https://launchpad.net/ubuntu/+source/rna-star/2.7.7a+dfsg-1/+build/20776819 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-039 4.15.0-129-generic #132-Ubuntu SMP Thu Dec 10 14:07:05 UTC 2020 aarch64 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 23:51:22 ntpdate[1573]: adjust time server 10.211.37.1 offset 0.000554 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20776819 --image-type chroot /home/buildd/filecache-default/d1fb963478283f19fe8f83381d93195a7691df38 Creating target for build PACKAGEBUILD-20776819 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20776819 Starting target for build PACKAGEBUILD-20776819 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20776819 '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-20776819 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20776819 Updating target for build PACKAGEBUILD-20776819 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 arm64 Packages [1352 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe arm64 Packages [12.7 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5395 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 Packages [143 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [56.2 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe arm64 Packages [766 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [337 kB] Fetched 21.8 MB in 8s (2600 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-aarch64-linux-gnu binutils-common 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 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 104 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 79.0 MB of archives. After this operation, 57.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcrypt-dev arm64 1:4.4.17-1ubuntu1 [109 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libc6-dev arm64 2.32-0ubuntu6 [1723 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libc-dev-bin arm64 2.32-0ubuntu6 [28.7 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcrypt1 arm64 1:4.4.17-1ubuntu1 [80.8 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 linux-libc-dev arm64 5.8.0-34.37+21.04.1 [1119 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc-common all 1.3.1-1 [7452 B] Get:7 http://ftpmaster.internal/ubuntu hirsute/main arm64 libk5crypto3 arm64 1.17-10ubuntu1 [79.6 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgssapi-krb5-2 arm64 1.17-10ubuntu1 [112 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5-3 arm64 1.17-10ubuntu1 [314 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5support0 arm64 1.17-10ubuntu1 [30.2 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libssl1.1 arm64 1.1.1f-1ubuntu5 [1157 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc-dev arm64 1.3.1-1 [185 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc3 arm64 1.3.1-1 [73.3 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main arm64 libisl23 arm64 0.23-1 [586 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libcc1-0 arm64 10.2.1-2ubuntu3 [46.4 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libctf0 arm64 2.35.50.20201218-1ubuntu3 [90.8 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libctf-nobfd0 arm64 2.35.50.20201218-1ubuntu3 [90.2 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.35.50.20201218-1ubuntu3 [2505 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libbinutils arm64 2.35.50.20201218-1ubuntu3 [611 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils-common arm64 2.35.50.20201218-1ubuntu3 [216 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils arm64 2.35.50.20201218-1ubuntu3 [3368 B] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 gcc-10-base arm64 10.2.1-2ubuntu3 [19.3 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libgcc-s1 arm64 10.2.1-2ubuntu3 [34.6 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libgomp1 arm64 10.2.1-2ubuntu3 [93.6 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libitm1 arm64 10.2.1-2ubuntu3 [24.2 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libatomic1 arm64 10.2.1-2ubuntu3 [9824 B] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libasan6 arm64 10.2.1-2ubuntu3 [2026 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 liblsan0 arm64 10.2.1-2ubuntu3 [800 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libtsan0 arm64 10.2.1-2ubuntu3 [1972 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libubsan1 arm64 10.2.1-2ubuntu3 [765 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 g++-10 arm64 10.2.1-2ubuntu3 [8916 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libstdc++-10-dev arm64 10.2.1-2ubuntu3 [1719 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libgcc-10-dev arm64 10.2.1-2ubuntu3 [911 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 gcc-10 arm64 10.2.1-2ubuntu3 [15.8 MB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 cpp-10 arm64 10.2.1-2ubuntu3 [7783 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libstdc++6 arm64 