https://launchpad.net/ubuntu/+source/rna-star/2.7.7a+dfsg-1/+build/20776818 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-041 4.15.0-129-generic #132-Ubuntu SMP Thu Dec 10 14:02:26 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 6 Jan 23:53:09 ntpdate[1833]: adjust time server 10.211.37.1 offset -0.000146 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20776818 --image-type chroot /home/buildd/filecache-default/720a8366e1260e086c1691fe6381a3f2b1c21d81 Creating target for build PACKAGEBUILD-20776818 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20776818 Starting target for build PACKAGEBUILD-20776818 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20776818 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20776818 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20776818 Updating target for build PACKAGEBUILD-20776818 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [269 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main amd64 Packages [1386 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe amd64 Packages [13.0 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5395 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 Packages [156 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [56.2 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 Packages [820 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [337 kB] Fetched 22.2 MB in 6s (3472 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libisl23 libperl5.32 libxxhash0 perl-modules-5.32 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils coreutils cpp-10 dash dpkg dpkg-dev fakeroot g++-10 gcc-10 gcc-10-base grep init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgomp1 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 liblz4-1 libmount1 libmpc3 libncurses6 libncursesw6 libnpth0 libp11-kit0 libpcre2-8-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login mount ncurses-base ncurses-bin openssl passwd perl perl-base readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata util-linux 105 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 86.0 MB of archives. After this operation, 54.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcrypt-dev amd64 1:4.4.17-1ubuntu1 [105 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6-dev amd64 2.32-0ubuntu6 [2131 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-dev-bin amd64 2.32-0ubuntu6 [30.9 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcrypt1 amd64 1:4.4.17-1ubuntu1 [78.8 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 linux-libc-dev amd64 5.8.0-34.37+21.04.1 [1138 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtirpc-common all 1.3.1-1 [7452 B] Get:7 http://ftpmaster.internal/ubuntu hirsute/main amd64 libk5crypto3 amd64 1.17-10ubuntu1 [79.2 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgssapi-krb5-2 amd64 1.17-10ubuntu1 [121 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main amd64 libkrb5-3 amd64 1.17-10ubuntu1 [332 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main amd64 libkrb5support0 amd64 1.17-10ubuntu1 [30.7 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu5 [1324 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtirpc-dev amd64 1.3.1-1 [183 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtirpc3 amd64 1.3.1-1 [76.9 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main amd64 libisl23 amd64 0.23-1 [652 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcc1-0 amd64 10.2.1-2ubuntu3 [48.7 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf0 amd64 2.35.50.20201218-1ubuntu3 [95.3 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf-nobfd0 amd64 2.35.50.20201218-1ubuntu3 [94.6 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.35.50.20201218-1ubuntu3 [1825 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libbinutils amd64 2.35.50.20201218-1ubuntu3 [576 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-common amd64 2.35.50.20201218-1ubuntu3 [216 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils amd64 2.35.50.20201218-1ubuntu3 [3388 B] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10-base amd64 10.2.1-2ubuntu3 [19.3 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-s1 amd64 10.2.1-2ubuntu3 [41.7 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgomp1 amd64 10.2.1-2ubuntu3 [102 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libitm1 amd64 10.2.1-2ubuntu3 [26.3 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libatomic1 amd64 10.2.1-2ubuntu3 [9288 B] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libasan6 amd64 10.2.1-2ubuntu3 [2060 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 liblsan0 amd64 10.2.1-2ubuntu3 [834 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtsan0 amd64 10.2.1-2ubuntu3 [2009 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libubsan1 amd64 10.2.1-2ubuntu3 [784 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libquadmath0 amd64 10.2.1-2ubuntu3 [146 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 g++-10 amd64 10.2.1-2ubuntu3 [9759 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++-10-dev amd64 10.2.1-2ubuntu3 [1754 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-10-dev