.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:78:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedFlush()': BAMoutput.cpp:72:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR-ssse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-ssse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -mssse3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 "INSTALL=install --strip-program=true" SFX=-sse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funPrimaryAlignMark.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_classifyAlign.cpp opal.cpp: In static member function 'static __mxxxi SimdSW::add(const __mxxxi&, const __mxxxi&)': opal.cpp:103:67: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 103 | static inline __mxxxi add(const __mxxxi& a, const __mxxxi& b) { return _mmxxx_adds_epi8(a, b); } | ^ In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function 'simde__m256i simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, long long unsigned int, int&)': SuffixArrayFuns.cpp:234:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 234 | register int64 ii; | ^~ SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': SuffixArrayFuns.cpp:359:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 359 | register uint saind=0; | ^~~~~ SuffixArrayFuns.cpp:362:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~ SuffixArrayFuns.cpp:365:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 365 | register char g2=(char) g1; | ^~ SuffixArrayFuns.cpp:379:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersGenome.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:225:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bam_cat.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortUnmapped.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:78:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedFlush()': BAMoutput.cpp:72:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o STAR-sse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -msse3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' dh_auto_clean ; dh_auto_build -- SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -j20 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cd source && make -j20 "INSTALL=install --strip-program=true" SFX=-plain "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.7.11b+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' systemFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funPrimaryAlignMark.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_classifyAlign.cpp opal.cpp: In static member function 'static __mxxxi SimdSW::add(const __mxxxi&, const __mxxxi&)': opal.cpp:103:67: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 103 | static inline __mxxxi add(const __mxxxi& a, const __mxxxi& b) { return _mmxxx_adds_epi8(a, b); } | ^ In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function 'simde__m256i simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_waspMap.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:225:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bam_cat.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+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 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' BAMbinSortUnmapped.cpp BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:78:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ 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()); | ~~~~~~^~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedFlush()': BAMoutput.cpp:72:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now Transcript.h:10:7: warning: type 'struct Transcript' violates the C++ One Definition Rule [-Wodr] 10 | class Transcript { | ^ Transcript.h:10:7: note: a different type is defined in another translation unit 10 | class Transcript { | ^ Transcript.h:12:10: note: the first difference of corresponding definitions is field 'exons' 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:12:10: note: a field of same name but different type is defined in another translation unit 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:10:7: note: array types have different bounds 10 | class Transcript { | ^ ReadAlign.h:22:7: warning: type 'struct ReadAlign' violates the C++ One Definition Rule [-Wodr] 22 | class ReadAlign { | ^ ReadAlign.h:22:7: note: a different type is defined in another translation unit 22 | class ReadAlign { | ^ ReadAlign.h:57:20: note: the first difference of corresponding definitions is field 'trA' 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ ReadAlign.h:57:20: note: a field of same name but different type is defined in another translation unit 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ Transcript.h:10:7: note: type 'struct Transcript' itself violates the C++ One Definition Rule 10 | class Transcript { | ^ ReadAlign.h:214:14: warning: type of 'calcCIGAR' does not match original declaration [-Wlto-type-mismatch] 214 | void calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate); | ^ ReadAlign_calcCIGAR.cpp:3:6: note: 'calcCIGAR' was previously declared here 3 | void ReadAlign::calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate) { | ^ In function 'min': lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] In function 'min': lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] lto-wrapper: warning: using serial compilation of 23 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information lto-wrapper: warning: using serial compilation of 23 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information In function 'searchDatabase_', inlined from 'searchDatabase' at opal/opal.cpp:1013:21, inlined from 'opalSearchDatabase' at opal/opal.cpp:1465:46, inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ In function 'opalSearchDatabase', inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:1450:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1450 | bool *skip = new bool[dbLength]; | ^ /usr/include/c++/13/new: In member function 'mapChunk': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'searchDatabase_', inlined from 'searchDatabase' at opal/opal.cpp:1013:21, inlined from 'opalSearchDatabase' at opal/opal.cpp:1465:46, inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ In function 'opalSearchDatabase', inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: opal/opal.cpp:1450:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1450 | bool *skip = new bool[dbLength]; | ^ /usr/include/c++/13/new: In member function 'mapChunk': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ opal/opal.cpp: In function 'min': opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ opal/opal.cpp: In function 'min': opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' cp source/STAR-plain source/STARlong-plain /build/reproducible-path/rna-star-2.7.11b+dfsg/debian/rna-star/usr/lib/rna-star/bin/ make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' set -i; for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ if lscpu | grep -q ${SIMD} ; then \ debian/tests/run_test.sh /build/reproducible-path/rna-star-2.7.11b+dfsg/source/STAR-${SIMD} ; \ fi ; done /bin/sh: line 1: set: -i: invalid option set: usage: set [-abefhkmnptuvxBCEHPT] [-o option-name] [--] [-] [arg ...] make[1]: *** [debian/rules:50: override_dh_auto_test] Error 2 make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+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: user script /srv/workspace/pbuilder/354062/tmp/hooks/C01_cleanup starting debug output: disk usage on i-capture-the-hostname at Fri May 31 09:21:57 UTC 2024 Filesystem Size Used Avail Use% Mounted on tmpfs 40G 0 40G 0% /dev/shm I: user script /srv/workspace/pbuilder/354062/tmp/hooks/C01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/354062 and its subdirectories