https://launchpad.net/ubuntu/+source/rna-star/2.7.7a+dfsg-1/+build/20776820 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-007 4.15.0-129-generic #132-Ubuntu SMP Thu Dec 10 13:57:56 UTC 2020 ppc64le 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 23:33:08 ntpdate[1869]: adjust time server 10.211.37.1 offset 0.001885 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20776820 --image-type chroot /home/buildd/filecache-default/562b8b0d733db483afe9600af35c69ac54075a74 Creating target for build PACKAGEBUILD-20776820 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20776820 Starting target for build PACKAGEBUILD-20776820 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20776820 '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-20776820 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20776820 Updating target for build PACKAGEBUILD-20776820 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 ppc64el Packages [1343 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el 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 ppc64el Packages [144 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [56.2 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe ppc64el Packages [758 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [337 kB] Fetched 22.1 MB in 5s (4492 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-powerpc64le-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 80.2 MB of archives. After this operation, 52.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcrypt-dev ppc64el 1:4.4.17-1ubuntu1 [131 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libc6-dev ppc64el 2.32-0ubuntu6 [2132 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libc-dev-bin ppc64el 2.32-0ubuntu6 [31.5 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcrypt1 ppc64el 1:4.4.17-1ubuntu1 [99.8 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el linux-libc-dev ppc64el 5.8.0-34.37+21.04.1 [1134 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libtirpc-common all 1.3.1-1 [7452 B] Get:7 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libk5crypto3 ppc64el 1.17-10ubuntu1 [105 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libgssapi-krb5-2 ppc64el 1.17-10ubuntu1 [135 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libkrb5-3 ppc64el 1.17-10ubuntu1 [375 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libkrb5support0 ppc64el 1.17-10ubuntu1 [34.8 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libssl1.1 ppc64el 1.1.1f-1ubuntu5 [1363 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libtirpc-dev ppc64el 1.3.1-1 [208 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libtirpc3 ppc64el 1.3.1-1 [88.9 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libisl23 ppc64el 0.23-1 [713 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libcc1-0 ppc64el 10.2.1-2ubuntu3 [42.0 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libctf0 ppc64el 2.35.50.20210106-1ubuntu2 [97.3 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libctf-nobfd0 ppc64el 2.35.50.20210106-1ubuntu2 [95.8 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.35.50.20210106-1ubuntu2 [1703 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libbinutils ppc64el 2.35.50.20210106-1ubuntu2 [569 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el binutils-common ppc64el 2.35.50.20210106-1ubuntu2 [216 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el binutils ppc64el 2.35.50.20210106-1ubuntu2 [3384 B] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el gcc-10-base ppc64el 10.2.1-2ubuntu3 [19.4 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libgcc-s1 ppc64el 10.2.1-2ubuntu3 [30.1 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libgomp1 ppc64el 10.2.1-2ubuntu3 [109 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libitm1 ppc64el 10.2.1-2ubuntu3 [28.5 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libatomic1 ppc64el 10.2.1-2ubuntu3 [9984 B] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libasan6 ppc64el 10.2.1-2ubuntu3 [2107 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el liblsan0 ppc64el 10.2.1-2ubuntu3 [848 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libtsan0 ppc64el 10.2.1-2ubuntu3 [2031 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libubsan1 ppc64el 10.2.1-2ubuntu3 [800 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libquadmath0 ppc64el 10.2.1-2ubuntu3 [149 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el g++-10 ppc64el 10.2.1-2ubuntu3 [8185 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libstdc++-10-dev ppc64el 10.2.1-2ubuntu3 [1793 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libgcc-10-dev ppc64el 