amd64 10.2.1-2ubuntu3 [2344 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10 amd64 10.2.1-2ubuntu3 [17.4 MB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 cpp-10 amd64 10.2.1-2ubuntu3 [8575 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++6 amd64 10.2.1-2ubuntu3 [501 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmpc3 amd64 1.2.0-1 [44.3 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main amd64 libzstd1 amd64 1.4.8+dfsg-1 [304 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6 amd64 2.32-0ubuntu6 [2683 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-files amd64 11ubuntu16 [60.5 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main amd64 bash amd64 5.1-1ubuntu1 [673 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main amd64 bsdutils amd64 1:2.36.1-1ubuntu2 [86.8 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main amd64 coreutils amd64 8.32-4ubuntu2 [1353 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main amd64 tar amd64 1.32+dfsg-1 [279 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main amd64 dpkg amd64 1.20.5ubuntu3 [1172 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main amd64 dash amd64 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [87.1 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main amd64 grep amd64 3.6-1 [155 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main amd64 login amd64 1:4.8.1-1ubuntu7 [220 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main amd64 libncursesw6 amd64 6.2+20201114-2 [132 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtinfo6 amd64 6.2+20201114-2 [87.3 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main amd64 ncurses-bin amd64 6.2+20201114-2 [173 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main amd64 perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main amd64 libperl5.32 amd64 5.32.0-6 [4064 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main amd64 perl amd64 5.32.0-6 [225 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main amd64 perl-base amd64 5.32.0-6 [1562 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main amd64 util-linux amd64 2.36.1-1ubuntu2 [1073 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdebconfclient0 amd64 0.255ubuntu1 [6184 B] Get:60 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-passwd amd64 3.5.48 [47.5 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 init-system-helpers all 1.60 [37.8 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-bin amd64 2.32-0ubuntu6 [642 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main amd64 ncurses-base all 6.2+20201114-2 [18.4 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main amd64 sysvinit-utils amd64 2.96-5ubuntu1 [20.8 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxxhash0 amd64 0.8.0-1 [16.1 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgcrypt20 amd64 1.8.7-2ubuntu1 [424 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblz4-1 amd64 1.9.3-0ubuntu1 [56.0 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-sysv amd64 247.1-4ubuntu1 [10.3 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:70 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap-ng0 amd64 0.7.9-2.2build1 [11.0 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit1 amd64 1:2.8.5-3ubuntu3 [39.0 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpcre2-8-0 amd64 10.35-2ubuntu1 [204 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main amd64 libselinux1 amd64 3.1-2build2 [69.4 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage-common all 3.1-1build2 [10.0 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage1 amd64 3.1-1build2 [86.9 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main amd64 passwd amd64 1:4.8.1-1ubuntu7 [797 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 adduser all 3.118ubuntu4 [163 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-timesyncd amd64 247.1-4ubuntu1 [28.1 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapparmor1 amd64 3.0.0-0ubuntu5 [35.5 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main amd64 libblkid1 amd64 2.36.1-1ubuntu2 [132 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libudev1 amd64 247.1-4ubuntu1 [69.1 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdevmapper1.02.1 amd64 2:1.02.167-1ubuntu4 [128 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main amd64 libuuid1 amd64 2.36.1-1ubuntu2 [21.6 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcryptsetup12 amd64 2:2.3.4-1ubuntu1 [195 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main amd64 libip4tc2 amd64 1.8.5-3ubuntu4 [18.7 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libseccomp2 amd64 2.4.3-1ubuntu6 [41.9 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main amd64 mount amd64 2.36.1-1ubuntu2 [121 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd amd64 247.1-4ubuntu1 [3988 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libsystemd0 amd64 247.1-4ubuntu1 [276 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapt-pkg6.0 amd64 2.1.15 [851 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main amd64 apt amd64 2.1.15 [1318 