10.2.1-2ubuntu3 [462 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmpc3 arm64 1.2.0-1 [42.3 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main arm64 libzstd1 arm64 1.4.8+dfsg-1 [274 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libc6 arm64 2.32-0ubuntu6 [2246 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main arm64 base-files arm64 11ubuntu16 [60.4 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main arm64 bash arm64 5.1-1ubuntu1 [632 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main arm64 bsdutils arm64 1:2.36.1-1ubuntu2 [82.6 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main arm64 coreutils arm64 8.32-4ubuntu2 [1258 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main arm64 tar arm64 1.32+dfsg-1 [262 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main arm64 dpkg arm64 1.20.5ubuntu3 [1156 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main arm64 dash arm64 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [84.1 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main arm64 grep arm64 3.6-1 [147 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main arm64 login arm64 1:4.8.1-1ubuntu7 [217 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main arm64 libncurses6 arm64 6.2+20201114-2 [92.6 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main arm64 libncursesw6 arm64 6.2+20201114-2 [120 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtinfo6 arm64 6.2+20201114-2 [81.6 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main arm64 ncurses-bin arm64 6.2+20201114-2 [168 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main arm64 libperl5.32 arm64 5.32.0-6 [3875 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl arm64 5.32.0-6 [225 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl-base arm64 5.32.0-6 [1430 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main arm64 util-linux arm64 2.36.1-1ubuntu2 [1034 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdebconfclient0 arm64 0.255ubuntu1 [6132 B] Get:59 http://ftpmaster.internal/ubuntu hirsute/main arm64 base-passwd arm64 3.5.48 [46.6 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 init-system-helpers all 1.60 [37.8 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libc-bin arm64 2.32-0ubuntu6 [520 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main arm64 ncurses-base all 6.2+20201114-2 [18.4 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main arm64 sysvinit-utils arm64 2.96-5ubuntu1 [20.4 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxxhash0 arm64 0.8.0-1 [16.8 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcrypt20 arm64 1.8.7-2ubuntu1 [354 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblz4-1 arm64 1.9.3-0ubuntu1 [52.0 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 systemd-sysv arm64 247.1-4ubuntu1 [10.3 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main arm64 libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:69 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcap-ng0 arm64 0.7.9-2.2build1 [10.5 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main arm64 libaudit1 arm64 1:2.8.5-3ubuntu3 [38.1 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre2-8-0 arm64 10.35-2ubuntu1 [172 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main arm64 libselinux1 arm64 3.1-2build2 [65.4 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsemanage-common all 3.1-1build2 [10.0 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsemanage1 arm64 3.1-1build2 [80.6 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main arm64 passwd arm64 1:4.8.1-1ubuntu7 [773 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 adduser all 3.118ubuntu4 [163 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 systemd-timesyncd arm64 247.1-4ubuntu1 [26.4 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main arm64 libapparmor1 arm64 3.0.0-0ubuntu5 [34.3 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main arm64 libblkid1 arm64 2.36.1-1ubuntu2 [124 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libudev1 arm64 247.1-4ubuntu1 [63.3 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdevmapper1.02.1 arm64 2:1.02.167-1ubuntu4 [110 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main arm64 libuuid1 arm64 2.36.1-1ubuntu2 [21.0 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcryptsetup12 arm64 2:2.3.4-1ubuntu1 [177 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main arm64 libip4tc2 arm64 1.8.5-3ubuntu4 [18.2 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libseccomp2 arm64 2.4.3-1ubuntu6 [42.6 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main arm64 mount arm64 2.36.1-1ubuntu2 [117 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 systemd arm64 247.1-4ubuntu1 [3670 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libsystemd0 arm64 247.1-4ubuntu1 [254 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main arm64 libapt-pkg6.0 arm64 2.1.15 [768 