Mon Apr 22 11:27:27 UTC 2024 I: starting to build rna-star/trixie/arm64 on jenkins on '2024-04-22 11:27' Mon Apr 22 11:27:27 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/14655/console.log Mon Apr 22 11:27:27 UTC 2024 I: Downloading source for trixie/rna-star=2.7.11b+dfsg-1 --2024-04-22 11:27:27-- http://deb.debian.org/debian/pool/main/r/rna-star/rna-star_2.7.11b%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2174 (2.1K) [text/prs.lines.tag] Saving to: ‘rna-star_2.7.11b+dfsg-1.dsc’ 0K .. 100% 259M=0s 2024-04-22 11:27:27 (259 MB/s) - ‘rna-star_2.7.11b+dfsg-1.dsc’ saved [2174/2174] Mon Apr 22 11:27:27 UTC 2024 I: rna-star_2.7.11b+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rna-star Binary: rna-star Architecture: amd64 arm64 loong64 ppc64el mips64el Version: 2.7.11b+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Sascha Steinbiss , Homepage: https://github.com/alexdobin/STAR/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/rna-star Vcs-Git: https://salsa.debian.org/med-team/rna-star.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libhts-dev, xxd, zlib1g-dev, libsimde-dev Package-List: rna-star deb science optional arch=amd64,arm64,loong64,ppc64el,mips64el Checksums-Sha1: afb7185ca0a5fb12a0997f2aa90081cd4dd33c03 520964 rna-star_2.7.11b+dfsg.orig.tar.xz 5a7b46946e7c6d1be4b1528572311e63530f6fbe 379268 rna-star_2.7.11b+dfsg-1.debian.tar.xz Checksums-Sha256: b06b9c0074fd7ab018edf7549582ee4ae29ed807aa8238811d888bf9ff73eaab 520964 rna-star_2.7.11b+dfsg.orig.tar.xz 274ebcfc4a94c723c235f25b4339327859bc4a3f8d307fc8580413807bc9ef5f 379268 rna-star_2.7.11b+dfsg-1.debian.tar.xz Files: 003d1d688848cbc667285f514a8b62b5 520964 rna-star_2.7.11b+dfsg.orig.tar.xz aac759b75fd5702c49f96f20af1d2fbd 379268 rna-star_2.7.11b+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEESjHbWh7kCWyHOZiAkDZJKUwz+bcFAmXGUhQACgkQkDZJKUwz +bfTbRAAp97flBVsfkw0gFQsehWVkTn0eWE1Iq4ANPrymOWP4wyS0+iEZN1dT2RJ l1qOp5nv7EpStlQxo0qGqNltGwocQWFIAAxC115R+7CyGHNuyuvMgUjVJsP3oU4k uQ6LT4yceh/84aTCGLhGeTHoTNJE38NzKA3dr9zyWGBErXXSWTcEQuUdVk87/N97 KBcFOpT4Qy2SlQ0uQkZJdOYi17DwJKNmnBTTdymETiv/GpMcYg7L5TgyMs2PMv6+ e0+/8DwmXZV46QdtMlpQUjptkQn4kL7AhQ64t21DfTbVcD2YEPpO246CHkEdsGpm ogEluMvCBNZcXhfazdxBs4gsp5shuHH1qTnPiZd5k/a341toy+sPlbrUzEM3anDY uzE9BGguVYpVVP0ZiyDKVHXXTljAeaZt/PFHKcATA8DKEcE0HuZPVb+byavdLQ+j Eg+jkwxc452lIKAZyiUGPQQhMwUxSkqk27I/UqUiarB8R7Nqlk4Z5Loy566m+pK5 JiB+op3/4IUoaS89jR046zPHNNNE4cMijU+uKYvIIKIt+tMLaqgF3Iiez2QfZU8b afWqYRbO8IKVimxk2abpUmv4blzcrA18rlOLilTOe2FTQ+VBuq4kMZpwxwvfrFnx vZo7pQAGwTIrxonpfxgG8cNnyMCBknEINRMWzqrNIwYmTtGKWww= =F6Mc -----END PGP SIGNATURE----- Mon Apr 22 11:27:27 UTC 2024 I: Checking whether the package is not for us Mon Apr 22 11:27:27 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Mon Apr 22 11:27:27 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Mon Apr 22 11:31:02 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 21 23:27:30 -12 2024 I: pbuilder-time-stamp: 1713785250 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/533727/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='805b11cc2c914c1e8db7a97fd53ebca9' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='533727' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.r7MXFmYJ/pbuilderrc_VcVc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.r7MXFmYJ/b1 --logfile b1/build.log rna-star_2.7.11b+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:16 /bin -> usr/bin I: user script /srv/workspace/pbuilder/533727/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libhts-dev, 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 ... 19930 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on xxd; however: Package xxd is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} xxd{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 24.4 MB of archives. After unpacking 101 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3 [1127 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1 arm64 0.190-1+b1 [175 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libpsl5 arm64 0.21.2-1+b1 [59.0 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libssh2-1 arm64 1.11.0-4 [206 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libcurl3-gnutls arm64 8.5.0-2 [394 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.5.0-2 [510 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libhts3 arm64 1.19+ds-1 [412 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3+b1 [916 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.19+ds-1 [1603 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libsimde-dev all 0.8.0-1 [458 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 xxd arm64 2:9.1.0016-1 [94.0 kB] Fetched 24.4 MB in 0s (159 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 ... 