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 init amd64 1.60 [6040 B] Get:93 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libacl1 amd64 2.2.53-9 [17.6 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main amd64 libattr1 amd64 1:2.4.48-6 [12.9 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmount1 amd64 2.36.1-1ubuntu2 [147 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsmartcols1 amd64 2.36.1-1ubuntu2 [94.6 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main amd64 libidn2-0 amd64 2.3.0-4 [52.4 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main amd64 libp11-kit0 amd64 0.23.22-1 [191 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap2 amd64 1:2.44-1 [17.2 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main amd64 readline-common all 8.1-1 [54.1 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main amd64 libreadline8 amd64 8.1-1 [137 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsqlite3-0 amd64 3.34.0-1 [589 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 openssl amd64 1.1.1f-1ubuntu5 [621 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 tzdata all 2020f-1ubuntu1 [294 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main amd64 dpkg-dev all 1.20.5ubuntu3 [758 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdpkg-perl all 1.20.5ubuntu3 [232 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfakeroot amd64 1.25.3-1.1 [26.8 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main amd64 fakeroot amd64 1.25.3-1.1 [62.9 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnpth0 amd64 1.6-3 [8220 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 86.0 MB in 9s (9287 kB/s) (Reading database ... 12980 files and directories currently installed.) 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Setting up libquadmath0:amd64 (10.2.1-2ubuntu3) ... Setting up libmpc3:amd64 (1.2.0-1) ... Setting up libatomic1:amd64 (10.2.1-2ubuntu3) ... Setting up libncursesw6:amd64 (6.2+20201114-2) ... Setting up libk5crypto3:amd64 (1.17-10ubuntu1) ... Setting up libperl5.32:amd64 (5.32.0-6) ... Setting up libubsan1:amd64 (10.2.1-2ubuntu3) ... Setting up libcrypt-dev:amd64 (1:4.4.17-1ubuntu1) ... Setting up libkrb5-3:amd64 (1.17-10ubuntu1) ... Setting up libbinutils:amd64 (2.35.50.20201218-1ubuntu3) ... Setting up libisl23:amd64 (0.23-1) ... Setting up libc-dev-bin (2.32-0ubuntu6) ... Setting up openssl (1.1.1f-1ubuntu5) ... Setting up readline-common (8.1-1) ... Setting up libcc1-0:amd64 (10.2.1-2ubuntu3) ... Setting up liblsan0:amd64 (10.2.1-2ubuntu3) ... Setting up cpp-10 (10.2.1-2ubuntu3) ... Setting up libitm1:amd64 (10.2.1-2ubuntu3) ... Setting up libtsan0:amd64 (10.2.1-2ubuntu3) ... Setting up libctf0:amd64 (2.35.50.20201218-1ubuntu3) ... Setting up libgcc-10-dev:amd64 (10.2.1-2ubuntu3) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up perl (5.32.0-6) ... Setting up libgssapi-krb5-2:amd64 (1.17-10ubuntu1) ... Setting up libdpkg-perl (1.20.5ubuntu3) ... Setting up binutils-x86-64-linux-gnu (2.35.50.20201218-1ubuntu3) ... Setting up libtirpc3:amd64 (1.3.1-1) ... Setting up binutils (2.35.50.20201218-1ubuntu3) ... Setting up dpkg-dev (1.20.5ubuntu3) ... Setting up libtirpc-dev:amd64 (1.3.1-1) ... Setting up gcc-10 (10.2.1-2ubuntu3) ... Setting up libc6-dev:amd64 (2.32-0ubuntu6) ... Setting up libstdc++-10-dev:amd64 (10.2.1-2ubuntu3) ... Setting up g++-10 (10.2.1-2ubuntu3) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20776818 amd64 hirsute-proposed -c chroot:build-PACKAGEBUILD-20776818 --arch=amd64 --dist=hirsute-proposed --nolog -A rna-star_2.7.7a+dfsg-1.dsc Initiating build PACKAGEBUILD-20776818 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-129-generic #132-Ubuntu SMP Thu Dec 10 14:02:26 UTC 2020 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lgw01-amd64-041.buildd +==============================================================================+ | rna-star 2.7.7a+dfsg-1 (amd64) Wed, 06 Jan 2021 23:54:51 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.7a+dfsg-1 Source Version: 2.7.7a+dfsg-1 Distribution: hirsute-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20776818/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- rna-star_2.7.7a+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/rna-star-KOEwJO/rna-star-2.7.7a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-KOEwJO' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-sDOPVS/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-sDOPVS/apt_archive ./ InRelease Get:2 copy:/<>/resolver-sDOPVS/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-sDOPVS/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-sDOPVS/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-sDOPVS/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (53.9 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-sDOPVS/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (55.8 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64 ppc64el mips64el) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, zlib1g-dev Filtered Build-Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-rna-star-dummy' in '/<>/resolver-sDOPVS/apt_archive/sbuild-build-depends-rna-star-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-rna-star-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-sDOPVS/apt_archive ./ InRelease Get:2 copy:/<>/resolver-sDOPVS/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-sDOPVS/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-sDOPVS/apt_archive ./ Sources [517 B] Get:5 copy:/<>/resolver-sDOPVS/apt_archive ./ Packages [599 B] Fetched 2079 B in 0s (35.7 kB/s) Reading package lists... Reading package lists... Install rna-star build dependencies (apt-based resolver) -------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf vim-common xxd zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl vim | vim-gtk3 | vim-athena | vim-nox | vim-tiny The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-rna-star-dummy vim-common xxd zlib1g-dev 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 22.7 MB of archives. After this operation, 78.9 MB of additional disk space will be used. Get:1 copy:/<>/resolver-sDOPVS/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [892 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main amd64 bsdextrautils amd64 2.36.1-1ubuntu2 [77.3 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main amd64 libuchardet0 amd64 0.0.7-1 [68.0 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main amd64 groff-base amd64 1.22.4-5 [847 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpipeline1 amd64 1.5.3-1 [27.8 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main amd64 man-db amd64 2.9.3-2 [1117 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmagic-mgc amd64 1:5.39-3 [228 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmagic1 amd64 1:5.39-3 [80.6 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main amd64 file amd64 1:5.39-3 [23.7 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libelf1 amd64 0.182-3 [44.4 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main amd64 libicu67 amd64 67.1-5 [8618 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxml2 amd64 2.9.10+dfsg-6.3build1 [623 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main amd64 xxd amd64 2:8.2.1913-1ubuntu3 [50.1 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main amd64 vim-common all 2:8.2.1913-1ubuntu3 [80.0 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gettext-base amd64 0.21-3 [40.0 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpsl5 amd64 0.21.0-1.1ubuntu1 [52.3 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libsigsegv2 amd64 2.12-3 [14.0 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 m4 amd64 1.4.18-5 [200 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main amd64 autoconf all 2.69-14 [293 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main amd64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main amd64 automake all 1:1.16.3-2ubuntu1 [552 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 autopoint all 0.21-3 [423 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtool all 2.4.6-14 [161 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main amd64 dh-autoreconf all 19 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libdebhelper-perl all 13.3ubuntu4 [63.8 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:28 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main amd64 dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:30 http://ftpmaster.internal/ubuntu hirsute/main amd64 dwz amd64 0.13+20201015-2 [173 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gettext amd64 0.21-3 [824 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 debhelper all 13.3ubuntu4 [881 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-2 [41.8 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-2 [181 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main amd64 libbrotli1 amd64 1.0.9-2build2 [274 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-2 [29.7 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-2 [88.0 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-2 [47.6 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-2 [107 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-2 [207 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-2 [15.1 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-2 [96.5 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2ubuntu1 [14.7 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2ubuntu1 [49.3 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main amd64 libldap-2.4-2 amd64 2.4.56+dfsg-1ubuntu1 [156 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnghttp2-14 amd64 1.42.0-1 [72.1 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build2 [55.0 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main amd64 libssh-4 amd64 0.9.5-1 [172 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcurl3-gnutls amd64 7.72.0-1ubuntu1 [236 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcurl4-gnutls-dev amd64 7.72.0-1ubuntu1 [323 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libdeflate0 amd64 1.7-1 [52.7 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libdeflate-dev amd64 1.7-1 [45.7 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libhts3 amd64 1.11-4 [353 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblzma-dev amd64 5.2.4-1ubuntu1 [147 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu4 [156 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libhts-dev amd64 1.11-4 [3831 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 22.7 MB in 2s (14.9 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-1ubuntu2_amd64.deb ... Unpacking bsdextrautils (2.36.1-1ubuntu2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_amd64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... 