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main arm64 apt arm64 2.1.15 [1259 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 init arm64 1.60 [6036 B] Get:92 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libacl1 arm64 2.2.53-9 [16.7 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute/main arm64 libattr1 arm64 1:2.4.48-6 [12.6 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmount1 arm64 2.36.1-1ubuntu2 [137 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsmartcols1 arm64 2.36.1-1ubuntu2 [88.6 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main arm64 libidn2-0 arm64 2.3.0-4 [51.6 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main arm64 libp11-kit0 arm64 0.23.22-1 [183 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcap2 arm64 1:2.44-1 [16.7 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main arm64 readline-common all 8.1-1 [54.1 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main arm64 libreadline8 arm64 8.1-1 [129 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsqlite3-0 arm64 3.34.0-1 [542 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 openssl arm64 1.1.1f-1ubuntu5 [600 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 tzdata all 2020f-1ubuntu1 [294 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main arm64 dpkg-dev all 1.20.5ubuntu3 [758 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdpkg-perl all 1.20.5ubuntu3 [232 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfakeroot arm64 1.25.3-1.1 [26.6 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main arm64 fakeroot arm64 1.25.3-1.1 [62.4 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main arm64 libnpth0 arm64 1.6-3 [7824 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.0 MB in 4s (19.7 MB/s) (Reading database ... 12970 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu1_arm64.deb ... Unpacking libcrypt-dev:arm64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libc6-dev_2.32-0ubuntu6_arm64.deb ... Unpacking libc6-dev:arm64 (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libc-dev-bin_2.32-0ubuntu6_arm64.deb ... Unpacking libc-dev-bin (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu1_arm64.deb ... Unpacking libcrypt1:arm64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:arm64 (1:4.4.17-1ubuntu1) ... (Reading database ... 12969 files and directories currently installed.) Preparing to unpack .../00-linux-libc-dev_5.8.0-34.37+21.04.1_arm64.deb ... Unpacking linux-libc-dev:arm64 (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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Setting up libmpc3:arm64 (1.2.0-1) ... Setting up libatomic1:arm64 (10.2.1-2ubuntu3) ... Setting up libncursesw6:arm64 (6.2+20201114-2) ... Setting up libk5crypto3:arm64 (1.17-10ubuntu1) ... Setting up libperl5.32:arm64 (5.32.0-6) ... Setting up libubsan1:arm64 (10.2.1-2ubuntu3) ... Setting up libcrypt-dev:arm64 (1:4.4.17-1ubuntu1) ... Setting up libkrb5-3:arm64 (1.17-10ubuntu1) ... Setting up libbinutils:arm64 (2.35.50.20201218-1ubuntu3) ... Setting up libisl23:arm64 (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:arm64 (10.2.1-2ubuntu3) ... Setting up liblsan0:arm64 (10.2.1-2ubuntu3) ... Setting up cpp-10 (10.2.1-2ubuntu3) ... Setting up libitm1:arm64 (10.2.1-2ubuntu3) ... Setting up libtsan0:arm64 (10.2.1-2ubuntu3) ... Setting up libctf0:arm64 (2.35.50.20201218-1ubuntu3) ... Setting up libgcc-10-dev:arm64 (10.2.1-2ubuntu3) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up binutils-aarch64-linux-gnu (2.35.50.20201218-1ubuntu3) ... Setting up binutils (2.35.50.20201218-1ubuntu3) ... Setting up perl (5.32.0-6) ... Setting up libgssapi-krb5-2:arm64 (1.17-10ubuntu1) ... Setting up gcc-10 (10.2.1-2ubuntu3) ... Setting up libdpkg-perl (1.20.5ubuntu3) ... Setting up libtirpc3:arm64 (1.3.1-1) ... Setting up dpkg-dev (1.20.5ubuntu3) ... Setting up libtirpc-dev:arm64 (1.3.1-1) ... Setting up libc6-dev:arm64 (2.32-0ubuntu6) ... Setting up libstdc++-10-dev:arm64 (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-20776819 arm64 hirsute-proposed -c chroot:build-PACKAGEBUILD-20776819 --arch=arm64 --dist=hirsute-proposed --nolog rna-star_2.7.7a+dfsg-1.dsc Initiating build PACKAGEBUILD-20776819 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-129-generic #132-Ubuntu SMP Thu Dec 10 14:07:05 UTC 2020 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-039.buildd +==============================================================================+ | rna-star 2.7.7a+dfsg-1 (arm64) Wed, 06 Jan 2021 23:52:58 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.7a+dfsg-1 Source Version: 2.7.7a+dfsg-1 Distribution: hirsute-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20776819/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-QAQmUH/rna-star-2.7.7a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-QAQmUH' 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-oT5Fhw/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-oT5Fhw/apt_archive ./ InRelease Get:2 copy:/<>/resolver-oT5Fhw/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-oT5Fhw/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-oT5Fhw/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-oT5Fhw/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (33.7 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-oT5Fhw/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (29.5 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.