10.2.1-2ubuntu3 [1246 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el gcc-10 ppc64el 10.2.1-2ubuntu3 [14.5 MB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el cpp-10 ppc64el 10.2.1-2ubuntu3 [7072 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libstdc++6 ppc64el 10.2.1-2ubuntu3 [540 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libmpc3 ppc64el 1.2.0-1 [47.1 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libzstd1 ppc64el 1.4.8+dfsg-1 [327 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libc6 ppc64el 2.32-0ubuntu6 [2680 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main ppc64el base-files ppc64el 11ubuntu16 [60.7 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main ppc64el bash ppc64el 5.1-1ubuntu1 [748 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main ppc64el bsdutils ppc64el 1:2.36.1-1ubuntu2 [91.9 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main ppc64el coreutils ppc64el 8.32-4ubuntu2 [1411 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main ppc64el tar ppc64el 1.32+dfsg-1 [317 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dpkg ppc64el 1.20.5ubuntu3 [1199 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dash ppc64el 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [100 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main ppc64el grep ppc64el 3.6-1 [160 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main ppc64el login ppc64el 1:4.8.1-1ubuntu7 [223 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libncurses6 ppc64el 6.2+20201114-2 [122 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libncursesw6 ppc64el 6.2+20201114-2 [153 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libtinfo6 ppc64el 6.2+20201114-2 [104 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main ppc64el ncurses-bin ppc64el 6.2+20201114-2 [180 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main ppc64el perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libperl5.32 ppc64el 5.32.0-6 [4020 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main ppc64el perl ppc64el 5.32.0-6 [225 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main ppc64el perl-base ppc64el 5.32.0-6 [1547 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main ppc64el util-linux ppc64el 2.36.1-1ubuntu2 [1118 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libdebconfclient0 ppc64el 0.255ubuntu1 [6148 B] Get:60 http://ftpmaster.internal/ubuntu hirsute/main ppc64el base-passwd ppc64el 3.5.48 [49.6 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el init-system-helpers all 1.60 [37.8 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libc-bin ppc64el 2.32-0ubuntu6 [647 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main ppc64el ncurses-base all 6.2+20201114-2 [18.4 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main ppc64el sysvinit-utils ppc64el 2.96-5ubuntu1 [22.8 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libxxhash0 ppc64el 0.8.0-1 [30.5 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libgcrypt20 ppc64el 1.8.7-2ubuntu1 [444 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main ppc64el liblz4-1 ppc64el 1.9.3-0ubuntu1 [70.0 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el systemd-sysv ppc64el 247.1-4ubuntu1 [10.3 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:70 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcap-ng0 ppc64el 0.7.9-2.2build1 [11.7 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libaudit1 ppc64el 1:2.8.5-3ubuntu3 [42.5 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libpcre2-8-0 ppc64el 10.35-2ubuntu1 [204 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libselinux1 ppc64el 3.1-2build2 [81.5 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsemanage-common all 3.1-1build2 [10.0 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsemanage1 ppc64el 3.1-1build2 [97.0 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main ppc64el passwd ppc64el 1:4.8.1-1ubuntu7 [804 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el adduser all 3.118ubuntu4 [163 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el systemd-timesyncd ppc64el 247.1-4ubuntu1 [28.6 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libapparmor1 ppc64el 3.0.0-0ubuntu5 [39.6 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libblkid1 ppc64el 2.36.1-1ubuntu2 [151 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libudev1 ppc64el 247.1-4ubuntu1 [82.5 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.167-1ubuntu4 [157 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libuuid1 ppc64el 2.36.1-1ubuntu2 [23.1 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcryptsetup12 