Tue Jul 21 07:09:41 UTC 2020 I: starting to build rna-star/buster/arm64 on jenkins on '2020-07-21 07:09' Tue Jul 21 07:09:41 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/12573/console.log Tue Jul 21 07:09:41 UTC 2020 I: Downloading source for buster/rna-star=2.7.0a+dfsg-1 --2020-07-21 07:09:41-- http://deb.debian.org/debian/pool/main/r/rna-star/rna-star_2.7.0a+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2166 (2.1K) Saving to: ‘rna-star_2.7.0a+dfsg-1.dsc’ 0K .. 100% 257M=0s 2020-07-21 07:09:41 (257 MB/s) - ‘rna-star_2.7.0a+dfsg-1.dsc’ saved [2166/2166] Tue Jul 21 07:09:41 UTC 2020 I: rna-star_2.7.0a+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: rna-star Binary: rna-star Architecture: amd64 arm64 ppc64el mips64el Version: 2.7.0a+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Sascha Steinbiss Homepage: https://github.com/alexdobin/STAR/ Standards-Version: 4.3.0 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 (>= 11), libhts-dev, vim-common, zlib1g-dev Package-List: rna-star deb science optional arch=amd64,arm64,ppc64el,mips64el Checksums-Sha1: ad75c4119ff0456610567526ab92303b1c1c0590 366860 rna-star_2.7.0a+dfsg.orig.tar.xz 8750164d22ea6998afab5fac7e1ca36cab0c1755 374944 rna-star_2.7.0a+dfsg-1.debian.tar.xz Checksums-Sha256: 05a7dc9dbf7d73a0d4b61821403d8082274a86f291d8782f79e62eceef86f23b 366860 rna-star_2.7.0a+dfsg.orig.tar.xz cc650464ac20bedac4e09a7d6a0ce2acb1f6425f8ec2597f462b524ea5a6414d 374944 rna-star_2.7.0a+dfsg-1.debian.tar.xz Files: 594ac9161a3e7c50633c1dde9c1ecc60 366860 rna-star_2.7.0a+dfsg.orig.tar.xz 4488bc797cab3bf84a967719be1cc092 374944 rna-star_2.7.0a+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAlxQ1LATHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0SKYD/9fgtzxqsZT0Wz3Bdm3/ghmKDOJ2Fa6 uJhY63JB//jtfAqi6lQku/b5RgEOKT5bLvzbQ841cCq0NuFnIVupX66hR32xKReu +u3KJlskhMiPvMCLLYrl1UOoAP+5QBNQ2c65pJSmzzj/Vwogz9yVojUC3i7zCjj6 KQEqrR1SdgPOeXTVDVTYuZVfitbS67epqGZMUDNCxT1oZxZ9NLEvr4KWL9O52Fa+ YVMIPCdVCtSxdlFQ/6FlgDmGeyeQH/WR3kyjlLkMj0P75Je6ixEkvuQ9QmVVCGyP ODP2QNRj1x1PtGI2OT+4yHwy5RHzNOxW8HCbK1cdZnv/is85bW3lF3/qUCC9akZq bWZqy/q0LeuAuv+B3kg5yMWJjz7vdVMUBKoZvBiwnk+fICXOOck0dRRegl8waUTx 6L3yh61NWGNql0EOTDeUTnGJxyyuD2It+wqoUhKpjXLgzDu1wCPgxZ1qVL9P79+y VIz7J7bwe+0U0ao3u4XAiKhYnp2IFMKu92ckLTm+ItB3BOUakpAtnU299PJJAzZg xvOO/cbgjnMtS1P+1ptKXS/4bkNDEUAOiRP0mQsr/PH4LewIMA1BHSE8Gr159Z/Q nilrzoe30Ovx+0bg+3LZBShduSmLzBWivOHanCjUq2pMId6olB4M4i1EIhDAYnDn RL/NqPf4uFjGTA== =Etje -----END PGP SIGNATURE----- Tue Jul 21 07:09:41 UTC 2020 I: Checking whether the package is not for us Tue Jul 21 07:09:41 UTC 2020 I: Starting 1st build on remote node codethink-sled10-arm64.debian.net. Tue Jul 21 07:09:41 UTC 2020 I: Preparing to do remote build '1' on codethink-sled10-arm64.debian.net. Tue Jul 21 07:17:04 UTC 2020 I: Deleting $TMPDIR on codethink-sled10-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 20 19:09:51 -12 2020 I: pbuilder-time-stamp: 1595315391 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [rna-star_2.7.0a+dfsg-1.dsc] I: copying [./rna-star_2.7.0a+dfsg.orig.tar.xz] I: copying [./rna-star_2.7.0a+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Jan 29 10:33:20 2019 -12 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.7.0a+dfsg-1.dsc dpkg-source: info: extracting rna-star in rna-star-2.7.0a+dfsg dpkg-source: info: unpacking rna-star_2.7.0a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.0a+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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31312/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='31312' 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/tmp.gcPuT4WEJu/pbuilderrc_bage --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.gcPuT4WEJu/b1 --logfile b1/build.log rna-star_2.7.0a+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled10-arm64 4.4.0-185-generic #215-Ubuntu SMP Mon Jun 8 21:55:24 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 19 20:26 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/31312/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 (>= 11), libhts-dev, vim-common, zlib1g-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 ... 19168 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 (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on vim-common; however: Package vim-common is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-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} bsdmainutils{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} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} vim-common{a} xxd{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info vim vim-athena vim-gtk vim-gtk3 vim-nox vim-tiny wget xdg-user-dirs 0 packages upgraded, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 27.2 MB of archives. After unpacking 85.