19930 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%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_arm64.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/rna-star-2.7.11b+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rna-star_2.7.11b+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 arm64 debian/rules clean dh clean --sourcedirectory=source dh_auto_clean -O--sourcedirectory=source cd source && make -j12 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' dh_auto_build -- 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 -mbranch-protection=standard -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 -mbranch-protection=standard -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR STARlong cd source && make -j12 "INSTALL=install --strip-program=true" "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 -mbranch-protection=standard -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 -mbranch-protection=standard -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR STARlong make[2]: Entering directory '/build/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Transcriptome_classifyAlign.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -O3 -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 -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' GTF.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' Variation.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 -mbranch-protection=standard -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 -mbranch-protection=standard -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' ReadAlign_waspMap.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.11b+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -D'COMPILATION_TIME_PLACE="2024-02-09T16:04:19+00:00 "' bam_cat.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -O3 -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); | ~~~~~~~~~~^~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedFlush()': BAMoutput.cpp:72:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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) { | ^ 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 '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 '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) | ^ make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg/source' 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' debian/tests/run_test.sh /build/reproducible-path/rna-star-2.7.11b+dfsg/source/STAR /build/reproducible-path/rna-star-2.7.11b+dfsg/source/STAR --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.11b+dfsg/debian/tests/foo.gtf STAR version: 2.7.11b compiled: 2024-02-09T16:04:19+00:00 Apr 22 11:30:25 ..... started STAR run Apr 22 11:30:25 ... starting to generate Genome files Apr 22 11:30:25 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Apr 22 11:30:25 ... starting to sort Suffix Array. This may take a long time... Apr 22 11:30:25 ... sorting Suffix Array chunks and saving them to disk... Apr 22 11:30:25 ... loading chunks from disk, packing SA... Apr 22 11:30:25 ... finished generating suffix array Apr 22 11:30:25 ... generating Suffix Array index Apr 22 11:30:25 ... completed Suffix Array index Apr 22 11:30:25 ... writing Genome to disk ... Apr 22 11:30:25 ... writing Suffix Array to disk ... Apr 22 11:30:25 ... writing SAindex to disk Apr 22 11:30:26 ..... finished successfully /build/reproducible-path/rna-star-2.7.11b+dfsg/source/STAR --runThreadN 1 --genomeDir . --readFilesIn reads.fastq STAR version: 2.7.11b compiled: 2024-02-09T16:04:19+00:00 Apr 22 11:30:26 ..... started STAR run Apr 22 11:30:26 ..... loading genome Apr 22 11:30:26 ..... started mapping Apr 22 11:30:26 ..... finished mapping Apr 22 11:30:26 ..... finished successfully make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=source dh_prep -O--sourcedirectory=source debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_install source/STAR source/STARlong usr/bin/ make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_installdocs -O--sourcedirectory=source