ppc64el 2:2.3.4-1ubuntu1 [228 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libip4tc2 ppc64el 1.8.5-3ubuntu4 [22.0 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libseccomp2 ppc64el 2.4.3-1ubuntu6 [47.7 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main ppc64el mount ppc64el 2.36.1-1ubuntu2 [128 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el systemd ppc64el 247.1-4ubuntu1 [4205 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libsystemd0 ppc64el 247.1-4ubuntu1 [318 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libapt-pkg6.0 ppc64el 2.1.15 [932 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main ppc64el apt ppc64el 2.1.15 [1329 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el init ppc64el 1.60 [6040 B] Get:93 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libacl1 ppc64el 2.2.53-9 [19.1 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libattr1 ppc64el 1:2.4.48-6 [13.8 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libmount1 ppc64el 2.36.1-1ubuntu2 [166 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsmartcols1 ppc64el 2.36.1-1ubuntu2 [107 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libidn2-0 ppc64el 2.3.0-4 [55.3 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libp11-kit0 ppc64el 0.23.22-1 [203 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcap2 ppc64el 1:2.44-1 [19.8 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main ppc64el readline-common all 8.1-1 [54.1 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libreadline8 ppc64el 8.1-1 [151 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsqlite3-0 ppc64el 3.34.0-1 [628 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el openssl ppc64el 1.1.1f-1ubuntu5 [621 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el tzdata all 2020f-1ubuntu1 [294 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dpkg-dev all 1.20.5ubuntu3 [758 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libdpkg-perl all 1.20.5ubuntu3 [232 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libfakeroot ppc64el 1.25.3-1.1 [28.6 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main ppc64el fakeroot ppc64el 1.25.3-1.1 [66.4 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libnpth0 ppc64el 1.6-3 [8640 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 80.2 MB in 2s (44.1 MB/s) (Reading database ... 12922 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu1_ppc64el.deb ... Unpacking libcrypt-dev:ppc64el (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libc6-dev_2.32-0ubuntu6_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libc-dev-bin_2.32-0ubuntu6_ppc64el.deb ... Unpacking libc-dev-bin (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu1_ppc64el.deb ... Unpacking libcrypt1:ppc64el (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:ppc64el (1:4.4.17-1ubuntu1) ... (Reading database ... 12921 files and directories currently installed.) Preparing to unpack .../00-linux-libc-dev_5.8.0-34.37+21.04.1_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (5.8.0-34.37+21.04.1) over (5.8.0-25.26) ... Preparing to unpack .../01-libtirpc-common_1.3.1-1_all.deb ... Unpacking libtirpc-common (1.3.1-1) over (1.2.6-1build1) ... 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Unpacking dpkg-dev (1.20.5ubuntu3) over (1.20.5ubuntu2) ... Preparing to unpack .../07-libdpkg-perl_1.20.5ubuntu3_all.deb ... Unpacking libdpkg-perl (1.20.5ubuntu3) over (1.20.5ubuntu2) ... Preparing to unpack .../08-libfakeroot_1.25.3-1.1_ppc64el.deb ... Unpacking libfakeroot:ppc64el (1.25.3-1.1) over (1.25.2-1) ... Preparing to unpack .../09-fakeroot_1.25.3-1.1_ppc64el.deb ... Unpacking fakeroot (1.25.3-1.1) over (1.25.2-1) ... Preparing to unpack .../10-libnpth0_1.6-3_ppc64el.deb ... Unpacking libnpth0:ppc64el (1.6-3) over (1.6-2) ... Setting up init (1.60) ... Setting up libtirpc-common (1.3.1-1) ... Setting up perl-modules-5.32 (5.32.0-6) ... Setting up libsqlite3-0:ppc64el (3.34.0-1) ... Setting up binutils-common:ppc64el (2.35.50.20210106-1ubuntu2) ... Setting up linux-libc-dev:ppc64el (5.8.0-34.37+21.04.1) ... Setting up libctf-nobfd0:ppc64el (2.35.50.20210106-1ubuntu2) ... Setting up libnpth0:ppc64el (1.6-3) ... Setting up libgomp1:ppc64el (10.2.1-2ubuntu3) ... Setting up libcap2:ppc64el (1:2.44-1) ... Setting up libfakeroot:ppc64el (1.25.3-1.1) ... Setting up libasan6:ppc64el (10.2.1-2ubuntu3) ... Setting up libkrb5support0:ppc64el (1.17-10ubuntu1) ... Setting up tzdata (2020f-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 6 23:33:41 UTC 2021. Universal Time is now: Wed Jan 6 23:33:41 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.25.3-1.1) ... Setting up