https://launchpad.net/ubuntu/+source/rna-star/2.7.8a+dfsg-2/+build/21143309 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-002 4.15.0-136-generic #140-Ubuntu SMP Thu Jan 28 05:23:14 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_194~476~ubuntu18.04.1 python3-lpbuildd_194~476~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... 11 Mar 02:34:01 ntpdate[1781]: adjust time server 10.211.37.1 offset -0.053849 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-21143309 --image-type chroot /home/buildd/filecache-default/d1fb963478283f19fe8f83381d93195a7691df38 Creating target for build PACKAGEBUILD-21143309 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-21143309 Starting target for build PACKAGEBUILD-21143309 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-21143309 '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-21143309 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-21143309 Updating target for build PACKAGEBUILD-21143309 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 [1372 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe arm64 Packages [12.9 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5445 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 Packages [87.6 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [30.9 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe arm64 Packages [219 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [97.6 kB] Fetched 21.2 MB in 4s (5006 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: gcc-11-base libisl23 libperl5.32 libxxhash0 lto-disabled-list 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 ca-certificates coreutils cpp-10 dash dpkg dpkg-dev e2fsprogs fakeroot findutils g++-10 gcc-10 gcc-10-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan6 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libffi8ubuntu1 libgcc-10-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed6 libidn2-0 libip4tc2 libitm1 libjson-c5 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblockfile-bin liblockfile1 liblsan0 liblz4-1 liblzma5 libmount1 libmpc3 libncurses6 libncursesw6 libnettle8 libnpth0 libp11-kit0 libpcre2-8-0 libpcre3 libpng16-16 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave mount ncurses-base ncurses-bin openssl passwd patch perl perl-base pkgbinarymangler readline-common sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata ubuntu-keyring util-linux xz-utils zlib1g 139 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 84.1 MB of archives. After this operation, 58.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcrypt-dev arm64 1:4.4.17-1ubuntu2 [109 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute/main arm64 libc6-dev arm64 2.33-0ubuntu2 [1719 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main arm64 libc-dev-bin arm64 2.33-0ubuntu2 [18.3 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcrypt1 arm64 1:4.4.17-1ubuntu2 [80.9 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 linux-libc-dev arm64 5.11.0-11.12 [1135 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc-common all 1.3.1-1build1 [7316 B] Get:7 http://ftpmaster.internal/ubuntu hirsute/main arm64 libk5crypto3 arm64 1.18.3-4 [77.9 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgssapi-krb5-2 arm64 1.18.3-4 [119 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5-3 arm64 1.18.3-4 [309 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5support0 arm64 1.18.3-4 [30.3 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcom-err2 arm64 1.45.7-1ubuntu2 [10.1 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main arm64 libssl1.1 arm64 1.1.1j-1ubuntu1 [1158 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc-dev arm64 1.3.1-1build1 [185 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc3 arm64 1.3.1-1build1 [73.0 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main arm64 libc6 arm64 2.33-0ubuntu2 [2254 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main arm64 libc-bin arm64 2.33-0ubuntu2 [532 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main arm64 gcc-11-base arm64 11-20210306-1ubuntu1 [18.9 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcc-s1 arm64 11-20210306-1ubuntu1 [34.4 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main arm64 base-files arm64 11ubuntu18 [60.4 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main arm64 bash arm64 5.1-1ubuntu1 [632 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main arm64 bsdutils arm64 1:2.36.1-7ubuntu2 [83.3 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main arm64 coreutils arm64 8.32-4ubuntu2 [1258 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main arm64 tar arm64 1.34+dfsg-1build1 [264 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main arm64 dpkg arm64 1.20.7.1ubuntu3 [1241 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main arm64 dash arm64 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [84.1 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main arm64 findutils arm64 4.8.0-1ubuntu1 [323 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main arm64 grep arm64 3.6-1 [147 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main arm64 gzip arm64 1.10-2ubuntu3 [92.1 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main arm64 login arm64 1:4.8.1-1ubuntu8 [217 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main arm64 libncurses6 arm64 6.2+20201114-2build1 [92.5 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main arm64 libncursesw6 arm64 6.2+20201114-2build1 [120 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtinfo6 arm64 6.2+20201114-2build1 [81.4 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main arm64 ncurses-bin arm64 6.2+20201114-2build1 [168 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl-modules-5.32 all 5.32.1-2 [2755 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main arm64 libperl5.32 arm64 5.32.1-2 [3858 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl arm64 5.32.1-2 [225 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl-base arm64 5.32.1-2 [1430 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgdbm6 arm64 1.19-2 [26.5 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgdbm-compat4 arm64 1.19-2 [6020 B] Get:40 http://ftpmaster.internal/ubuntu hirsute/main arm64 zlib1g arm64 1:1.2.11.dfsg-2ubuntu5 [51.1 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main arm64 util-linux arm64 2.36.1-7ubuntu2 [1031 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdebconfclient0 arm64 0.256ubuntu3 [6032 B] Get:43 http://ftpmaster.internal/ubuntu hirsute/main arm64 base-passwd arm64 3.5.49 [46.6 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main arm64 init-system-helpers all 1.60 [37.8 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main arm64 ncurses-base all 6.2+20201114-2build1 [18.4 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main arm64 sysvinit-utils arm64 2.96-5ubuntu1 [20.4 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxxhash0 arm64 0.8.0-2 [16.9 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgpg-error0 arm64 1.38-2build1 [60.3 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcrypt20 arm64 1.8.7-2ubuntu2 [352 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblz4-1 arm64 1.9.3-1build1 [51.8 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblzma5 arm64 5.2.5-1.0build1 [89.8 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main arm64 libstdc++6 arm64 11-20210306-1ubuntu1 [533 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgmp10 arm64 2:6.2.1+dfsg-1ubuntu1 [214 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main arm64 libnettle8 arm64 3.7-2.1 [152 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main arm64 libhogweed6 arm64 3.7-2.1 [191 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main arm64 libidn2-0 arm64 2.3.0-5 [51.3 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main arm64 libffi8ubuntu1 arm64 3.4~20200819gead65ca871-0ubuntu5 [17.4 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main arm64 libp11-kit0 arm64 0.23.22-1 [183 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgnutls30 arm64 3.7.0-5ubuntu1 [844 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main arm64 systemd-sysv arm64 247.3-1ubuntu4 [10.3 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main arm64 libaudit-common all 1:3.0-2ubuntu1 [4836 B] Get:62 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcap-ng0 arm64 0.7.9-2.2build1 [10.5 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main arm64 libaudit1 arm64 1:3.0-2ubuntu1 [39.5 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre2-8-0 arm64 10.36-2ubuntu4 [173 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main arm64 libselinux1 arm64 3.1-3build1 [65.3 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsemanage-common all 3.1-1build2 [10.0 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsemanage1 arm64 3.1-1build2 [80.6 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main arm64 passwd arm64 1:4.8.1-1ubuntu8 [770 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main arm64 adduser all 3.118ubuntu5 [156 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main arm64 systemd-timesyncd arm64 247.3-1ubuntu4 [26.3 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main arm64 libapparmor1 arm64 3.0.0-0ubuntu6 [34.2 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main arm64 libargon2-1 arm64 0~20171227-0.2build21.04.0 [18.5 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main arm64 libblkid1 arm64 2.36.1-7ubuntu2 [125 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main arm64 libudev1 arm64 247.3-1ubuntu4 [64.2 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdevmapper1.02.1 arm64 2:1.02.175-2ubuntu3 [111 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main arm64 libjson-c5 arm64 0.15-2build1 [29.4 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main arm64 libuuid1 arm64 2.36.1-7ubuntu2 [21.6 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcryptsetup12 arm64 2:2.3.4-1ubuntu3 [177 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main arm64 libip4tc2 arm64 1.8.7-1ubuntu2 [18.2 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkmod2 arm64 28-1ubuntu2 [41.0 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main arm64 libseccomp2 arm64 2.5.1-1ubuntu1 [41.8 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main arm64 mount arm64 2.36.1-7ubuntu2 [117 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main arm64 systemd arm64 247.3-1ubuntu4 [3674 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsystemd0 arm64 247.3-1ubuntu4 [255 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main arm64 libzstd1 arm64 1.4.8+dfsg-2build1 [275 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main arm64 libapt-pkg6.0 arm64 2.2.1 [777 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 gpgv arm64 2.2.20-1ubuntu3 [184 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main arm64 ubuntu-keyring all 2020.06.17.1build1 [22.1 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main arm64 apt arm64 2.2.1 [1275 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main arm64 logsave arm64 1.45.7-1ubuntu2 [10.8 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main arm64 libext2fs2 arm64 1.45.7-1ubuntu2 [179 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute/main arm64 e2fsprogs arm64 1.45.7-1ubuntu2 [509 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute/main arm64 init arm64 1.60 [6036 B] Get:94 http://ftpmaster.internal/ubuntu hirsute/main arm64 libacl1 arm64 2.2.53-10build1 [16.0 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main arm64 libattr1 arm64 1:2.4.48-6build1 [12.5 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmount1 arm64 2.36.1-7ubuntu2 [137 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre3 arm64 2:8.39-13build2 [211 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsmartcols1 arm64 2.36.1-7ubuntu2 [88.9 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgomp1 arm64 11-20210306-1ubuntu1 [98.2 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main arm64 libitm1 arm64 11-20210306-1ubuntu1 [24.1 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main arm64 libatomic1 arm64 11-20210306-1ubuntu1 [9852 B] Get:102 http://ftpmaster.internal/ubuntu hirsute/main arm64 libasan6 arm64 10.2.1-21ubuntu1 [2025 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblsan0 arm64 10.2.1-21ubuntu1 [799 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtsan0 arm64 10.2.1-21ubuntu1 [1971 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main arm64 libubsan1 arm64 10.2.1-21ubuntu1 [764 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main arm64 g++-10 arm64 10.2.1-21ubuntu1 [8919 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main arm64 gcc-10 arm64 10.2.1-21ubuntu1 [15.8 MB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main arm64 libstdc++-10-dev arm64 10.2.1-21ubuntu1 [1716 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcc-10-dev arm64 10.2.1-21ubuntu1 [910 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute/main arm64 libisl23 arm64 0.23-1 [586 kB] Get:111 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmpc3 arm64 1.2.0-1 [42.3 kB] Get:112 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcc1-0 arm64 11-20210306-1ubuntu1 [46.6 kB] Get:113 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libctf0 arm64 2.36.1-5ubuntu1 [89.5 kB] Get:114 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libctf-nobfd0 arm64 2.36.1-5ubuntu1 [92.9 kB] Get:115 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.36.1-5ubuntu1 [2523 kB] Get:116 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libbinutils arm64 2.36.1-5ubuntu1 [619 kB] Get:117 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils arm64 2.36.1-5ubuntu1 [3352 B] Get:118 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils-common arm64 2.36.1-5ubuntu1 [217 kB] Get:119 http://ftpmaster.internal/ubuntu hirsute/main arm64 cpp-10 arm64 10.2.1-21ubuntu1 [7784 kB] Get:120 http://ftpmaster.internal/ubuntu hirsute/main arm64 gcc-10-base arm64 10.2.1-21ubuntu1 [20.3 kB] Get:121 http://ftpmaster.internal/ubuntu hirsute/main arm64 libss2 arm64 1.45.7-1ubuntu2 [10.8 kB] Get:122 http://ftpmaster.internal/ubuntu hirsute/main arm64 sensible-utils all 0.0.14 [13.5 kB] Get:123 http://ftpmaster.internal/ubuntu hirsute/main arm64 openssl arm64 1.1.1j-1ubuntu1 [599 kB] Get:124 http://ftpmaster.internal/ubuntu hirsute/main arm64 ca-certificates all 20210119build1 [147 kB] Get:125 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcap2 arm64 1:2.44-1build1 [16.2 kB] Get:126 http://ftpmaster.internal/ubuntu hirsute/main arm64 readline-common all 8.1-1 [54.1 kB] Get:127 http://ftpmaster.internal/ubuntu hirsute/main arm64 libreadline8 arm64 8.1-1 [129 kB] Get:128 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libsqlite3-0 arm64 3.34.1-3 [541 kB] Get:129 http://ftpmaster.internal/ubuntu hirsute/main arm64 tzdata all 2021a-1ubuntu1 [294 kB] Get:130 http://ftpmaster.internal/ubuntu hirsute/main arm64 xz-utils arm64 5.2.5-1.0build1 [80.2 kB] Get:131 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpng16-16 arm64 1.6.37-3build2 [174 kB] Get:132 http://ftpmaster.internal/ubuntu hirsute/main arm64 dpkg-dev all 1.20.7.1ubuntu3 [935 kB] Get:133 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdpkg-perl all 1.20.7.1ubuntu3 [233 kB] Get:134 http://ftpmaster.internal/ubuntu hirsute/main arm64 patch arm64 2.7.6-7 [97.8 kB] Get:135 http://ftpmaster.internal/ubuntu hirsute/main arm64 lto-disabled-list all 1 [1996 B] Get:136 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfakeroot arm64 1.25.3-1.1ubuntu2 [27.1 kB] Get:137 http://ftpmaster.internal/ubuntu hirsute/main arm64 fakeroot arm64 1.25.3-1.1ubuntu2 [62.3 kB] Get:138 http://ftpmaster.internal/ubuntu hirsute/main arm64 libassuan0 arm64 2.5.4-1ubuntu1 [33.2 kB] Get:139 http://ftpmaster.internal/ubuntu hirsute/main arm64 libnpth0 arm64 1.6-3 [7824 B] Get:140 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 gpg arm64 2.2.20-1ubuntu3 [445 kB] Get:141 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 gpgconf arm64 2.2.20-1ubuntu3 [117 kB] Get:142 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 gpg-agent arm64 2.2.20-1ubuntu3 [216 kB] Get:143 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblockfile-bin arm64 1.17-1 [11.5 kB] Get:144 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblockfile1 arm64 1.17-1 [6460 B] Get:145 http://ftpmaster.internal/ubuntu hirsute/main arm64 pkgbinarymangler all 147 [31.