dh_installchangelogs -O--sourcedirectory=source dh_installman -O--sourcedirectory=source dh_installsystemduser -O--sourcedirectory=source dh_perl -O--sourcedirectory=source dh_link -O--sourcedirectory=source dh_strip_nondeterminism -O--sourcedirectory=source debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_fixperms -O--sourcedirectory=source dh_missing -O--sourcedirectory=source dh_dwz -a -O--sourcedirectory=source dh_strip -a -O--sourcedirectory=source dh_makeshlibs -a -O--sourcedirectory=source dh_shlibdeps -a -O--sourcedirectory=source dh_installdeb -O--sourcedirectory=source debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.0-1), " make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.11b+dfsg' dh_md5sums -O--sourcedirectory=source dh_builddeb -O--sourcedirectory=source dpkg-deb: building package 'rna-star' in '../rna-star_2.7.11b+dfsg-1_arm64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.11b+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rna-star_2.7.11b+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../rna-star_2.7.11b+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/533727 and its subdirectories I: Current time: Sun Apr 21 23:30:59 -12 2024 I: pbuilder-time-stamp: 1713785459 Mon Apr 22 11:31:03 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Mon Apr 22 11:31:03 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Mon Apr 22 11:34:30 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Mon Apr 22 11:34:31 UTC 2024 I: rna-star_2.7.11b+dfsg-1_arm64.changes: Format: 1.8 Date: Fri, 09 Feb 2024 23:04:19 +0700 Source: rna-star Binary: rna-star rna-star-dbgsym Architecture: arm64 Version: 2.7.11b+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Lance Lin Description: rna-star - ultrafast universal RNA-seq aligner Closes: 1045634 Changes: rna-star (2.7.11b+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * d/rules: Remove override_dh_auto_clean * d/clean: Remove generated files (Closes: #1045634) * d/patches: Add patch to fix typos Checksums-Sha1: 5769008c7f123d18ea2bd3ace12d0df0b7fb5adb 17105332 rna-star-dbgsym_2.7.11b+dfsg-1_arm64.deb f5c27b075a7d9f2828317a703a0b3b87db0b7766 6257 rna-star_2.7.11b+dfsg-1_arm64.buildinfo 1c2a3a98d72bd16e860b268e45a31659f343d76b 711568 rna-star_2.7.11b+dfsg-1_arm64.deb Checksums-Sha256: e6396161d0faf4eddd66cf10597f5d8a82755ae3ffab87f0b6f185daf8808f7b 17105332 rna-star-dbgsym_2.7.11b+dfsg-1_arm64.deb ab3b06ed6898d874b674a72733c885fbb304772c4529307925ac57dd8035aa2c 6257 rna-star_2.7.11b+dfsg-1_arm64.buildinfo fb104b84e991f5253232a98301b5666fb03159e1e7f5e267cbebc895864c01a6 711568 rna-star_2.7.11b+dfsg-1_arm64.deb Files: 963d1b8c56eed4bd26632b000d42284c 17105332 debug optional rna-star-dbgsym_2.7.11b+dfsg-1_arm64.deb 08bc2baf7d70dac6d4ed8ad4b7f67b28 6257 science optional rna-star_2.7.11b+dfsg-1_arm64.buildinfo 244ab031ccfb6c79f1a413fa0b105fd8 711568 science optional rna-star_2.7.11b+dfsg-1_arm64.deb Mon Apr 22 11:34:32 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_10-14655.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.r7MXFmYJ/rna-star_2.7.11b+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.r7MXFmYJ/rna-star_2.7.11b+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.r7MXFmYJ/rna-star_2.7.11b+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.r7MXFmYJ/b1/rna-star_2.7.11b+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.r7MXFmYJ/b2/rna-star_2.7.11b+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.505s) 0.505s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.199s) 0.199s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 807ms CPU time consumed: 807ms Mon Apr 22 11:34:33 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 22 11:34:33 UTC 2024 I: rna-star from trixie built successfully and reproducibly on arm64. Mon Apr 22 11:34:35 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Apr 22 11:34:35 UTC 2024 I: Submitting 8.0K b1/rna-star_2.7.11b+dfsg-1_arm64.buildinfo.asc Mon Apr 22 11:34:37 UTC 2024 I: Submitting 8.0K b2/rna-star_2.7.11b+dfsg-1_arm64.buildinfo.asc Mon Apr 22 11:34:37 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 22 11:34:37 UTC 2024 I: Done submitting .buildinfo files. Mon Apr 22 11:34:37 UTC 2024 I: Removing signed rna-star_2.7.11b+dfsg-1_arm64.buildinfo.asc files: removed './b1/rna-star_2.7.11b+dfsg-1_arm64.buildinfo.asc' removed './b2/rna-star_2.7.11b+dfsg-1_arm64.buildinfo.asc'