libncurses6:ppc64el (6.2+20201114-2) ... Setting up libquadmath0:ppc64el (10.2.1-2ubuntu3) ... Setting up libmpc3:ppc64el (1.2.0-1) ... Setting up libatomic1:ppc64el (10.2.1-2ubuntu3) ... Setting up libncursesw6:ppc64el (6.2+20201114-2) ... Setting up libk5crypto3:ppc64el (1.17-10ubuntu1) ... Setting up libperl5.32:ppc64el (5.32.0-6) ... Setting up libubsan1:ppc64el (10.2.1-2ubuntu3) ... Setting up libcrypt-dev:ppc64el (1:4.4.17-1ubuntu1) ... Setting up libkrb5-3:ppc64el (1.17-10ubuntu1) ... Setting up libbinutils:ppc64el (2.35.50.20210106-1ubuntu2) ... Setting up libisl23:ppc64el (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:ppc64el (10.2.1-2ubuntu3) ... Setting up liblsan0:ppc64el (10.2.1-2ubuntu3) ... Setting up cpp-10 (10.2.1-2ubuntu3) ... Setting up libitm1:ppc64el (10.2.1-2ubuntu3) ... Setting up libtsan0:ppc64el (10.2.1-2ubuntu3) ... Setting up libctf0:ppc64el (2.35.50.20210106-1ubuntu2) ... Setting up libgcc-10-dev:ppc64el (10.2.1-2ubuntu3) ... Setting up libreadline8:ppc64el (8.1-1) ... Setting up perl (5.32.0-6) ... Setting up libgssapi-krb5-2:ppc64el (1.17-10ubuntu1) ... Setting up libdpkg-perl (1.20.5ubuntu3) ... Setting up binutils-powerpc64le-linux-gnu (2.35.50.20210106-1ubuntu2) ... Setting up libtirpc3:ppc64el (1.3.1-1) ... Setting up binutils (2.35.50.20210106-1ubuntu2) ... Setting up dpkg-dev (1.20.5ubuntu3) ... Setting up libtirpc-dev:ppc64el (1.3.1-1) ... Setting up gcc-10 (10.2.1-2ubuntu3) ... Setting up libc6-dev:ppc64el (2.32-0ubuntu6) ... Setting up libstdc++-10-dev:ppc64el (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-20776820 ppc64el hirsute-proposed -c chroot:build-PACKAGEBUILD-20776820 --arch=ppc64el --dist=hirsute-proposed --nolog rna-star_2.7.7a+dfsg-1.dsc Initiating build PACKAGEBUILD-20776820 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-129-generic #132-Ubuntu SMP Thu Dec 10 13:57:56 UTC 2020 ppc64le sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-ppc64el-007.buildd +==============================================================================+ | rna-star 2.7.7a+dfsg-1 (ppc64el) Wed, 06 Jan 2021 23:33:42 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.7a+dfsg-1 Source Version: 2.7.7a+dfsg-1 Distribution: hirsute-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20776820/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-RM2aT1/rna-star-2.7.7a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-RM2aT1' 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-s1Jk66/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-s1Jk66/apt_archive ./ InRelease Get:2 copy:/<>/resolver-s1Jk66/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-s1Jk66/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-s1Jk66/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-s1Jk66/apt_archive ./ Packages [434 B] Fetched 1740 B in 0s (83.8 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-s1Jk66/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14869 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.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 (ppc64el 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-s1Jk66/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-s1Jk66/apt_archive ./ InRelease Get:2 copy:/<>/resolver-s1Jk66/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-s1Jk66/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-s1Jk66/apt_archive ./ Sources [517 B] Get:5 copy:/<>/resolver-s1Jk66/apt_archive ./ Packages [600 B] Fetched 2080 B in 0s (91.2 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 23.7 MB of archives. After this operation, 87.1 MB of additional disk space will be used. Get:1 copy:/<>/resolver-s1Jk66/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [888 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main ppc64el bsdextrautils ppc64el 2.36.1-1ubuntu2 [83.5 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libuchardet0 ppc64el 0.0.7-1 [71.0 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main ppc64el groff-base ppc64el 1.22.4-5 [922 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libpipeline1 ppc64el 1.5.3-1 [29.6 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main ppc64el man-db ppc64el 2.9.3-2 [1148 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libmagic-mgc ppc64el 1:5.39-3 [228 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libmagic1 ppc64el 1:5.39-3 [93.4 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main ppc64el file ppc64el 1:5.39-3 [24.7 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libelf1 ppc64el 0.182-3 [52.4 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libicu67 ppc64el 67.1-5 [8813 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libxml2 