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 (arm64 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-oT5Fhw/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-oT5Fhw/apt_archive ./ InRelease Get:2 copy:/<>/resolver-oT5Fhw/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-oT5Fhw/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-oT5Fhw/apt_archive ./ Sources [517 B] Get:5 copy:/<>/resolver-oT5Fhw/apt_archive ./ Packages [598 B] Fetched 2078 B in 0s (30.5 kB/s) Reading package lists... Reading package lists... Install rna-star build dependencies (apt-based resolver) -------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf vim-common xxd zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl vim | vim-gtk3 | vim-athena | vim-nox | vim-tiny The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-rna-star-dummy vim-common xxd zlib1g-dev 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 22.2 MB of archives. After this operation, 77.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-oT5Fhw/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [888 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main arm64 bsdextrautils arm64 2.36.1-1ubuntu2 [73.8 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main arm64 libuchardet0 arm64 0.0.7-1 [68.0 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main arm64 groff-base arm64 1.22.4-5 [797 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpipeline1 arm64 1.5.3-1 [26.1 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main arm64 man-db arm64 2.9.3-2 [1100 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmagic-mgc arm64 1:5.39-3 [228 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmagic1 arm64 1:5.39-3 [75.1 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main arm64 file arm64 1:5.39-3 [23.6 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libelf1 arm64 0.182-3 [43.4 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main arm64 libicu67 arm64 67.1-5 [8457 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxml2 arm64 2.9.10+dfsg-6.3build1 [558 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main arm64 xxd arm64 2:8.2.1913-1ubuntu3 [49.5 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main arm64 vim-common all 2:8.2.1913-1ubuntu3 [80.0 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 gettext-base arm64 0.21-3 [38.8 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpsl5 arm64 0.21.0-1.1ubuntu1 [52.0 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libsigsegv2 arm64 2.12-3 [13.8 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 m4 arm64 1.4.18-5 [194 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main arm64 autoconf all 2.69-14 [293 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main arm64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main arm64 automake all 1:1.16.3-2ubuntu1 [552 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 autopoint all 0.21-3 [423 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtool all 2.4.6-14 [161 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main arm64 dh-autoreconf all 19 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libdebhelper-perl all 13.3ubuntu4 [63.8 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:28 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main arm64 dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:30 http://ftpmaster.internal/ubuntu hirsute/main arm64 dwz arm64 0.13+20201015-2 [153 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 gettext arm64 0.21-3 [775 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 debhelper all 13.3ubuntu4 [881 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-2 [39.4 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-2 [150 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main arm64 libbrotli1 arm64 1.0.9-2build2 [262 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-2 [27.9 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-2 [84.8 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-2 [47.2 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-2 [98.6 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-2 [192 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-2 [14.8 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-2 [88.4 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2ubuntu1 [14.9 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2ubuntu1 [48.4 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main