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 xxd arm64 2:8.1.0875-5 [139 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 vim-common all 2:8.1.0875-5 [195 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u2 [216 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libcurl3-gnutls arm64 7.64.0-4+deb10u1 [310 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libdeflate0 arm64 1.2-1 [51.4 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libhts2 arm64 1.9-11 [277 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 liblzma-dev arm64 5.2.4-1 [209 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libhts-dev arm64 1.9-11 [4338 kB] Fetched 27.2 MB in 2s (12.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/rna-star-2.7.0a+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.0a+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/rna-star-2.7.0a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/build/rna-star-2.7.0a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/build/rna-star-2.7.0a+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/build/rna-star-2.7.0a+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/rna-star-2.7.0a+dfsg' cd source && /usr/bin/make CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/rna-star-2.7.0a+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp blocksOverlap.cpp SoloReadFeature_record.cpp ChimericDetection_chimericDetectionMult.cpp outputSJ.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp SoloReadBarcode_getCBandUMI.cpp signalFromBAM.cpp Chain.cpp ReadAlign_calcCIGAR.cpp sjdbLoadFromStream.cpp sjAlignSplit.cpp SoloReadFeature_inputRecords.cpp Parameters_closeReadsFiles.cpp ReadAlign_CIGAR.cpp SoloFeature_collapseUMI.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp ReadAlign_chimericDetection.cpp SoloRead_record.cpp BAMfunctions.cpp ReadAlign.cpp Genome_insertSequences.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp Transcript_generateCigarP.cpp ThreadControl.cpp BAMbinSortUnmapped.cpp ReadAlign_chimericDetectionOld.cpp sjdbInsertJunctions.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp BAMoutput.cpp SoloReadBarcode.cpp genomeParametersWrite.cpp ParametersSolo.cpp ChimericAlign.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_chimericDetectionOldOutput.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp ChimericAlign_chimericJunctionOutput.cpp genomeSAindex.cpp stringSubstituteAll.cpp ChimericDetection.cpp Transcript_variationOutput.cpp SharedMemory.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_oneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_outputVariation.cpp Parameters_readSAMheader.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp genomeScanFastaFiles.cpp ReadAlign_mapOneRead.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Genome_genomeGenerate.cpp Variation.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp readLoad.cpp binarySearch2.cpp SoloReadFeature.cpp Solo.cpp Transcriptome_geneCountsAddAlign.cpp sjdbPrepare.cpp ChimericSegment.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature.cpp Solo_outputResults.cpp BAMbinSortByCoordinate.cpp SoloReadFeature_getFeature.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp STAR.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp Transcriptome.cpp bam_cat.c Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp blocksOverlap.cpp SoloReadFeature_record.cpp ChimericDetection_chimericDetectionMult.cpp outputSJ.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp SoloReadBarcode_getCBandUMI.cpp signalFromBAM.cpp Chain.cpp ReadAlign_calcCIGAR.cpp sjdbLoadFromStream.cpp sjAlignSplit.cpp SoloReadFeature_inputRecords.cpp Parameters_closeReadsFiles.cpp ReadAlign_CIGAR.cpp SoloFeature_collapseUMI.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp ReadAlign_chimericDetection.cpp SoloRead_record.cpp BAMfunctions.cpp ReadAlign.cpp Genome_insertSequences.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp Transcript_generateCigarP.cpp ThreadControl.cpp BAMbinSortUnmapped.cpp ReadAlign_chimericDetectionOld.cpp sjdbInsertJunctions.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp BAMoutput.cpp SoloReadBarcode.cpp genomeParametersWrite.cpp ParametersSolo.cpp ChimericAlign.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_chimericDetectionOldOutput.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp ChimericAlign_chimericJunctionOutput.cpp genomeSAindex.cpp stringSubstituteAll.cpp ChimericDetection.cpp Transcript_variationOutput.cpp SharedMemory.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_oneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_outputVariation.cpp Parameters_readSAMheader.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp genomeScanFastaFiles.cpp ReadAlign_mapOneRead.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Genome_genomeGenerate.cpp Variation.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp readLoad.cpp binarySearch2.cpp SoloReadFeature.cpp Solo.cpp Transcriptome_geneCountsAddAlign.cpp sjdbPrepare.cpp ChimericSegment.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature.cpp Solo_outputResults.cpp BAMbinSortByCoordinate.cpp SoloReadFeature_getFeature.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp STAR.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp Transcriptome.cpp bam_cat.c 'rm' -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp blocksOverlap.cpp SoloReadFeature_record.cpp ChimericDetection_chimericDetectionMult.cpp outputSJ.