ppc64el 2.9.10+dfsg-6.3build1 [656 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main ppc64el xxd ppc64el 2:8.2.1913-1ubuntu3 [50.4 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main ppc64el vim-common all 2:8.2.1913-1ubuntu3 [80.0 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el gettext-base ppc64el 0.21-3 [44.7 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libpsl5 ppc64el 0.21.0-1.1ubuntu1 [54.0 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libsigsegv2 ppc64el 2.12-3 [14.5 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el m4 ppc64el 1.4.18-5 [208 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main ppc64el autoconf all 2.69-14 [293 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main ppc64el autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main ppc64el automake all 1:1.16.3-2ubuntu1 [552 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el autopoint all 0.21-3 [423 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libtool all 2.4.6-14 [161 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dh-autoreconf all 19 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el libdebhelper-perl all 13.3ubuntu4 [63.8 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsub-override-perl all 0.09-2 [9532 B] Get:28 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:30 http://ftpmaster.internal/ubuntu hirsute/main ppc64el dwz ppc64el 0.13+20201015-2 [156 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el gettext ppc64el 0.21-3 [897 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main ppc64el debhelper all 13.3ubuntu4 [881 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libroken18-heimdal ppc64el 7.7.0+dfsg-2 [46.4 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libasn1-8-heimdal ppc64el 7.7.0+dfsg-2 [176 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libbrotli1 ppc64el 1.0.9-2build2 [304 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libheimbase1-heimdal ppc64el 7.7.0+dfsg-2 [32.4 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libhcrypto4-heimdal ppc64el 7.7.0+dfsg-2 [108 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libwind0-heimdal ppc64el 7.7.0+dfsg-2 [48.9 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libhx509-5-heimdal ppc64el 7.7.0+dfsg-2 [120 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libkrb5-26-heimdal ppc64el 7.7.0+dfsg-2 [234 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libheimntlm0-heimdal ppc64el 7.7.0+dfsg-2 [17.4 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libgssapi3-heimdal ppc64el 7.7.0+dfsg-2 [105 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsasl2-modules-db ppc64el 2.1.27+dfsg-2ubuntu1 [16.8 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libsasl2-2 ppc64el 2.1.27+dfsg-2ubuntu1 [60.0 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libldap-2.4-2 ppc64el 2.4.56+dfsg-1ubuntu1 [176 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libnghttp2-14 ppc64el 1.42.0-1 [83.7 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build2 [59.2 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libssh-4 ppc64el 0.9.5-1 [195 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcurl3-gnutls ppc64el 7.72.0-1ubuntu1 [259 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main ppc64el libcurl4-gnutls-dev ppc64el 7.72.0-1ubuntu1 [363 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el libdeflate0 ppc64el 1.7-1 [47.6 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el libdeflate-dev ppc64el 1.7-1 [40.3 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el libhts3 ppc64el 1.11-4 [433 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main ppc64el liblzma-dev ppc64el 5.2.4-1ubuntu1 [164 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-2ubuntu4 [166 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/universe ppc64el libhts-dev ppc64el 1.11-4 [3961 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.7 MB in 3s (6812 kB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14869 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-1ubuntu2_ppc64el.deb ... Unpacking bsdextrautils (2.36.1-1ubuntu2) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../01-libuchardet0_0.0.7-1_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_ppc64el.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../03-libpipeline1_1.5.3-1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_ppc64el.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.39-3_ppc64el.deb ... Unpacking libmagic-mgc (1:5.39-3) ... 