arm64 libldap-2.4-2 arm64 2.4.56+dfsg-1ubuntu1 [145 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main arm64 libnghttp2-14 arm64 1.42.0-1 [68.6 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build2 [53.1 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main arm64 libssh-4 arm64 0.9.5-1 [160 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcurl3-gnutls arm64 7.72.0-1ubuntu1 [215 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcurl4-gnutls-dev arm64 7.72.0-1ubuntu1 [312 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdeflate0 arm64 1.7-1 [47.2 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdeflate-dev arm64 1.7-1 [43.2 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libhts3 arm64 1.11-4 [320 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblzma-dev arm64 5.2.4-1ubuntu1 [144 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu4 [154 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libhts-dev arm64 1.11-4 [3833 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 22.2 MB in 1s (16.8 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-1ubuntu2_arm64.deb ... Unpacking bsdextrautils (2.36.1-1ubuntu2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_arm64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_arm64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... 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Preparing to unpack .../57-sbuild-build-depends-rna-star-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up libpsl5:arm64 (0.21.0-1.1ubuntu1) ... Setting up bsdextrautils (2.36.1-1ubuntu2) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-5) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3ubuntu4) ... Setting up libbrotli1:arm64 (1.0.9-2build2) ... Setting up libnghttp2-14:arm64 (1.42.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up gettext-base (0.21-3) ... Setting up file (1:5.39-3) ... Setting up xxd (2:8.2.1913-1ubuntu3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2ubuntu1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up vim-common (2:8.2.1913-1ubuntu3) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:arm64 (2.12-3) ... Setting up autopoint (0.21-3) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:arm64 (0.9.5-1) ... Setting up libroken18-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up liblzma-dev:arm64 (5.2.4-1ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu4) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:arm64 (1.7-1) ... Setting up libelf1:arm64 (0.182-3) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.3build1) ... Setting up libheimbase1-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up gettext (0.21-3) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-5) ... Setting up libhcrypto4-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libwind0-heimdal:arm64 (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:arm64 (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:arm64 (7.7.0+dfsg-2) ... Setting up libheimntlm0-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:arm64 (2.4.56+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.72.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:arm64 (7.72.0-1ubuntu1) ... Setting up libhts3:arm64 (1.11-4) ... Setting up libhts-dev:arm64 (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 arm64 (aarch64) Toolchain package versions: binutils_2.35.50.20201218-1ubuntu3 dpkg-dev_1.20.5ubuntu3 g++-10_10.2.1-2ubuntu3 gcc-10_10.2.1-2ubuntu3 libc6-dev_2.32-0ubuntu6 libstdc++-10-dev_10.2.1-2ubuntu3 libstdc++6_10.2.1-2ubuntu3 linux-libc-dev_5.8.0-34.37+21.04.1 Package versions: adduser_3.118ubuntu4 advancecomp_2.1-2.1build1 apt_2.1.15 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1-1ubuntu1 binutils_2.35.50.20201218-1ubuntu3 binutils-aarch64-linux-gnu_2.35.50.20201218-1ubuntu3 binutils-common_2.35.50.20201218-1ubuntu3 bsdextrautils_2.36.1-1ubuntu2 bsdutils_1:2.36.1-1ubuntu2 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.32-4ubuntu2 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.1-2ubuntu3 dash_0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 debconf_1.5.74 debhelper_13.3ubuntu4 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.5ubuntu3 dpkg-dev_1.20.5ubuntu3 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.7.0-1ubuntu2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.1-2ubuntu3 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.1-2ubuntu3 gcc-10-base_10.2.1-2ubuntu3 gettext_0.21-3 gettext-base_0.21-3 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.60 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-9 libapparmor1_3.0.0-0ubuntu5 libapt-pkg6.0_2.1.15 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.1-2ubuntu3 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.2.1-2ubuntu3 libattr1_1:2.4.48-6 libaudit-common_1:2.8.5-3ubuntu3 libaudit1_1:2.8.5-3ubuntu3 libbinutils_2.35.50.20201218-1ubuntu3 libblkid1_2.36.1-1ubuntu2 libbrotli1_1.0.9-2build2 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu6 libc-dev-bin_2.32-0ubuntu6 libc6_2.32-0ubuntu6 libc6-dev_2.32-0ubuntu6 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1 libcc1-0_10.2.1-2ubuntu3 libcom-err2_1.45.6-1ubuntu1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.4-1ubuntu1 libctf-nobfd0_2.35.50.20201218-1ubuntu3 libctf0_2.35.50.20201218-1ubuntu3 libcurl3-gnutls_7.72.0-1ubuntu1 libcurl4-gnutls-dev_7.72.