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp SoloReadBarcode_getCBandUMI.cpp signalFromBAM.cpp Chain.cpp ReadAlign_calcCIGAR.cpp sjdbLoadFromStream.cpp sjAlignSplit.cpp SoloReadFeature_inputRecords.cpp Parameters_closeReadsFiles.cpp ReadAlign_CIGAR.cpp SoloFeature_collapseUMI.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp ReadAlign_chimericDetection.cpp SoloRead_record.cpp BAMfunctions.cpp ReadAlign.cpp Genome_insertSequences.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp Transcript_generateCigarP.cpp ThreadControl.cpp BAMbinSortUnmapped.cpp ReadAlign_chimericDetectionOld.cpp sjdbInsertJunctions.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp BAMoutput.cpp SoloReadBarcode.cpp genomeParametersWrite.cpp ParametersSolo.cpp ChimericAlign.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_chimericDetectionOldOutput.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp ChimericAlign_chimericJunctionOutput.cpp genomeSAindex.cpp stringSubstituteAll.cpp ChimericDetection.cpp Transcript_variationOutput.cpp SharedMemory.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_oneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_outputVariation.cpp Parameters_readSAMheader.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp genomeScanFastaFiles.cpp ReadAlign_mapOneRead.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Genome_genomeGenerate.cpp Variation.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp readLoad.cpp binarySearch2.cpp SoloReadFeature.cpp Solo.cpp Transcriptome_geneCountsAddAlign.cpp sjdbPrepare.cpp ChimericSegment.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature.cpp Solo_outputResults.cpp BAMbinSortByCoordinate.cpp SoloReadFeature_getFeature.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp STAR.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp Transcriptome.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 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_collapseUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' STAR.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:350:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(P.inOut->outBAMfileUnsorted); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:354:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(P.inOut->outQuantBAMfile); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' alignSmithWaterman.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' loadGTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::__cxx11::string, std::vector >)': Parameters_readSAMheader.cpp:26:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(com1.c_str()); ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -Wall -Wextra -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bam_cat.c bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] if (h) bam_hdr_write(fp, h); ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] 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] 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] 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] 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] 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] 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] bgzf_raw_write(fp, ebuf, es); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMoutput.cpp BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] 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] bgzf_write(bgzfBAM,bamArray,binBytes1); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMfunctions.cpp BAMfunctions.cpp: In function 'std::__cxx11::string bam_cigarString(bam1_t*)': BAMfunctions.cpp:12:25: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < c->n_cigar; ++i) { ~~^~~~~~~~~~~~ BAMfunctions.cpp: In function 'int bam_read1_fromArray(char*, bam1_t*)': BAMfunctions.cpp:59:16: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:76:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,"BAM\001",4); ~~~~~~~~~~^~~~~~~~~~~~~~~~ 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] bgzf_write(fp,(char*) &hlen,sizeof(hlen)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:79:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,samh.c_str(),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] bgzf_write(fp,(char*) &nchr,sizeof(nchr)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:85:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,(char*) &rlen,sizeof(rlen)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:86:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] bgzf_write(fp,(char*) &slen,sizeof(slen)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(fp); ~~~~~~~~~~^~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::__cxx11::string, Parameters&, Genome&)': BAMbinSortByCoordinate.cpp:66:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBin,ib, *((uint32*) ib)+sizeof(uint32) ); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:69:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfBin); ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::__cxx11::string, std::__cxx11::string, Parameters&)': bamRemoveDuplicates.cpp:125:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] bam_hdr_write(bgzfOut, bamHeader); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:152:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfOut,bamRaw,bamS); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:248:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfOut,bamRaw,bamLength); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:249:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfOut); ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::__cxx11::string, Parameters&, Genome&)': BAMbinSortUnmapped.cpp:52:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBin, bamIn[it], bamSize.at(it)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:69:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfBin); ~~~~~~~~~~^~~~~~~~~ g++ -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/rna-star-2.7.0a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_collapseUMI.o SoloFeature_outputResults.o SoloFeature_processRecords.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o InOutStreams.o SequenceFuns.o Genome.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 ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericStitching.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.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 -Bstatic -lhts -Bdynamic -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:61:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(("ls -lL " + rfName + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Parameters_openReadsFiles.cpp: In member function 'openReadsFiles': Parameters_openReadsFiles.cpp:33:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered] for (uint imate=0;imate../rna-star_2.7.0a+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) 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/31312 and its subdirectories I: Current time: Mon Jul 20 19:17:00 -12 2020 I: pbuilder-time-stamp: 1595315820 Tue Jul 21 07:17:06 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled15-arm64.debian.net. Tue Jul 21 07:17:06 UTC 2020 I: Preparing to do remote build '2' on codethink-sled15-arm64.debian.net. Tue Jul 21 07:25:16 UTC 2020 I: Deleting $TMPDIR on codethink-sled15-arm64.debian.net. Tue Jul 21 07:25:18 UTC 2020 I: rna-star_2.7.0a+dfsg-1_arm64.changes: Format: 1.8 Date: Tue, 29 Jan 2019 22:58:57 +0100 Source: rna-star Binary: rna-star rna-star-dbgsym Architecture: arm64 Version: 2.7.0a+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.7.0a+dfsg-1) unstable; urgency=medium . * New upstream release. This release introduces STARsolo for: mapping, demultiplexing and gene quantification for single cell RNA-seq. . * Standards-Version: 4.3.0 - no changes required Checksums-Sha1: 3f6b5a4872eb3375a17583b381c81b6cb7e9d3a0 7154768 rna-star-dbgsym_2.7.0a+dfsg-1_arm64.deb d880625b84c581adb8f609596adfac0a549289e8 5495 rna-star_2.7.0a+dfsg-1_arm64.buildinfo 67f183202840fbe2ec879547c69f00421107293c 418628 rna-star_2.7.0a+dfsg-1_arm64.deb Checksums-Sha256: 8dc330016d875144613e1d4fc4325208bd2919c08cddf7be3ebc7c7ba0acadd7 7154768 rna-star-dbgsym_2.7.0a+dfsg-1_arm64.deb a0891551265ed20f21afae7b501a19eb9b77821bd2f5d09597b049739bb06957 5495 rna-star_2.7.0a+dfsg-1_arm64.buildinfo d2c38a93f16c8c11127ff371612351f3350aee297962b6e59df44e1a2c857cb0 418628 rna-star_2.7.0a+dfsg-1_arm64.deb Files: 30dc4dd9fb7ac1bc06b89fb36850525c 7154768 debug optional rna-star-dbgsym_2.7.0a+dfsg-1_arm64.deb 89814aeea6b6284137d2548665fa3c8b 5495 science optional rna-star_2.7.0a+dfsg-1_arm64.buildinfo ce93be511c231edec1d9a573efb6888a 418628 science optional rna-star_2.7.0a+dfsg-1_arm64.deb Tue Jul 21 07:25:19 UTC 2020 I: diffoscope 152 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.gcPuT4WEJu/rna-star_2.7.0a+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.gcPuT4WEJu/rna-star_2.7.0a+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.gcPuT4WEJu/rna-star_2.7.0a+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.gcPuT4WEJu/b1/rna-star_2.7.0a+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.gcPuT4WEJu/b2/rna-star_2.7.0a+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: 0.335s) 0.335s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.123s) 0.122s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 21 07:25:21 UTC 2020 I: diffoscope 152 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 21 07:25:21 UTC 2020 I: rna-star from buster built successfully and reproducibly on arm64. Tue Jul 21 07:25:22 UTC 2020 I: Submitting .buildinfo files to external archives: Tue Jul 21 07:25:22 UTC 2020 I: Submitting 8.0K b1/rna-star_2.7.0a+dfsg-1_arm64.buildinfo.asc Tue Jul 21 07:25:23 UTC 2020 I: Submitting 8.0K b2/rna-star_2.7.0a+dfsg-1_arm64.buildinfo.asc Tue Jul 21 07:25:24 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 21 07:25:24 UTC 2020 I: Done submitting .buildinfo files. Tue Jul 21 07:25:24 UTC 2020 I: Removing signed rna-star_2.7.0a+dfsg-1_arm64.buildinfo.asc files: removed './b1/rna-star_2.7.0a+dfsg-1_arm64.buildinfo.asc' removed './b2/rna-star_2.7.0a+dfsg-1_arm64.buildinfo.asc'