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Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-5) ... Setting up libhcrypto4-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libwind0-heimdal:ppc64el (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:ppc64el (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:ppc64el (7.7.0+dfsg-2) ... Setting up libheimntlm0-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:ppc64el (2.4.56+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:ppc64el (7.72.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:ppc64el (7.72.0-1ubuntu1) ... Setting up libhts3:ppc64el (1.11-4) ... Setting up libhts-dev:ppc64el (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 ppc64el (ppc64le) Toolchain package versions: binutils_2.35.50.20210106-1ubuntu2 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_2.35.50.20210106-1ubuntu2 binutils-common_2.35.50.20210106-1ubuntu2 binutils-powerpc64le-linux-gnu_2.35.50.20210106-1ubuntu2 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_2.35.50.20210106-1ubuntu2 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_2.35.50.20210106-1ubuntu2 libctf0_2.35.50.20210106-1ubuntu2 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-20776820 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20776820 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20776820 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 ppc64el 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-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a 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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_addBAMtags.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 -O3 -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 -O3 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bam_cat.c g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O3 -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 -O3 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' serviceFuns.cpp bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O3 -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 -O3 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O3 -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 -O3 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMfunctions.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O3 -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 -O3 -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 -O3 -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 -O3 -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); | ~~~~~~~~~~^~~~ 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 -O3 -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 -O3 -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 -O3 -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 -O3 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamRemoveDuplicates.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); | ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O3 -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 -O3 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortUnmapped.cpp 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 -O3 -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 -O3 -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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParametersSolo.cpp: In member function ‘initialize’: ParametersSolo.cpp:10:6: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 10 | void ParametersSolo::initialize(Parameters *pPin) | ^ ParametersGenome.h: In member function ‘__ct_base ’: ParametersGenome.h:8:7: note: the layout of aggregates containing vectors with 2-byte alignment has changed in GCC 5 8 | class ParametersGenome {//"constant" genome parameters - user input | ^ Parameters.cpp: In member function ‘inputParameters’: Parameters.cpp:293:6: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 293 | void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters: default, from files, from command line | ^ ReadAlignChunk.cpp: In member function ‘__ct_base ’: ReadAlignChunk.cpp:5:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 5 | ReadAlignChunk::ReadAlignChunk(Parameters& Pin, Genome &genomeIn, Transcriptome *TrIn, int iChunk) : P(Pin), mapGen(genomeIn) {//initialize chunk | ^ ParametersChimeric_initialize.cpp: In member function ‘initialize’: ParametersChimeric_initialize.cpp:8:12: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 8 | out.bam=false; | ^ Genome.h: In member function ‘operator=.isra’: Genome.h:86:12: note: the layout of aggregates containing vectors with 2-byte alignment has changed in GCC 5 86 | struct { | ^ 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 06 23:35:49 ..... started STAR run Jan 06 23:35:49 ... starting to generate Genome files Jan 06 23:35:49 ..... 