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.1 MB in 1s (58.5 MB/s) (Reading database ... 12970 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu2_arm64.deb ... Unpacking libcrypt-dev:arm64 (1:4.4.17-1ubuntu2) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libc6-dev_2.33-0ubuntu2_arm64.deb ... Unpacking libc6-dev:arm64 (2.33-0ubuntu2) over (2.32-0ubuntu3) ... Preparing to unpack .../libc-dev-bin_2.33-0ubuntu2_arm64.deb ... Unpacking libc-dev-bin (2.33-0ubuntu2) over (2.32-0ubuntu3) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu2_arm64.deb ... Unpacking libcrypt1:arm64 (1:4.4.17-1ubuntu2) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:arm64 (1:4.4.17-1ubuntu2) ... (Reading database ... 12968 files and directories currently installed.) Preparing to unpack .../00-linux-libc-dev_5.11.0-11.12_arm64.deb ... Unpacking linux-libc-dev:arm64 (5.11.0-11.12) over (5.8.0-25.26) ... Preparing to unpack .../01-libtirpc-common_1.3.1-1build1_all.deb ... Unpacking libtirpc-common (1.3.1-1build1) over (1.2.6-1build1) ... Preparing to unpack .../02-libk5crypto3_1.18.3-4_arm64.deb ... Unpacking libk5crypto3:arm64 (1.18.3-4) over (1.17-10) ... Preparing to unpack .../03-libgssapi-krb5-2_1.18.3-4_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.18.3-4) over (1.17-10) ... Preparing to unpack .../04-libkrb5-3_1.18.3-4_arm64.deb ... Unpacking libkrb5-3:arm64 (1.18.3-4) over (1.17-10) ... Preparing to unpack .../05-libkrb5support0_1.18.3-4_arm64.deb ... Unpacking libkrb5support0:arm64 (1.18.3-4) over (1.17-10) ... Preparing to unpack .../06-libcom-err2_1.45.7-1ubuntu2_arm64.deb ... Unpacking libcom-err2:arm64 (1.45.7-1ubuntu2) over (1.45.6-1ubuntu1) ... Preparing to unpack .../07-libssl1.1_1.1.1j-1ubuntu1_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1j-1ubuntu1) over (1.1.1f-1ubuntu4) ... Preparing to unpack .../08-libtirpc-dev_1.3.1-1build1_arm64.deb ... Unpacking libtirpc-dev:arm64 (1.3.1-1build1) over (1.2.6-1build1) ... Preparing to unpack .../09-libtirpc3_1.3.1-1build1_arm64.deb ... Unpacking libtirpc3:arm64 (1.3.1-1build1) over (1.2.6-1build1) ... Preparing to unpack .../10-libc6_2.33-0ubuntu2_arm64.deb ... Unpacking libc6:arm64 (2.33-0ubuntu2) over (2.32-0ubuntu3) ... Setting up libc6:arm64 (2.33-0ubuntu2) ... (Reading database ... 12970 files and directories currently installed.) Preparing to unpack .../libc-bin_2.33-0ubuntu2_arm64.deb ... Unpacking libc-bin (2.33-0ubuntu2) over (2.32-0ubuntu3) ... Setting up libc-bin (2.33-0ubuntu2) ... Selecting previously unselected package gcc-11-base:arm64. (Reading database ... 12970 files and directories currently installed.) Preparing to unpack .../gcc-11-base_11-20210306-1ubuntu1_arm64.deb ... Unpacking gcc-11-base:arm64 (11-20210306-1ubuntu1) ... Setting up gcc-11-base:arm64 (11-20210306-1ubuntu1) ... (Reading database ... 12975 files and directories currently installed.) Preparing to unpack .../libgcc-s1_11-20210306-1ubuntu1_arm64.deb ... Unpacking libgcc-s1:arm64 (11-20210306-1ubuntu1) over (10.2.0-13ubuntu1) ... Setting up libgcc-s1:arm64 (11-20210306-1ubuntu1) ... (Reading database ... 12975 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu18_arm64.deb ... Unpacking base-files (11ubuntu18) over (11ubuntu14) ... Setting up base-files (11ubuntu18) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12975 files and directories currently installed.) Preparing to unpack .../bash_5.1-1ubuntu1_arm64.deb ... Unpacking bash (5.1-1ubuntu1) over (5.0-6ubuntu2) ... Setting up bash (5.1-1ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12975 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.36.1-7ubuntu2_arm64.deb ... Unpacking bsdutils (1:2.36.1-7ubuntu2) over (1:2.36-3ubuntu1) ... Setting up bsdutils (1:2.36.1-7ubuntu2) ... (Reading database ... 12975 files and directories currently installed.) Preparing to unpack .../coreutils_8.32-4ubuntu2_arm64.deb ... Unpacking coreutils (8.32-4ubuntu2) over (8.32-3ubuntu1) ... Setting up coreutils (8.32-4ubuntu2) ... (Reading database ... 12975 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1build1_arm64.deb ... Unpacking tar (1.34+dfsg-1build1) over (1.30+dfsg-7) ... Setting up tar (1.34+dfsg-1build1) ... (Reading database ... 12975 files and directories currently installed.) Preparing to unpack .../dpkg_1.20.7.1ubuntu3_arm64.deb ... Unpacking dpkg (1.20.7.1ubuntu3) over (1.20.5ubuntu2) ... Setting up dpkg (1.20.7.1ubuntu3) ... Installing new version of config file /etc/cron.daily/dpkg ... (Reading database ... 12989 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1_arm64.deb ... Unpacking dash (0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1) over (0.5.10.2-7) ... Setting up dash (0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1) ... (Reading database ... 12989 files and directories currently installed.) Preparing to unpack .../findutils_4.8.0-1ubuntu1_arm64.deb ... Unpacking findutils (4.8.0-1ubuntu1) over (4.7.0-1ubuntu2) ... Setting up findutils (4.8.0-1ubuntu1) ... (Reading database ... 12989 files and directories currently installed.) Preparing to unpack .../archives/grep_3.6-1_arm64.deb ... Unpacking grep (3.6-1) over (3.4-1) ... Setting up grep (3.6-1) ... (Reading database ... 12990 files and directories currently installed.) Preparing to unpack .../gzip_1.10-2ubuntu3_arm64.deb ... Unpacking gzip (1.10-2ubuntu3) over (1.10-2ubuntu1) ... Setting up gzip (1.10-2ubuntu3) ... (Reading database ... 12990 files and directories currently installed.) Preparing to unpack .../login_1%3a4.8.1-1ubuntu8_arm64.deb ... Unpacking login (1:4.8.1-1ubuntu8) over (1:4.8.1-1ubuntu6) ... Setting up login (1:4.8.1-1ubuntu8) ... Installing new version of config file /etc/login.defs ... (Reading database ... 12990 files and directories currently installed.) Preparing to unpack .../libncurses6_6.2+20201114-2build1_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2build1) over (6.2-1) ... Preparing to unpack .../libncursesw6_6.2+20201114-2build1_arm64.deb ... Unpacking libncursesw6:arm64 (6.2+20201114-2build1) over (6.2-1) ... Preparing to unpack .../libtinfo6_6.2+20201114-2build1_arm64.deb ... Unpacking libtinfo6:arm64 (6.2+20201114-2build1) over (6.2-1) ... Setting up libtinfo6:arm64 (6.2+20201114-2build1) ... (Reading database ... 12990 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.2+20201114-2build1_arm64.deb ... Unpacking ncurses-bin (6.2+20201114-2build1) over (6.2-1) ... Setting up ncurses-bin (6.2+20201114-2build1) ... (Reading database ... 12990 files and directories currently installed.) Preparing to unpack .../perl_5.32.1-2_arm64.deb ... Unpacking perl (5.32.1-2) over (5.30.3-4) ... Selecting previously unselected package perl-modules-5.32. Preparing to unpack .../perl-modules-5.32_5.32.1-2_all.deb ... Unpacking perl-modules-5.32 (5.32.1-2) ... Selecting previously unselected package libperl5.32:arm64. Preparing to unpack .../libperl5.32_5.32.1-2_arm64.deb ... Unpacking libperl5.32:arm64 (5.32.1-2) ... Preparing to unpack .../perl-base_5.32.1-2_arm64.deb ... Unpacking perl-base (5.32.1-2) over (5.30.3-4) ... Setting up perl-base (5.32.1-2) ... (Reading database ... 14918 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.19-2_arm64.deb ... Unpacking libgdbm6:arm64 (1.19-2) over (1.18.1-5.1) ... Preparing to unpack .../libgdbm-compat4_1.19-2_arm64.deb ... Unpacking libgdbm-compat4:arm64 (1.19-2) over (1.18.1-5.1) ... Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-2ubuntu5_arm64.deb ... Unpacking zlib1g:arm64 (1:1.2.11.dfsg-2ubuntu5) over (1:1.2.11.dfsg-2ubuntu4) ... Setting up zlib1g:arm64 (1:1.2.11.dfsg-2ubuntu5) ... (Reading database ... 14918 files and directories currently installed.) Preparing to unpack .../util-linux_2.36.1-7ubuntu2_arm64.deb ... Unpacking util-linux (2.36.1-7ubuntu2) over (2.36-3ubuntu1) ... Setting up util-linux (2.36.1-7ubuntu2) ... Installing new version of config file /etc/init.d/hwclock.sh ... (Reading database ... 14919 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.256ubuntu3_arm64.deb ... Unpacking libdebconfclient0:arm64 (0.256ubuntu3) over (0.252ubuntu1) ... Setting up libdebconfclient0:arm64 (0.256ubuntu3) ... (Reading database ... 