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Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:amd64 (2.12-3) ... Setting up autopoint (0.21-3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:amd64 (0.9.5-1) ... Setting up libroken18-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up liblzma-dev:amd64 (5.2.4-1ubuntu1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu4) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:amd64 (1.7-1) ... Setting up libelf1:amd64 (0.182-3) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.3build1) ... Setting up libheimbase1-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up gettext (0.21-3) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-5) ... Setting up libhcrypto4-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libwind0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13+20201015-2) ... Setting up groff-base (1.22.4-5) ... Setting up automake (1:1.16.3-2ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:amd64 (2.4.56+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:amd64 (7.72.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:amd64 (7.72.0-1ubuntu1) ... Setting up libhts3:amd64 (1.11-4) ... Setting up libhts-dev:amd64 (1.11-4) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.3ubuntu4) ... Setting up sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-129-generic amd64 (x86_64) Toolchain package versions: binutils_2.35.50.20201218-1ubuntu3 dpkg-dev_1.20.5ubuntu3 g++-10_10.2.1-2ubuntu3 gcc-10_10.2.1-2ubuntu3 libc6-dev_2.32-0ubuntu6 libstdc++-10-dev_10.2.1-2ubuntu3 libstdc++6_10.2.1-2ubuntu3 linux-libc-dev_5.8.0-34.37+21.04.1 Package versions: adduser_3.118ubuntu4 advancecomp_2.1-2.1build1 apt_2.1.15 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1-1ubuntu1 binutils_2.35.50.20201218-1ubuntu3 binutils-common_2.35.50.20201218-1ubuntu3 binutils-x86-64-linux-gnu_2.35.50.20201218-1ubuntu3 bsdextrautils_2.36.1-1ubuntu2 bsdutils_1:2.36.1-1ubuntu2 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.32-4ubuntu2 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.1-2ubuntu3 dash_0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 debconf_1.5.74 debhelper_13.3ubuntu4 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.5ubuntu3 dpkg-dev_1.20.5ubuntu3 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.7.0-1ubuntu2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.1-2ubuntu3 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.1-2ubuntu3 gcc-10-base_10.2.1-2ubuntu3 gettext_0.21-3 gettext-base_0.21-3 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.60 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-9 libapparmor1_3.0.0-0ubuntu5 libapt-pkg6.0_2.1.15 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.1-2ubuntu3 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.2.1-2ubuntu3 libattr1_1:2.4.48-6 libaudit-common_1:2.8.5-3ubuntu3 libaudit1_1:2.8.5-3ubuntu3 libbinutils_2.35.50.20201218-1ubuntu3 libblkid1_2.36.1-1ubuntu2 libbrotli1_1.0.9-2build2 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu6 libc-dev-bin_2.32-0ubuntu6 libc6_2.32-0ubuntu6 libc6-dev_2.32-0ubuntu6 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1 libcc1-0_10.2.1-2ubuntu3 libcom-err2_1.45.6-1ubuntu1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.4-1ubuntu1 libctf-nobfd0_2.35.50.20201218-1ubuntu3 libctf0_2.35.50.20201218-1ubuntu3 libcurl3-gnutls_7.72.0-1ubuntu1 libcurl4-gnutls-dev_7.72.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.255ubuntu1 libdebhelper-perl_13.3ubuntu4 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdevmapper1.02.1_2:1.02.167-1ubuntu4 libdpkg-perl_1.20.5ubuntu3 libelf1_0.182-3 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.3-1.1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.1-2ubuntu3 libgcc-s1_10.2.1-2ubuntu3 libgcrypt20_1.8.7-2ubuntu1 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.6.15-4ubuntu2 libgomp1_10.2.1-2ubuntu3 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10ubuntu1 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.11-4 libhts3_1.11-4 libhx509-5-heimdal_7.7.0+dfsg-2 libicu67_67.1-5 libidn2-0_2.3.0-4 libip4tc2_1.8.5-3ubuntu4 libisl22_0.22.1-1 libisl23_0.23-1 libitm1_10.2.1-2ubuntu3 libjson-c5_0.15-1 libk5crypto3_1.17-10ubuntu1 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10ubuntu1 libkrb5support0_1.17-10ubuntu1 libldap-2.4-2_2.4.56+dfsg-1ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.2.1-2ubuntu3 liblz4-1_1.9.3-0ubuntu1 liblzma-dev_5.2.4-1ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-1ubuntu2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-0ubuntu3 libnsl2_1.3.0-0ubuntu3 