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 06 23:35:49 ... starting to sort Suffix Array. This may take a long time... Jan 06 23:35:49 ... sorting Suffix Array chunks and saving them to disk... Jan 06 23:35:49 ... loading chunks from disk, packing SA... Jan 06 23:35:49 ... finished generating suffix array Jan 06 23:35:49 ... generating Suffix Array index Jan 06 23:35:49 ... completed Suffix Array index Jan 06 23:35:49 ... writing Genome to disk ... Jan 06 23:35:49 ... writing Suffix Array to disk ... Jan 06 23:35:49 ... writing SAindex to disk Jan 06 23:35:49 ..... finished successfully Jan 06 23:35:49 ..... started STAR run Jan 06 23:35:49 ..... loading genome Jan 06 23:35:49 ..... started mapping Jan 06 23:35:49 ..... finished mapping Jan 06 23:35:49 ..... finished successfully make[1]: Leaving directory '/<>/rna-star-2.7.7a+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a 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 -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a 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: 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_ppc64el.deb'. 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_ppc64el.deb'. Renaming rna-star-dbgsym_2.7.7a+dfsg-1_ppc64el.deb to rna-star-dbgsym_2.7.7a+dfsg-1_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../rna-star_2.7.7a+dfsg-1_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-01-06T23:36:05Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.7.7a+dfsg-1_ppc64el.changes: --------------------------------------- Format: 1.8 Date: Wed, 06 Jan 2021 16:28:02 +0530 Source: rna-star Binary: rna-star Architecture: ppc64el 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: c020b919e1bbd9fc1ec6ae9f8bb35209e15a6c08 6121068 rna-star-dbgsym_2.7.7a+dfsg-1_ppc64el.ddeb 997e77ad0e1f9db1fb7cbf9398be4e9a40641423 6838 rna-star_2.7.7a+dfsg-1_ppc64el.buildinfo 68e5e9e3b3803c2ffc3d43f6eb0b5c91e5fe519d 602624 rna-star_2.7.7a+dfsg-1_ppc64el.deb Checksums-Sha256: 7a9ebfd4da81e1c50d2feb45c1965cca46740131b656c3aa0fd630acdca18cee 6121068 rna-star-dbgsym_2.7.7a+dfsg-1_ppc64el.ddeb 5148bc2f788c2ff845c43f0f45bdbb78ea831817b78054b827069e7d9dce2587 6838 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rna-star-dbgsym_2.7.7a+dfsg-1_ppc64el.ddeb 68e5e9e3b3803c2ffc3d43f6eb0b5c91e5fe519d 602624 rna-star_2.7.7a+dfsg-1_ppc64el.deb Checksums-Sha256: 7a9ebfd4da81e1c50d2feb45c1965cca46740131b656c3aa0fd630acdca18cee 6121068 rna-star-dbgsym_2.7.7a+dfsg-1_ppc64el.ddeb 4fbd90c7fd3f9da023fc9597aa59bff8a8de58951ae556fcdb83995b8740fa32 602624 rna-star_2.7.7a+dfsg-1_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Wed, 06 Jan 2021 23:36:05 +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 (= 2.35.50.20210106-1ubuntu2), binutils-common (= 2.35.50.20210106-1ubuntu2), binutils-powerpc64le-linux-gnu (= 2.35.50.20210106-1ubuntu2), bsdextrautils (= 2.36.1-1ubuntu2), bsdutils (= 1:2.36.1-1ubuntu2), build-essential (= 12.8ubuntu3), 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libaudit-common (= 1:2.8.5-3ubuntu3), libaudit1 (= 1:2.8.5-3ubuntu3), libbinutils (= 2.35.50.20210106-1ubuntu2), 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), libctf-nobfd0 (= 2.35.50.20210106-1ubuntu2), libctf0 (= 2.35.50.20210106-1ubuntu2), 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), libdpkg-perl (= 1.20.5ubuntu3), libelf1 (= 0.182-3), 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), libisl23 (= 0.23-1), libitm1 (= 10.2.1-2ubuntu3), libk5crypto3 (= 1.17-10ubuntu1), libkeyutils1 (= 1.6.1-2ubuntu1), 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), 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), 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_ppc64el.deb ---------------------------------- new Debian package, version 2.0. size 602624 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: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1383 Depends: libc6 (>= 2.29), libgcc-s1 (>= 4.2), 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 1164192 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: ppc64el Build Type: any Build-Space: n/a Build-Time: 129 Distribution: hirsute-proposed Host Architecture: ppc64el Install-Time: 13 Job: rna-star_2.7.7a+dfsg-1.dsc Machine Architecture: ppc64el Package: rna-star Package-Time: 143 Source-Version: 2.7.7a+dfsg-1 Space: n/a Status: successful Version: 2.7.7a+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-01-06T23:36:05Z Build needed 00:02:23, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=ppc64el PACKAGEBUILD-20776820 Scanning for processes to kill in build PACKAGEBUILD-20776820