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.255ubuntu1 libdebhelper-perl_13.3ubuntu4 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdevmapper1.02.1_2:1.02.167-1ubuntu4 libdpkg-perl_1.20.5ubuntu3 libelf1_0.182-3 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.3-1.1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.1-2ubuntu3 libgcc-s1_10.2.1-2ubuntu3 libgcrypt20_1.8.7-2ubuntu1 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.6.15-4ubuntu2 libgomp1_10.2.1-2ubuntu3 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10ubuntu1 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.11-4 libhts3_1.11-4 libhx509-5-heimdal_7.7.0+dfsg-2 libicu67_67.1-5 libidn2-0_2.3.0-4 libip4tc2_1.8.5-3ubuntu4 libisl22_0.22.1-1 libisl23_0.23-1 libitm1_10.2.1-2ubuntu3 libjson-c5_0.15-1 libk5crypto3_1.17-10ubuntu1 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10ubuntu1 libkrb5support0_1.17-10ubuntu1 libldap-2.4-2_2.4.56+dfsg-1ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.2.1-2ubuntu3 liblz4-1_1.9.3-0ubuntu1 liblzma-dev_5.2.4-1ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-1ubuntu2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-0ubuntu3 libnsl2_1.3.0-0ubuntu3 libnss-nis_3.1-0ubuntu4 libnss-nisplus_1.3-0ubuntu4 libp11-kit0_0.23.22-1 libpam-modules_1.3.1-5ubuntu6 libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpcre2-8-0_10.35-2ubuntu1 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libperl5.32_5.32.0-6 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpsl5_0.21.0-1.1ubuntu1 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-20776819 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20776819 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20776819 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 arm64 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 -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" cd source && make -j4 "INSTALL=install --strip-program=true" "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>/rna-star-2.7.7a+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_collapseUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_processRecords.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool)’: SoloFeature_outputResults.cpp:45:17: warning: ignoring return value of ‘int symlink(const char*, const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | symlink("../../../SJ.out.tab", (outputPrefix1+pSolo.outFileNames[1]).c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_samAttributes.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:184:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 184 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:188:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 188 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bam_cat.c bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMoutput.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortByCoordinate.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:77:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 77 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:79:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 79 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:82:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:86:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:90:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamRemoveDuplicates.cpp 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 -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortUnmapped.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:125:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:152:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:248:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 248 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:249:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 249 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.7a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_collapseUMI.