libnss-nis_3.1-0ubuntu4 libnss-nisplus_1.3-0ubuntu4 libp11-kit0_0.23.22-1 libpam-modules_1.3.1-5ubuntu6 libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpcre2-8-0_10.35-2ubuntu1 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libperl5.32_5.32.0-6 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpsl5_0.21.0-1.1ubuntu1 libquadmath0_10.2.1-2ubuntu3 libreadline8_8.1-1 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27+dfsg-2ubuntu1 libseccomp2_2.4.3-1ubuntu6 libselinux1_3.1-2build2 libsemanage-common_3.1-1build2 libsemanage1_3.1-1build2 libsepol1_3.1-1 libsigsegv2_2.12-3 libsmartcols1_2.36.1-1ubuntu2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1ubuntu1 libssh-4_0.9.5-1 libssl1.1_1.1.1f-1ubuntu5 libstdc++-10-dev_10.2.1-2ubuntu3 libstdc++6_10.2.1-2ubuntu3 libsub-override-perl_0.09-2 libsystemd0_247.1-4ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-14 libtsan0_10.2.1-2ubuntu3 libubsan1_10.2.1-2ubuntu3 libuchardet0_0.0.7-1 libudev1_247.1-4ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36.1-1ubuntu2 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-6.3build1 libxxhash0_0.8.0-1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.8.0-34.37+21.04.1 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu7 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-5 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36.1-1ubuntu2 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 openssl_1.1.1f-1ubuntu5 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu7 patch_2.7.6-6 perl_5.32.0-6 perl-base_5.32.0-6 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 readline-common_8.1-1 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rna-star-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 systemd_247.1-4ubuntu1 systemd-sysv_247.1-4ubuntu1 systemd-timesyncd_247.1-4ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.32+dfsg-1 tzdata_2020f-1ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.36.1-1ubuntu2 vim-common_2:8.2.1913-1ubuntu3 xxd_2:8.2.1913-1ubuntu3 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Jan 6 16:38:48 2021 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.7.7a+dfsg-1.dsc dpkg-source: info: extracting rna-star in /<>/rna-star-2.7.7a+dfsg dpkg-source: info: unpacking rna-star_2.7.7a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.7a+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 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-20776818 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20776818 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20776818 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.7a+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/rna-star-2.7.7a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/rna-star-2.7.7a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/rna-star-2.7.7a+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/<>/rna-star-2.7.7a+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/<>/rna-star-2.7.7a+dfsg' dh_auto_build --sourcedirectory=source -- CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" cd source && make -j4 "INSTALL=install --strip-program=true" "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>/rna-star-2.7.7a+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 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 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.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp 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 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.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 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.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_collapseUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_transformGenome.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool)’: SoloFeature_outputResults.cpp:45:17: warning: ignoring return value of ‘int symlink(const char*, const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | symlink("../../../SJ.out.tab", (outputPrefix1+pSolo.outFileNames[1]).c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_samAttributes.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:184:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 184 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:188:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+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 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=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMoutput.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortByCoordinate.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:77:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 77 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ 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] 79 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:82:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 86 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:90:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamRemoveDuplicates.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortUnmapped.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:125:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:152:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:248:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 248 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:249:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 249 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ 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=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_collapseUMI.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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:52:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/rna-star-2.7.7a+dfsg/source' make[1]: Leaving directory '/<>/rna-star-2.7.7a+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/rna-star-2.7.7a+dfsg' debian/tests/run_test.sh /<>/rna-star-2.7.7a+dfsg/source/STAR Jan 07 00:00:44 ..... started STAR run Jan 07 00:00:44 ... starting to generate Genome files Jan 07 00:00:44 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Jan 07 00:00:44 ... starting to sort Suffix Array. This may take a long time... Jan 07 00:00:44 ... sorting Suffix Array chunks and saving them to disk... Jan 07 00:00:44 ... loading chunks from disk, packing SA... Jan 07 00:00:44 ... finished generating suffix array Jan 07 00:00:44 ... generating Suffix Array index Jan 07 00:00:44 ... completed Suffix Array index Jan 07 00:00:44 ... writing Genome to disk ... Jan 07 00:00:44 ... writing Suffix Array to disk ... Jan 07 00:00:44 ... writing SAindex to disk Jan 07 00:00:44 ..... finished successfully Jan 07 00:00:44 ..... started STAR run Jan 07 00:00:44 ..... loading genome Jan 07 00:00:44 ..... started mapping Jan 07 00:00:45 ..... finished mapping Jan 07 00:00:45 ..... finished successfully make[1]: Leaving directory '/<>/rna-star-2.7.7a+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/<>/rna-star-2.7.7a+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>/rna-star-2.7.7a+dfsg' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing rna-star (in debian/rna-star); do_strip: , oemstrip: pkgstriptranslations: processing rna-star-dbgsym (in debian/.debhelper/rna-star/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/rna-star/DEBIAN/control, package rna-star, directory debian/rna-star pkgstripfiles: Truncating usr/share/doc/rna-star/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package rna-star ... pkgstripfiles: No PNG files. dpkg-deb: building package 'rna-star' in '../rna-star_2.7.7a+dfsg-1_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/rna-star/dbgsym-root/DEBIAN/control, package rna-star-dbgsym, directory debian/.debhelper/rna-star/dbgsym-root dpkg-deb: building package 'rna-star-dbgsym' in 'debian/.debhelper/scratch-space/build-rna-star/rna-star-dbgsym_2.7.7a+dfsg-1_amd64.deb'. Renaming rna-star-dbgsym_2.7.7a+dfsg-1_amd64.deb to rna-star-dbgsym_2.7.7a+dfsg-1_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../rna-star_2.7.7a+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-01-07T00:01:08Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.7.7a+dfsg-1_amd64.changes: ------------------------------------- Format: 1.8 Date: Wed, 06 Jan 2021 16:28:02 +0530 Source: rna-star Binary: rna-star Architecture: amd64 Version: 2.7.7a+dfsg-1 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nilesh Patra Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.7.7a+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.5.1 (routine-update) * Switch watch version to 4 Checksums-Sha1: cad223b0e8da7e6bdaf6dea9675cad59bbda16c5 5807124 rna-star-dbgsym_2.7.7a+dfsg-1_amd64.ddeb 6520db3a6098871cb890812c33a2218ebe663796 6817 rna-star_2.7.7a+dfsg-1_amd64.buildinfo a7b3de47b10793059bfebe79a8d1afd6d8538842 571624 rna-star_2.7.7a+dfsg-1_amd64.deb Checksums-Sha256: 856f23f2209fcfe23962b957e35ca6df70cf854e3b51be39ba6ca9fb6b12863f 5807124 rna-star-dbgsym_2.7.7a+dfsg-1_amd64.ddeb 5db08e7fee29cfcefca93dc8de5d40fdf8944911e7d67a13568a7cfbc1c6cc91 6817 rna-star_2.7.7a+dfsg-1_amd64.buildinfo 96d0ac14b6bb313231c1a7ab887ad6ff1ba25c166316d5d98a023f86ee45124d 571624 rna-star_2.7.7a+dfsg-1_amd64.deb Files: 608366cd4a4d16c2cc4788430dad124f 5807124 debug optional rna-star-dbgsym_2.7.7a+dfsg-1_amd64.ddeb 4758aedde1e448b97bd9ebe05704f52b 6817 science optional rna-star_2.7.7a+dfsg-1_amd64.buildinfo 65351738cbd6d279158ee4e33151220b 571624 science optional rna-star_2.7.7a+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: rna-star Binary: rna-star rna-star-dbgsym Architecture: amd64 Version: 2.7.7a+dfsg-1 Checksums-Md5: 608366cd4a4d16c2cc4788430dad124f 5807124 rna-star-dbgsym_2.7.7a+dfsg-1_amd64.ddeb 65351738cbd6d279158ee4e33151220b 571624 rna-star_2.7.7a+dfsg-1_amd64.deb Checksums-Sha1: cad223b0e8da7e6bdaf6dea9675cad59bbda16c5 5807124 rna-star-dbgsym_2.7.7a+dfsg-1_amd64.ddeb a7b3de47b10793059bfebe79a8d1afd6d8538842 571624 rna-star_2.7.7a+dfsg-1_amd64.deb Checksums-Sha256: 856f23f2209fcfe23962b957e35ca6df70cf854e3b51be39ba6ca9fb6b12863f 5807124 rna-star-dbgsym_2.7.7a+dfsg-1_amd64.ddeb 96d0ac14b6bb313231c1a7ab887ad6ff1ba25c166316d5d98a023f86ee45124d 571624 rna-star_2.7.7a+dfsg-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 