14919 files and directories currently installed.) Preparing to unpack .../base-passwd_3.5.49_arm64.deb ... Unpacking base-passwd (3.5.49) over (3.5.47) ... Setting up base-passwd (3.5.49) ... Changing home-directory of irc from /var/run/ircd to /run/ircd 1 changes have been made, rewriting files Writing passwd-file to /etc/passwd Writing shadow-file to /etc/shadow Writing group-file to /etc/group (Reading database ... 14919 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.60_all.deb ... Unpacking init-system-helpers (1.60) over (1.58) ... Setting up init-system-helpers (1.60) ... (Reading database ... 14918 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.2+20201114-2build1_all.deb ... Unpacking ncurses-base (6.2+20201114-2build1) over (6.2-1) ... Setting up ncurses-base (6.2+20201114-2build1) ... (Reading database ... 14918 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_2.96-5ubuntu1_arm64.deb ... Unpacking sysvinit-utils (2.96-5ubuntu1) over (2.96-3ubuntu1) ... Setting up sysvinit-utils (2.96-5ubuntu1) ... Selecting previously unselected package libxxhash0:arm64. (Reading database ... 14918 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.0-2_arm64.deb ... Unpacking libxxhash0:arm64 (0.8.0-2) ... Setting up libxxhash0:arm64 (0.8.0-2) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.38-2build1_arm64.deb ... Unpacking libgpg-error0:arm64 (1.38-2build1) over (1.38-2) ... Setting up libgpg-error0:arm64 (1.38-2build1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.8.7-2ubuntu2_arm64.deb ... Unpacking libgcrypt20:arm64 (1.8.7-2ubuntu2) over (1.8.5-5ubuntu2) ... Setting up libgcrypt20:arm64 (1.8.7-2ubuntu2) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.3-1build1_arm64.deb ... Unpacking liblz4-1:arm64 (1.9.3-1build1) over (1.9.2-2) ... Setting up liblz4-1:arm64 (1.9.3-1build1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.5-1.0build1_arm64.deb ... Unpacking liblzma5:arm64 (5.2.5-1.0build1) over (5.2.4-1ubuntu1) ... Setting up liblzma5:arm64 (5.2.5-1.0build1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libstdc++6_11-20210306-1ubuntu1_arm64.deb ... Unpacking libstdc++6:arm64 (11-20210306-1ubuntu1) over (10.2.0-13ubuntu1) ... Setting up libstdc++6:arm64 (11-20210306-1ubuntu1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.2.1+dfsg-1ubuntu1_arm64.deb ... Unpacking libgmp10:arm64 (2:6.2.1+dfsg-1ubuntu1) over (2:6.2.0+dfsg-6ubuntu1) ... Setting up libgmp10:arm64 (2:6.2.1+dfsg-1ubuntu1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libnettle8_3.7-2.1_arm64.deb ... Unpacking libnettle8:arm64 (3.7-2.1) over (3.6-2) ... Setting up libnettle8:arm64 (3.7-2.1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.7-2.1_arm64.deb ... Unpacking libhogweed6:arm64 (3.7-2.1) over (3.6-2) ... Setting up libhogweed6:arm64 (3.7-2.1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.0-5_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.0-5) over (2.3.0-1) ... Setting up libidn2-0:arm64 (2.3.0-5) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu5_arm64.deb ... Unpacking libffi8ubuntu1:arm64 (3.4~20200819gead65ca871-0ubuntu5) over (3.4~20200819gead65ca871-0ubuntu3) ... Setting up libffi8ubuntu1:arm64 (3.4~20200819gead65ca871-0ubuntu5) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.23.22-1_arm64.deb ... Unpacking libp11-kit0:arm64 (0.23.22-1) over (0.23.21-2build1) ... Setting up libp11-kit0:arm64 (0.23.22-1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.0-5ubuntu1_arm64.deb ... Unpacking libgnutls30:arm64 (3.7.0-5ubuntu1) over (3.6.15-4ubuntu2) ... Setting up libgnutls30:arm64 (3.7.0-5ubuntu1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../systemd-sysv_247.3-1ubuntu4_arm64.deb ... Unpacking systemd-sysv (247.3-1ubuntu4) over (246.6-1ubuntu1) ... Preparing to unpack .../libaudit-common_1%3a3.0-2ubuntu1_all.deb ... Unpacking libaudit-common (1:3.0-2ubuntu1) over (1:2.8.5-3ubuntu1) ... Setting up libaudit-common (1:3.0-2ubuntu1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.9-2.2build1_arm64.deb ... Unpacking libcap-ng0:arm64 (0.7.9-2.2build1) over (0.7.9-2.2) ... Setting up libcap-ng0:arm64 (0.7.9-2.2build1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0-2ubuntu1_arm64.deb ... Unpacking libaudit1:arm64 (1:3.0-2ubuntu1) over (1:2.8.5-3ubuntu1) ... Setting up libaudit1:arm64 (1:3.0-2ubuntu1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.36-2ubuntu4_arm64.deb ... Unpacking libpcre2-8-0:arm64 (10.36-2ubuntu4) over (10.34-7) ... Setting up libpcre2-8-0:arm64 (10.36-2ubuntu4) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libselinux1_3.1-3build1_arm64.deb ... Unpacking libselinux1:arm64 (3.1-3build1) over (3.1-2) ... Setting up libselinux1:arm64 (3.1-3build1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.1-1build2_all.deb ... Unpacking libsemanage-common (3.1-1build2) over (3.1-1) ... Setting up libsemanage-common (3.1-1build2) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libsemanage1_3.1-1build2_arm64.deb ... Unpacking libsemanage1:arm64 (3.1-1build2) over (3.1-1) ... Setting up libsemanage1:arm64 (3.1-1build2) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.8.1-1ubuntu8_arm64.deb ... Unpacking passwd (1:4.8.1-1ubuntu8) over (1:4.8.1-1ubuntu6) ... Setting up passwd (1:4.8.1-1ubuntu8) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../adduser_3.118ubuntu5_all.deb ... Unpacking adduser (3.118ubuntu5) over (3.118ubuntu2) ... Setting up adduser (3.118ubuntu5) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../systemd-timesyncd_247.3-1ubuntu4_arm64.deb ... Unpacking systemd-timesyncd (247.3-1ubuntu4) over (246.6-1ubuntu1) ... Preparing to unpack .../libapparmor1_3.0.0-0ubuntu6_arm64.deb ... Unpacking libapparmor1:arm64 (3.0.0-0ubuntu6) over (3.0.0-0ubuntu1) ... Preparing to unpack .../libargon2-1_0~20171227-0.2build21.04.0_arm64.deb ... Unpacking libargon2-1:arm64 (0~20171227-0.2build21.04.0) over (0~20171227-0.2build20.10.0) ... Preparing to unpack .../libblkid1_2.36.1-7ubuntu2_arm64.deb ... Unpacking libblkid1:arm64 (2.36.1-7ubuntu2) over (2.36-3ubuntu1) ... Setting up libblkid1:arm64 (2.36.1-7ubuntu2) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libudev1_247.3-1ubuntu4_arm64.deb ... Unpacking libudev1:arm64 (247.3-1ubuntu4) over (246.6-1ubuntu1) ... Setting up libudev1:arm64 (247.3-1ubuntu4) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.175-2ubuntu3_arm64.deb ... Unpacking libdevmapper1.02.1:arm64 (2:1.02.175-2ubuntu3) over (2:1.02.167-1ubuntu3) ... Preparing to unpack .../libjson-c5_0.15-2build1_arm64.deb ... Unpacking libjson-c5:arm64 (0.15-2build1) over (0.15-1) ... Preparing to unpack .../libuuid1_2.36.1-7ubuntu2_arm64.deb ... Unpacking libuuid1:arm64 (2.36.1-7ubuntu2) over (2.36-3ubuntu1) ... Setting up libuuid1:arm64 (2.36.1-7ubuntu2) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../libcryptsetup12_2%3a2.3.4-1ubuntu3_arm64.deb ... Unpacking libcryptsetup12:arm64 (2:2.3.4-1ubuntu3) over (2:2.3.3-1ubuntu6) ... Preparing to unpack .../libip4tc2_1.8.7-1ubuntu2_arm64.deb ... Unpacking libip4tc2:arm64 (1.8.7-1ubuntu2) over (1.8.5-3ubuntu1) ... Preparing to unpack .../libkmod2_28-1ubuntu2_arm64.deb ... Unpacking libkmod2:arm64 (28-1ubuntu2) over (27+20200310-2ubuntu1) ... Preparing to unpack .../libseccomp2_2.5.1-1ubuntu1_arm64.deb ... Unpacking libseccomp2:arm64 (2.5.1-1ubuntu1) over (2.4.3-1ubuntu4) ... Setting up libseccomp2:arm64 (2.5.1-1ubuntu1) ... (Reading database ... 14923 files and directories currently installed.) Preparing to unpack .../mount_2.36.1-7ubuntu2_arm64.deb ... Unpacking mount (2.36.1-7ubuntu2) over (2.36-3ubuntu1) ... Preparing to unpack .../systemd_247.3-1ubuntu4_arm64.deb ... Unpacking systemd (247.3-1ubuntu4) over (246.6-1ubuntu1) ... Preparing to unpack .../libsystemd0_247.3-1ubuntu4_arm64.deb ... Unpacking libsystemd0:arm64 (247.3-1ubuntu4) over (246.6-1ubuntu1) ... Setting up libsystemd0:arm64 (247.3-1ubuntu4) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../libzstd1_1.4.8+dfsg-2build1_arm64.deb ... Unpacking libzstd1:arm64 (1.4.8+dfsg-2build1) over (1.4.5+dfsg-4) ... Setting up libzstd1:arm64 (1.4.8+dfsg-2build1) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.2.1_arm64.deb ... Unpacking libapt-pkg6.0:arm64 (2.2.1) over (2.1.10) ... Setting up libapt-pkg6.0:arm64 (2.2.1) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.20-1ubuntu3_arm64.deb ... Unpacking gpgv (2.2.20-1ubuntu3) over (2.2.20-1ubuntu1) ... Setting up gpgv (2.2.20-1ubuntu3) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../ubuntu-keyring_2020.06.17.1build1_all.deb ... Unpacking ubuntu-keyring (2020.06.17.1build1) over (2020.06.17.1) ... Setting up ubuntu-keyring (2020.06.17.1build1) ... (Reading database ... 