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:52:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/rna-star-2.7.7a+dfsg/source' make[1]: Leaving directory '/<>/rna-star-2.7.7a+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/rna-star-2.7.7a+dfsg' debian/tests/run_test.sh /<>/rna-star-2.7.7a+dfsg/source/STAR Jan 07 00:00:19 ..... started STAR run Jan 07 00:00:19 ... starting to generate Genome files Jan 07 00:00:19 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 Jan 07 00:00:19 ... starting to sort Suffix Array. This may take a long time... Jan 07 00:00:19 ... sorting Suffix Array chunks and saving them to disk... Jan 07 00:00:19 ... loading chunks from disk, packing SA... Jan 07 00:00:19 ... finished generating suffix array Jan 07 00:00:19 ... generating Suffix Array index Jan 07 00:00:19 ... completed Suffix Array index Jan 07 00:00:19 ... writing Genome to disk ... Jan 07 00:00:19 ... writing Suffix Array to disk ... Jan 07 00:00:19 ... writing SAindex to disk Jan 07 00:00:19 ..... finished successfully Jan 07 00:00:19 ..... started STAR run Jan 07 00:00:19 ..... loading genome Jan 07 00:00:19 ..... started mapping Jan 07 00:00:20 ..... finished mapping Jan 07 00:00:20 ..... 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: 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. 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' in '../rna-star_2.7.7a+dfsg-1_arm64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in 'debian/.debhelper/scratch-space/build-rna-star/rna-star-dbgsym_2.7.7a+dfsg-1_arm64.deb'. Renaming rna-star-dbgsym_2.7.7a+dfsg-1_arm64.deb to rna-star-dbgsym_2.7.7a+dfsg-1_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../rna-star_2.7.7a+dfsg-1_arm64.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 2021-01-07T00:00:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.7.7a+dfsg-1_arm64.changes: ------------------------------------- Format: 1.8 Date: Wed, 06 Jan 2021 16:28:02 +0530 Source: rna-star Binary: rna-star Architecture: arm64 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: 9286bd3a7968b87765729977c946b0044173e960 5626168 rna-star-dbgsym_2.7.7a+dfsg-1_arm64.ddeb 3b1affa4a69606f07a4b115914b1f749771b22e9 6783 rna-star_2.7.7a+dfsg-1_arm64.buildinfo 00ce4866af82e15ca2c35cbd65fb9404c872082d 527792 rna-star_2.7.7a+dfsg-1_arm64.deb Checksums-Sha256: ca3c7b61d2e76407f1f666461721a6090c2ec49aad4fcbaee52c75c5ac9575a5 5626168 rna-star-dbgsym_2.7.7a+dfsg-1_arm64.ddeb effc9cb2be8e6d0c1c43106db9ebf9dd5b75848e04abb2ba617124b3ea3c06a2 6783 rna-star_2.7.7a+dfsg-1_arm64.buildinfo 5131d18254c82565640de2853aab2c13132a6d2b3026cf13c4319bb96583f495 527792 rna-star_2.7.7a+dfsg-1_arm64.deb Files: 5058579ab1e55094df8a8a6d5071a4f9 5626168 debug optional rna-star-dbgsym_2.7.7a+dfsg-1_arm64.ddeb b8cc066cb885e9784f496e685b989f07 6783 science optional rna-star_2.7.7a+dfsg-1_arm64.buildinfo 3764693783aa05675936f600b174ec08 527792 science optional rna-star_2.7.7a+dfsg-1_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: rna-star Binary: rna-star rna-star-dbgsym Architecture: arm64 Version: 2.7.7a+dfsg-1 Checksums-Md5: 5058579ab1e55094df8a8a6d5071a4f9 5626168 rna-star-dbgsym_2.7.7a+dfsg-1_arm64.ddeb 3764693783aa05675936f600b174ec08 527792 rna-star_2.7.7a+dfsg-1_arm64.deb Checksums-Sha1: 9286bd3a7968b87765729977c946b0044173e960 5626168 rna-star-dbgsym_2.7.7a+dfsg-1_arm64.ddeb 00ce4866af82e15ca2c35cbd65fb9404c872082d 527792 rna-star_2.7.7a+dfsg-1_arm64.deb Checksums-Sha256: ca3c7b61d2e76407f1f666461721a6090c2ec49aad4fcbaee52c75c5ac9575a5 5626168 rna-star-dbgsym_2.7.7a+dfsg-1_arm64.ddeb 5131d18254c82565640de2853aab2c13132a6d2b3026cf13c4319bb96583f495 527792 rna-star_2.7.7a+dfsg-1_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Thu, 07 Jan 2021 00:00:51 +0000 Build-Path: /<>/rna-star-2.7.7a+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-14), automake (= 1:1.16.3-2ubuntu1), autopoint (= 0.21-3), autotools-dev (= 20180224.1+nmu1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.1-1ubuntu1), binutils (= 2.35.50.20201218-1ubuntu3), binutils-aarch64-linux-gnu (= 2.35.50.20201218-1ubuntu3), binutils-common (= 2.35.50.20201218-1ubuntu3), bsdextrautils (= 2.36.1-1ubuntu2), bsdutils (= 1:2.36.1-1ubuntu2), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), coreutils (= 8.32-4ubuntu2), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 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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), 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_arm64.deb -------------------------------- new Debian package, version 2.0. size 527792 bytes: control archive=1424 bytes. 1447 bytes, 25 lines control 602 bytes, 9 lines md5sums Package: rna-star Version: 2.7.7a+dfsg-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1099 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 873280 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: arm64 Build Type: any Build-Space: n/a Build-Time: 437 Distribution: hirsute-proposed Host Architecture: arm64 Install-Time: 33 Job: rna-star_2.7.7a+dfsg-1.dsc Machine Architecture: arm64 Package: rna-star Package-Time: 474 Source-Version: 2.7.7a+dfsg-1 Space: n/a Status: successful Version: 2.7.7a+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-01-07T00:00:52Z Build needed 00:07:54, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20776819 Scanning for processes to kill in build PACKAGEBUILD-20776819