07 Jan 2021 00:01:07 +0000 Build-Path: /<>/rna-star-2.7.7a+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-14), automake (= 1:1.16.3-2ubuntu1), autopoint (= 0.21-3), autotools-dev (= 20180224.1+nmu1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.1-1ubuntu1), binutils (= 2.35.50.20201218-1ubuntu3), binutils-common (= 2.35.50.20201218-1ubuntu3), binutils-x86-64-linux-gnu (= 2.35.50.20201218-1ubuntu3), bsdextrautils (= 2.36.1-1ubuntu2), bsdutils (= 1:2.36.1-1ubuntu2), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), coreutils (= 8.32-4ubuntu2), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 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libmpfr6 (= 4.1.0-3), libnettle8 (= 3.6-2), libnghttp2-14 (= 1.42.0-1), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), libp11-kit0 (= 0.23.22-1), libpam-modules (= 1.3.1-5ubuntu6), libpam-modules-bin (= 1.3.1-5ubuntu6), libpam-runtime (= 1.3.1-5ubuntu6), libpam0g (= 1.3.1-5ubuntu6), libpcre2-8-0 (= 10.35-2ubuntu1), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.0-6), libpipeline1 (= 1.5.3-1), libpsl5 (= 0.21.0-1.1ubuntu1), libquadmath0 (= 10.2.1-2ubuntu3), libroken18-heimdal (= 7.7.0+dfsg-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build2), libsasl2-2 (= 2.1.27+dfsg-2ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg-2ubuntu1), libseccomp2 (= 2.4.3-1ubuntu6), libselinux1 (= 3.1-2build2), libsigsegv2 (= 2.12-3), libsmartcols1 (= 2.36.1-1ubuntu2), libsqlite3-0 (= 3.34.0-1), libssh-4 (= 0.9.5-1), libssl1.1 (= 1.1.1f-1ubuntu5), libstdc++-10-dev (= 10.2.1-2ubuntu3), libstdc++6 (= 10.2.1-2ubuntu3), libsub-override-perl (= 0.09-2), libsystemd0 (= 247.1-4ubuntu1), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2+20201114-2), libtirpc-common (= 1.3.1-1), libtirpc-dev (= 1.3.1-1), libtirpc3 (= 1.3.1-1), libtool (= 2.4.6-14), libtsan0 (= 10.2.1-2ubuntu3), libubsan1 (= 10.2.1-2ubuntu3), libuchardet0 (= 0.0.7-1), libudev1 (= 247.1-4ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36.1-1ubuntu2), libwind0-heimdal (= 7.7.0+dfsg-2), libxml2 (= 2.9.10+dfsg-6.3build1), libzstd1 (= 1.4.8+dfsg-1), linux-libc-dev (= 5.8.0-34.37+21.04.1), login (= 1:4.8.1-1ubuntu7), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-5), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2+20201114-2), ncurses-bin (= 6.2+20201114-2), patch (= 2.7.6-6), perl (= 5.32.0-6), perl-base (= 5.32.0-6), perl-modules-5.32 (= 5.32.0-6), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu4), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.13), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.32+dfsg-1), util-linux (= 2.36.1-1ubuntu2), vim-common (= 2:8.2.1913-1ubuntu3), xxd (= 2:8.2.1913-1ubuntu3), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609930682" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ rna-star_2.7.7a+dfsg-1_amd64.deb -------------------------------- new Debian package, version 2.0. size 571624 bytes: control archive=1428 bytes. 1449 bytes, 25 lines control 602 bytes, 9 lines md5sums Package: rna-star Version: 2.7.7a+dfsg-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1252 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.3.1), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 9) Section: science Priority: optional Homepage: https://github.com/alexdobin/STAR/ Description: ultrafast universal RNA-seq aligner Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, the authors experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. drwxr-xr-x root/root 0 2021-01-06 10:58 ./ drwxr-xr-x root/root 0 2021-01-06 10:58 ./usr/ drwxr-xr-x root/root 0 2021-01-06 10:58 ./usr/bin/ -rwxr-xr-x root/root 1029168 2021-01-06 10:58 ./usr/bin/STAR drwxr-xr-x root/root 0 2021-01-06 10:58 ./usr/share/ drwxr-xr-x root/root 0 2021-01-06 10:58 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2021-01-06 10:57 ./usr/share/doc-base/rna-star drwxr-xr-x root/root 0 2021-01-06 10:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-01-06 10:58 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2021-01-06 10:57 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3240 2020-12-28 20:41 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 6799 2020-12-28 20:41 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 219849 2020-12-28 20:41 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 881 2021-01-06 10:58 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 2565 2021-01-06 10:58 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2021-01-06 10:58 ./usr/share/man/ drwxr-xr-x root/root 0 2021-01-06 10:58 ./usr/share/man/man1/ -rw-r--r-- root/root 824 2021-01-06 10:58 ./usr/share/man/man1/STAR.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 344 Distribution: hirsute-proposed Host Architecture: amd64 Install-Time: 30 Job: rna-star_2.7.7a+dfsg-1.dsc Machine Architecture: amd64 Package: rna-star Package-Time: 377 Source-Version: 2.7.7a+dfsg-1 Space: n/a Status: successful Version: 2.7.7a+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-01-07T00:01:08Z Build needed 00:06:17, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20776818 Scanning for processes to kill in build PACKAGEBUILD-20776818