14933 files and directories currently installed.) Preparing to unpack .../archives/apt_2.2.1_arm64.deb ... Unpacking apt (2.2.1) over (2.1.10) ... Setting up apt (2.2.1) ... Installing new version of config file /etc/kernel/postinst.d/apt-auto-removal ... (Reading database ... 14937 files and directories currently installed.) Preparing to unpack .../logsave_1.45.7-1ubuntu2_arm64.deb ... Unpacking logsave (1.45.7-1ubuntu2) over (1.45.6-1ubuntu1) ... Preparing to unpack .../libext2fs2_1.45.7-1ubuntu2_arm64.deb ... Unpacking libext2fs2:arm64 (1.45.7-1ubuntu2) over (1.45.6-1ubuntu1) ... Setting up libcom-err2:arm64 (1.45.7-1ubuntu2) ... Setting up libext2fs2:arm64 (1.45.7-1ubuntu2) ... (Reading database ... 14937 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.45.7-1ubuntu2_arm64.deb ... Unpacking e2fsprogs (1.45.7-1ubuntu2) over (1.45.6-1ubuntu1) ... Setting up libapparmor1:arm64 (3.0.0-0ubuntu6) ... Setting up libargon2-1:arm64 (0~20171227-0.2build21.04.0) ... Setting up libdevmapper1.02.1:arm64 (2:1.02.175-2ubuntu3) ... Setting up libjson-c5:arm64 (0.15-2build1) ... Setting up libssl1.1:arm64 (1.1.1j-1ubuntu1) ... Setting up libcryptsetup12:arm64 (2:2.3.4-1ubuntu3) ... Setting up libip4tc2:arm64 (1.8.7-1ubuntu2) ... Setting up libkmod2:arm64 (28-1ubuntu2) ... Setting up mount (2.36.1-7ubuntu2) ... Setting up systemd-timesyncd (247.3-1ubuntu4) ... Setting up systemd (247.3-1ubuntu4) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Installing new version of config file /etc/systemd/system.conf ... Initializing machine ID from random generator. Removing obsolete conffile /etc/pam.d/systemd-user ... Setting up systemd-sysv (247.3-1ubuntu4) ... (Reading database ... 14937 files and directories currently installed.) Preparing to unpack .../archives/init_1.60_arm64.deb ... Unpacking init (1.60) over (1.58) ... Preparing to unpack .../libacl1_2.2.53-10build1_arm64.deb ... Unpacking libacl1:arm64 (2.2.53-10build1) over (2.2.53-8) ... Setting up libacl1:arm64 (2.2.53-10build1) ... (Reading database ... 14937 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.4.48-6build1_arm64.deb ... Unpacking libattr1:arm64 (1:2.4.48-6build1) over (1:2.4.48-5) ... Setting up libattr1:arm64 (1:2.4.48-6build1) ... (Reading database ... 14937 files and directories currently installed.) Preparing to unpack .../libmount1_2.36.1-7ubuntu2_arm64.deb ... Unpacking libmount1:arm64 (2.36.1-7ubuntu2) over (2.36-3ubuntu1) ... Setting up libmount1:arm64 (2.36.1-7ubuntu2) ... (Reading database ... 14937 files and directories currently installed.) Preparing to unpack .../libpcre3_2%3a8.39-13build2_arm64.deb ... Unpacking libpcre3:arm64 (2:8.39-13build2) over (2:8.39-13) ... Setting up libpcre3:arm64 (2:8.39-13build2) ... (Reading database ... 14937 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.36.1-7ubuntu2_arm64.deb ... Unpacking libsmartcols1:arm64 (2.36.1-7ubuntu2) over (2.36-3ubuntu1) ... Setting up libsmartcols1:arm64 (2.36.1-7ubuntu2) ... (Reading database ... 14937 files and directories currently installed.) Preparing to unpack .../00-libgomp1_11-20210306-1ubuntu1_arm64.deb ... Unpacking libgomp1:arm64 (11-20210306-1ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../01-libitm1_11-20210306-1ubuntu1_arm64.deb ... Unpacking libitm1:arm64 (11-20210306-1ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../02-libatomic1_11-20210306-1ubuntu1_arm64.deb ... Unpacking libatomic1:arm64 (11-20210306-1ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../03-libasan6_10.2.1-21ubuntu1_arm64.deb ... Unpacking libasan6:arm64 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../04-liblsan0_10.2.1-21ubuntu1_arm64.deb ... Unpacking liblsan0:arm64 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../05-libtsan0_10.2.1-21ubuntu1_arm64.deb ... Unpacking libtsan0:arm64 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../06-libubsan1_10.2.1-21ubuntu1_arm64.deb ... Unpacking libubsan1:arm64 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../07-g++-10_10.2.1-21ubuntu1_arm64.deb ... Unpacking g++-10 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../08-gcc-10_10.2.1-21ubuntu1_arm64.deb ... Unpacking gcc-10 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../09-libstdc++-10-dev_10.2.1-21ubuntu1_arm64.deb ... Unpacking libstdc++-10-dev:arm64 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../10-libgcc-10-dev_10.2.1-21ubuntu1_arm64.deb ... Unpacking libgcc-10-dev:arm64 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Selecting previously unselected package libisl23:arm64. Preparing to unpack .../11-libisl23_0.23-1_arm64.deb ... Unpacking libisl23:arm64 (0.23-1) ... Preparing to unpack .../12-libmpc3_1.2.0-1_arm64.deb ... Unpacking libmpc3:arm64 (1.2.0-1) over (1.2.0~rc1-1) ... Preparing to unpack .../13-libcc1-0_11-20210306-1ubuntu1_arm64.deb ... Unpacking libcc1-0:arm64 (11-20210306-1ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../14-libctf0_2.36.1-5ubuntu1_arm64.deb ... Unpacking libctf0:arm64 (2.36.1-5ubuntu1) over (2.35.1-1ubuntu1) ... Preparing to unpack .../15-libctf-nobfd0_2.36.1-5ubuntu1_arm64.deb ... Unpacking libctf-nobfd0:arm64 (2.36.1-5ubuntu1) over (2.35.1-1ubuntu1) ... Preparing to unpack .../16-binutils-aarch64-linux-gnu_2.36.1-5ubuntu1_arm64.deb ... Unpacking binutils-aarch64-linux-gnu (2.36.1-5ubuntu1) over (2.35.1-1ubuntu1) ... Preparing to unpack .../17-libbinutils_2.36.1-5ubuntu1_arm64.deb ... Unpacking libbinutils:arm64 (2.36.1-5ubuntu1) over (2.35.1-1ubuntu1) ... Preparing to unpack .../18-binutils_2.36.1-5ubuntu1_arm64.deb ... Unpacking binutils (2.36.1-5ubuntu1) over (2.35.1-1ubuntu1) ... Preparing to unpack .../19-binutils-common_2.36.1-5ubuntu1_arm64.deb ... Unpacking binutils-common:arm64 (2.36.1-5ubuntu1) over (2.35.1-1ubuntu1) ... Preparing to unpack .../20-cpp-10_10.2.1-21ubuntu1_arm64.deb ... Unpacking cpp-10 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../21-gcc-10-base_10.2.1-21ubuntu1_arm64.deb ... Unpacking gcc-10-base:arm64 (10.2.1-21ubuntu1) over (10.2.0-13ubuntu1) ... Preparing to unpack .../22-libss2_1.45.7-1ubuntu2_arm64.deb ... Unpacking libss2:arm64 (1.45.7-1ubuntu2) over (1.45.6-1ubuntu1) ... Preparing to unpack .../23-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) over (0.0.13) ... Preparing to unpack .../24-openssl_1.1.1j-1ubuntu1_arm64.deb ... Unpacking openssl (1.1.1j-1ubuntu1) over (1.1.1f-1ubuntu4) ... Preparing to unpack .../25-ca-certificates_20210119build1_all.deb ... Unpacking ca-certificates (20210119build1) over (20200601) ... Preparing to unpack .../26-libcap2_1%3a2.44-1build1_arm64.deb ... Unpacking libcap2:arm64 (1:2.44-1build1) over (1:2.43-1) ... Preparing to unpack .../27-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) over (8.0-4) ... Preparing to unpack .../28-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) over (8.0-4) ... Preparing to unpack .../29-libsqlite3-0_3.34.1-3_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.34.1-3) over (3.33.0-1) ... Preparing to unpack .../30-tzdata_2021a-1ubuntu1_all.deb ... Unpacking tzdata (2021a-1ubuntu1) over (2020b-1ubuntu1) ... Preparing to unpack .../31-xz-utils_5.2.5-1.0build1_arm64.deb ... Unpacking xz-utils (5.2.5-1.0build1) over (5.2.4-1ubuntu1) ... Preparing to unpack .../32-libpng16-16_1.6.37-3build2_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.37-3build2) over (1.6.37-3) ... Preparing to unpack .../33-dpkg-dev_1.20.7.1ubuntu3_all.deb ... Unpacking dpkg-dev (1.20.7.1ubuntu3) over (1.20.5ubuntu2) ... Preparing to unpack .../34-libdpkg-perl_1.20.7.1ubuntu3_all.deb ... Unpacking libdpkg-perl (1.20.7.1ubuntu3) over (1.20.5ubuntu2) ... Preparing to unpack .../35-patch_2.7.6-7_arm64.deb ... Unpacking patch (2.7.6-7) over (2.7.6-6) ... Selecting previously unselected package lto-disabled-list. Preparing to unpack .../36-lto-disabled-list_1_all.deb ... Unpacking lto-disabled-list (1) ... Preparing to unpack .../37-libfakeroot_1.25.3-1.1ubuntu2_arm64.deb ... Unpacking libfakeroot:arm64 (1.25.3-1.1ubuntu2) over (1.25.2-1) ... Preparing to unpack .../38-fakeroot_1.25.3-1.1ubuntu2_arm64.deb ... Unpacking fakeroot (1.25.3-1.1ubuntu2) over (1.25.2-1) ... Preparing to unpack .../39-libassuan0_2.5.4-1ubuntu1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.4-1ubuntu1) over (2.5.3-7.1) ... Preparing to unpack .../40-libnpth0_1.6-3_arm64.deb ... Unpacking libnpth0:arm64 (1.6-3) over (1.6-2) ... Preparing to unpack .../41-gpg_2.2.20-1ubuntu3_arm64.deb ... Unpacking gpg (2.2.20-1ubuntu3) over (2.2.20-1ubuntu1) ... Preparing to unpack .../42-gpgconf_2.2.20-1ubuntu3_arm64.deb ... Unpacking gpgconf (2.2.20-1ubuntu3) over (2.2.20-1ubuntu1) ... Preparing to unpack .../43-gpg-agent_2.2.20-1ubuntu3_arm64.deb ... Unpacking gpg-agent (2.2.20-1ubuntu3) over (2.2.20-1ubuntu1) ... Preparing to unpack .../44-liblockfile-bin_1.17-1_arm64.deb ... Unpacking liblockfile-bin (1.17-1) over (1.16-1.1) ... Preparing to unpack .../45-liblockfile1_1.17-1_arm64.deb ... Unpacking liblockfile1:arm64 (1.17-1) over (1.16-1.1) ... Preparing to unpack .../46-pkgbinarymangler_147_all.deb ... Unpacking pkgbinarymangler (147) over (146) ... Setting up lto-disabled-list (1) ... Setting up liblockfile-bin (1.17-1) ... Setting up pkgbinarymangler (147) ... Setting up init (1.60) ... Setting up libtirpc-common (1.3.1-1build1) ... Setting up perl-modules-5.32 (5.32.1-2) ... Setting up libsqlite3-0:arm64 (3.34.1-3) ... Setting up binutils-common:arm64 (2.36.1-5ubuntu1) ... Setting up linux-libc-dev:arm64 (5.11.0-11.12) ... Setting up libctf-nobfd0:arm64 (2.36.1-5ubuntu1) ... Setting up libnpth0:arm64 (1.6-3) ... Setting up libassuan0:arm64 (2.5.4-1ubuntu1) ... Setting up libgomp1:arm64 (11-20210306-1ubuntu1) ... Setting up libcap2:arm64 (1:2.44-1build1) ... Setting up libfakeroot:arm64 (1.25.3-1.1ubuntu2) ... Setting up libkrb5support0:arm64 (1.18.3-4) ... Setting up tzdata (2021a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Mar 11 02:34:44 UTC 2021. Universal Time is now: Thu Mar 11 02:34:44 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.25.3-1.1ubuntu2) ... Setting up gcc-10-base:arm64 (10.2.1-21ubuntu1) ... Setting up libncurses6:arm64 (6.2+20201114-2build1) ... Setting up xz-utils (5.2.5-1.0build1) ... Setting up libpng16-16:arm64 (1.6.37-3build2) ... Setting up libmpc3:arm64 (1.2.0-1) ... Setting up libatomic1:arm64 (11-20210306-1ubuntu1) ... Setting up patch (2.7.6-7) ... Setting up libss2:arm64 (1.45.7-1ubuntu2) ... Setting up libncursesw6:arm64 (6.2+20201114-2build1) ... Setting up libk5crypto3:arm64 (1.18.3-4) ... Setting up logsave (1.45.7-1ubuntu2) ... Setting up libubsan1:arm64 (10.2.1-21ubuntu1) ... Setting up sensible-utils (0.0.14) ... Setting up libcrypt-dev:arm64 (1:4.4.17-1ubuntu2) ... Setting up libkrb5-3:arm64 (1.18.3-4) ... Setting up liblockfile1:arm64 (1.17-1) ... Setting up libbinutils:arm64 (2.36.1-5ubuntu1) ... Setting up libisl23:arm64 (0.23-1) ... Setting up libc-dev-bin (2.33-0ubuntu2) ... Setting up openssl (1.1.1j-1ubuntu1) ... Setting up readline-common (8.1-1) ... Setting up libcc1-0:arm64 (11-20210306-1ubuntu1) ... Setting up liblsan0:arm64 (10.2.1-21ubuntu1) ... Setting up cpp-10 (10.2.1-21ubuntu1) ... Setting up libitm1:arm64 (11-20210306-1ubuntu1) ... Setting up libgdbm6:arm64 (1.19-2) ... Setting up libtsan0:arm64 (10.2.1-21ubuntu1) ... Setting up libctf0:arm64 (2.36.1-5ubuntu1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up binutils-aarch64-linux-gnu (2.36.1-5ubuntu1) ... Setting up e2fsprogs (1.45.7-1ubuntu2) ... Setting up binutils (2.36.1-5ubuntu1) ... Setting up libasan6:arm64 (10.2.1-21ubuntu1) ... Setting up ca-certificates (20210119build1) ... Updating certificates in /etc/ssl/certs... 10 added, 7 removed; done. Setting up libgssapi-krb5-2:arm64 (1.18.3-4) ... Setting up libgdbm-compat4:arm64 (1.19-2) ... Setting up libperl5.32:arm64 (5.32.1-2) ... Setting up gpgconf (2.2.20-1ubuntu3) ... Setting up gpg (2.2.20-1ubuntu3) ... Setting up libtirpc3:arm64 (1.3.1-1build1) ... Setting up gpg-agent (2.2.20-1ubuntu3) ... Setting up libgcc-10-dev:arm64 (10.2.1-21ubuntu1) ... Setting up perl (5.32.1-2) ... Setting up libtirpc-dev:arm64 (1.3.1-1build1) ... Setting up gcc-10 (10.2.1-21ubuntu1) ... Setting up libdpkg-perl (1.20.7.1ubuntu3) ... Setting up libc6-dev:arm64 (2.33-0ubuntu2) ... Setting up libstdc++-10-dev:arm64 (10.2.1-21ubuntu1) ... Setting up g++-10 (10.2.1-21ubuntu1) ... Setting up dpkg-dev (1.20.7.1ubuntu3) ... Processing triggers for libc-bin (2.33-0ubuntu2) ... Processing triggers for ca-certificates (20210119build1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-21143309 arm64 hirsute-proposed -c chroot:build-PACKAGEBUILD-21143309 --arch=arm64 --dist=hirsute-proposed --nolog rna-star_2.7.8a+dfsg-2.dsc Initiating build PACKAGEBUILD-21143309 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-136-generic #140-Ubuntu SMP Thu Jan 28 05:23:14 UTC 2021 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-002.buildd +==============================================================================+ | rna-star 2.7.8a+dfsg-2 (arm64) Thu, 11 Mar 2021 02:34:52 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.8a+dfsg-2 Source Version: 2.7.8a+dfsg-2 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-21143309/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- rna-star_2.7.8a+dfsg-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/rna-star-eEgRpQ/rna-star-2.7.8a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-eEgRpQ' 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-YNFM98/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-YNFM98/apt_archive ./ InRelease Get:2 copy:/<>/resolver-YNFM98/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-YNFM98/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-YNFM98/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-YNFM98/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (68.6 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-YNFM98/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 (76.1 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14989 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, libsimde-dev Filtered Build-Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, zlib1g-dev, libsimde-dev dpkg-deb: building package 'sbuild-build-depends-rna-star-dummy' in '/<>/resolver-YNFM98/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-YNFM98/apt_archive ./ InRelease Get:2 copy:/<>/resolver-YNFM98/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-YNFM98/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-YNFM98/apt_archive ./ Sources [527 B] Get:5 copy:/<>/resolver-YNFM98/apt_archive ./ Packages [606 B] Fetched 2096 B in 0s (84.0 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 libsimde-dev 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 libsimde-dev 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, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 22.4 MB of archives. After this operation, 82.1 MB of additional disk space will be used. Get:1 copy:/<>/resolver-YNFM98/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [896 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main arm64 bsdextrautils arm64 2.36.1-7ubuntu2 [77.7 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 1.22.4-6 [809 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 2.9.4-2 [1136 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/main arm64 libelf1 arm64 0.183-4 [43.7 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main arm64 libicu67 arm64 67.1-6ubuntu1 [8456 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 2:8.2.2434-1ubuntu1 [49.4 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main arm64 vim-common all 2:8.2.2434-1ubuntu1 [80.0 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main arm64 gettext-base arm64 0.21-3ubuntu2 [38.6 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpsl5 arm64 0.21.0-1.2 [53.2 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsigsegv2 arm64 2.13-1 [14.0 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/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/main arm64 autopoint all 0.21-3ubuntu2 [422 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdebhelper-perl all 13.3.3ubuntu3 [61.1 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtool all 2.4.6-15 [161 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main arm64 dh-autoreconf all 20 [16.1 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 1.11.0-1 [17.0 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main arm64 dh-strip-nondeterminism all 1.11.0-1 [5236 B] Get:30 http://ftpmaster.internal/ubuntu hirsute/main arm64 dwz arm64 0.14-1 [89.4 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main arm64 gettext arm64 0.21-3ubuntu2 [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/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main arm64 debhelper all 13.3.3ubuntu3 [883 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 2.4.57+dfsg-2ubuntu1 [146 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main arm64 libnghttp2-14 arm64 1.43.0-1 [68.5 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 7.74.0-1ubuntu1 [223 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1ubuntu1 [321 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdeflate0 arm64 1.7-1ubuntu1 [47.4 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdeflate-dev arm64 1.7-1ubuntu1 [43.1 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 5.2.5-1.0build1 [148 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu5 [154 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libhts-dev arm64 1.11-4 [3833 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libsimde-dev all 0.7.2-4 [258 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 22.4 MB in 1s (17.6 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14989 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7ubuntu2_arm64.deb ... Unpacking bsdextrautils (2.36.1-7ubuntu2) ... 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_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... 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_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... 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) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../06-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../08-libelf1_0.183-4_arm64.deb ... Unpacking libelf1:arm64 (0.183-4) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../09-libicu67_67.1-6ubuntu1_arm64.deb ... Unpacking libicu67:arm64 (67.1-6ubuntu1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../10-libxml2_2.9.10+dfsg-6.3build1_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.3build1) ... Selecting previously unselected package xxd. Preparing to unpack .../11-xxd_2%3a8.2.2434-1ubuntu1_arm64.deb ... Unpacking xxd (2:8.2.2434-1ubuntu1) ... Selecting previously unselected package vim-common. Preparing to unpack .../12-vim-common_2%3a8.2.2434-1ubuntu1_all.deb ... Unpacking vim-common (2:8.2.2434-1ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../13-gettext-base_0.21-3ubuntu2_arm64.deb ... Unpacking gettext-base (0.21-3ubuntu2) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../14-libpsl5_0.21.0-1.2_arm64.deb ... Unpacking libpsl5:arm64 (0.21.0-1.2) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../15-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../16-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../17-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../18-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../19-automake_1%3a1.16.3-2ubuntu1_all.deb ... Unpacking automake (1:1.16.3-2ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../20-autopoint_0.21-3ubuntu2_all.deb ... Unpacking autopoint (0.21-3ubuntu2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../21-libdebhelper-perl_13.3.3ubuntu3_all.deb ... Unpacking libdebhelper-perl (13.3.3ubuntu3) ... Selecting previously unselected package libtool. Preparing to unpack .../22-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../23-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../24-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../25-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../26-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../27-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package dwz. Preparing to unpack .../28-dwz_0.14-1_arm64.deb ... Unpacking dwz (0.14-1) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.21-3ubuntu2_arm64.deb ... Unpacking gettext (0.21-3ubuntu2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_13.3.3ubuntu3_all.deb ... Unpacking debhelper (13.3.3ubuntu3) ... Selecting previously unselected package libroken18-heimdal:arm64. Preparing to unpack .../33-libroken18-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libroken18-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libasn1-8-heimdal:arm64. Preparing to unpack .../34-libasn1-8-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libasn1-8-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../35-libbrotli1_1.0.9-2build2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2build2) ... Selecting previously unselected package libheimbase1-heimdal:arm64. Preparing to unpack .../36-libheimbase1-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libheimbase1-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libhcrypto4-heimdal:arm64. Preparing to unpack .../37-libhcrypto4-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libhcrypto4-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libwind0-heimdal:arm64. Preparing to unpack .../38-libwind0-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libwind0-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libhx509-5-heimdal:arm64. Preparing to unpack .../39-libhx509-5-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libhx509-5-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libkrb5-26-heimdal:arm64. Preparing to unpack .../40-libkrb5-26-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libkrb5-26-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libheimntlm0-heimdal:arm64. Preparing to unpack .../41-libheimntlm0-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libheimntlm0-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libgssapi3-heimdal:arm64. Preparing to unpack .../42-libgssapi3-heimdal_7.7.0+dfsg-2_arm64.deb ... Unpacking libgssapi3-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../43-libsasl2-modules-db_2.1.27+dfsg-2ubuntu1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.27+dfsg-2ubuntu1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../44-libsasl2-2_2.1.27+dfsg-2ubuntu1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.27+dfsg-2ubuntu1) ... Selecting previously unselected package libldap-2.4-2:arm64. Preparing to unpack .../45-libldap-2.4-2_2.4.57+dfsg-2ubuntu1_arm64.deb ... Unpacking libldap-2.4-2:arm64 (2.4.57+dfsg-2ubuntu1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../46-libnghttp2-14_1.43.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.43.0-1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../47-librtmp1_2.4+20151223.gitfa8646d.1-2build2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build2) ... Selecting previously unselected package libssh-4:arm64. Preparing to unpack .../48-libssh-4_0.9.5-1_arm64.deb ... Unpacking libssh-4:arm64 (0.9.5-1) ... Selecting previously unselected package libcurl3-gnutls:arm64. Preparing to unpack .../49-libcurl3-gnutls_7.74.0-1ubuntu1_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.74.0-1ubuntu1) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../50-libcurl4-gnutls-dev_7.74.0-1ubuntu1_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (7.74.0-1ubuntu1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../51-libdeflate0_1.7-1ubuntu1_arm64.deb ... Unpacking libdeflate0:arm64 (1.7-1ubuntu1) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../52-libdeflate-dev_1.7-1ubuntu1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.7-1ubuntu1) ... Selecting previously unselected package libhts3:arm64. Preparing to unpack .../53-libhts3_1.11-4_arm64.deb ... Unpacking libhts3:arm64 (1.11-4) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../54-liblzma-dev_5.2.5-1.0build1_arm64.deb ... Unpacking liblzma-dev:arm64 (5.2.5-1.0build1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../55-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu5_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu5) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../56-libhts-dev_1.11-4_arm64.deb ... Unpacking libhts-dev:arm64 (1.11-4) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../57-libsimde-dev_0.7.2-4_all.deb ... Unpacking libsimde-dev (0.7.2-4) ... Selecting previously unselected package sbuild-build-depends-rna-star-dummy. Preparing to unpack .../58-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 libsimde-dev (0.7.2-4) ... Setting up libpsl5:arm64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-7ubuntu2) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-6ubuntu1) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.3ubuntu3) ... Setting up libbrotli1:arm64 (1.0.9-2build2) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1ubuntu1) ... Setting up gettext-base (0.21-3ubuntu2) ... Setting up file (1:5.39-3) ... Setting up xxd (2:8.2.2434-1ubuntu1) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2ubuntu1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up vim-common (2:8.2.2434-1ubuntu1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-3ubuntu2) ... 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 (5.2.5-1.0build1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu5) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:arm64 (1.7-1ubuntu1) ... Setting up libelf1:arm64 (0.183-4) ... 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 (1.11.0-1) ... Setting up gettext (0.21-3ubuntu2) ... Setting up libtool (2.4.6-15) ... 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 (1.11.0-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-6) ... 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 (2.9.4-2) ... 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 dh-autoreconf (20) ... Setting up libkrb5-26-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up debhelper (13.3.3ubuntu3) ... 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 (2.4.57+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:arm64 (7.74.0-1ubuntu1) ... Setting up libhts3:arm64 (1.11-4) ... Setting up libhts-dev:arm64 (1.11-4) ... Setting up sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.33-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-136-generic arm64 (aarch64) Toolchain package versions: binutils_2.36.1-5ubuntu1 dpkg-dev_1.20.7.1ubuntu3 g++-10_10.2.1-21ubuntu1 gcc-10_10.2.1-21ubuntu1 libc6-dev_2.33-0ubuntu2 libstdc++-10-dev_10.2.1-21ubuntu1 libstdc++6_11-20210306-1ubuntu1 linux-libc-dev_5.11.0-11.12 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1build1 apt_2.2.1 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3ubuntu2 autotools-dev_20180224.1+nmu1 base-files_11ubuntu18 base-passwd_3.5.49 bash_5.1-1ubuntu1 binutils_2.36.1-5ubuntu1 binutils-aarch64-linux-gnu_2.36.1-5ubuntu1 binutils-common_2.36.1-5ubuntu1 bsdextrautils_2.36.1-7ubuntu2 bsdutils_1:2.36.1-7ubuntu2 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20210119build1 coreutils_8.32-4ubuntu2 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.1-21ubuntu1 dash_0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 debconf_1.5.74 debhelper_13.3.3ubuntu3 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.7.1ubuntu3 dpkg-dev_1.20.7.1ubuntu3 dwz_0.14-1 e2fsprogs_1.45.7-1ubuntu2 fakeroot_1.25.3-1.1ubuntu2 file_1:5.39-3 findutils_4.8.0-1ubuntu1 g++_4:10.2.0-1ubuntu1 g++-10_10.2.1-21ubuntu1 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.1-21ubuntu1 gcc-10-base_10.2.1-21ubuntu1 gcc-11-base_11-20210306-1ubuntu1 gettext_0.21-3ubuntu2 gettext-base_0.21-3ubuntu2 gpg_2.2.20-1ubuntu3 gpg-agent_2.2.20-1ubuntu3 gpgconf_2.2.20-1ubuntu3 gpgv_2.2.20-1ubuntu3 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-2ubuntu3 hostname_3.23 init_1.60 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10build1 libapparmor1_3.0.0-0ubuntu6 libapt-pkg6.0_2.2.1 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build21.04.0 libasan6_10.2.1-21ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.4-1ubuntu1 libatomic1_11-20210306-1ubuntu1 libattr1_1:2.4.48-6build1 libaudit-common_1:3.0-2ubuntu1 libaudit1_1:3.0-2ubuntu1 libbinutils_2.36.1-5ubuntu1 libblkid1_2.36.1-7ubuntu2 libbrotli1_1.0.9-2build2 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.33-0ubuntu2 libc-dev-bin_2.33-0ubuntu2 libc6_2.33-0ubuntu2 libc6-dev_2.33-0ubuntu2 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1build1 libcc1-0_11-20210306-1ubuntu1 libcom-err2_1.45.7-1ubuntu2 libcrypt-dev_1:4.4.17-1ubuntu2 libcrypt1_1:4.4.17-1ubuntu2 libcryptsetup12_2:2.3.4-1ubuntu3 libctf-nobfd0_2.36.1-5ubuntu1 libctf0_2.36.1-5ubuntu1 libcurl3-gnutls_7.74.0-1ubuntu1 libcurl4-gnutls-dev_7.74.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.256ubuntu3 libdebhelper-perl_13.3.3ubuntu3 libdeflate-dev_1.7-1ubuntu1 libdeflate0_1.7-1ubuntu1 libdevmapper1.02.1_2:1.02.175-2ubuntu3 libdpkg-perl_1.20.7.1ubuntu3 libelf1_0.183-4 libext2fs2_1.45.7-1ubuntu2 libfakeroot_1.25.3-1.1ubuntu2 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu5 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-21ubuntu1 libgcc-s1_11-20210306-1ubuntu1 libgcrypt20_1.8.7-2ubuntu2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1ubuntu1 libgnutls30_3.7.0-5ubuntu1 libgomp1_11-20210306-1ubuntu1 libgpg-error0_1.38-2build1 libgssapi-krb5-2_1.18.3-4 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_3.7-2.1 libhts-dev_1.11-4 libhts3_1.11-4 libhx509-5-heimdal_7.7.0+dfsg-2 libicu67_67.1-6ubuntu1 libidn2-0_2.3.0-5 libip4tc2_1.8.7-1ubuntu2 libisl22_0.22.1-1 libisl23_0.23-1 libitm1_11-20210306-1ubuntu1 libjson-c5_0.15-2build1 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2ubuntu1 libkmod2_28-1ubuntu2 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libldap-2.4-2_2.4.57+dfsg-2ubuntu1 liblockfile-bin_1.17-1 liblockfile1_1.17-1 liblsan0_10.2.1-21ubuntu1 liblz4-1_1.9.3-1build1 liblzma-dev_5.2.5-1.0build1 liblzma5_5.2.5-1.0build1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-7ubuntu2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2build1 libncursesw6_6.2+20201114-2build1 libnettle8_3.7-2.1 libnghttp2-14_1.43.0-1 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_10.36-2ubuntu4 libpcre3_2:8.39-13build2 libperl5.30_5.30.3-4 libperl5.32_5.32.1-2 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3build2 libprocps8_2:3.3.16-5ubuntu2 libpsl5_0.21.0-1.2 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_2.5.1-1ubuntu1 libselinux1_3.1-3build1 libsemanage-common_3.1-1build2 libsemanage1_3.1-1build2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsimde-dev_0.7.2-4 libsmartcols1_2.36.1-7ubuntu2 libsqlite3-0_3.34.1-3 libss2_1.45.7-1ubuntu2 libssh-4_0.9.5-1 libssl1.1_1.1.1j-1ubuntu1 libstdc++-10-dev_10.2.1-21ubuntu1 libstdc++6_11-20210306-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_247.3-1ubuntu4 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2build1 libtirpc-common_1.3.1-1build1 libtirpc-dev_1.3.1-1build1 libtirpc3_1.3.1-1build1 libtool_2.4.6-15 libtsan0_10.2.1-21ubuntu1 libubsan1_10.2.1-21ubuntu1 libuchardet0_0.0.7-1 libudev1_247.3-1ubuntu4 libunistring2_0.9.10-4 libuuid1_2.36.1-7ubuntu2 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-6.3build1 libxxhash0_0.8.0-2 libzstd1_1.4.8+dfsg-2build1 linux-libc-dev_5.11.0-11.12 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu8 logsave_1.45.7-1ubuntu2 lsb-base_11.1.0ubuntu2 lto-disabled-list_1 m4_1.4.18-5 make_4.3-4ubuntu1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-7ubuntu2 ncurses-base_6.2+20201114-2build1 ncurses-bin_6.2+20201114-2build1 openssl_1.1.1j-1ubuntu1 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu8 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.1-2 pinentry-curses_1.1.0-4build1 pkgbinarymangler_147 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_0.0.14 systemd_247.3-1ubuntu4 systemd-sysv_247.3-1ubuntu4 systemd-timesyncd_247.3-1ubuntu4 sysvinit-utils_2.96-5ubuntu1 tar_1.34+dfsg-1build1 tzdata_2021a-1ubuntu1 ubuntu-keyring_2020.06.17.1build1 util-linux_2.36.1-7ubuntu2 vim-common_2:8.2.2434-1ubuntu1 xxd_2:8.2.2434-1ubuntu1 xz-utils_5.2.5-1.0build1 zlib1g_1:1.2.11.dfsg-2ubuntu5 zlib1g-dev_1:1.2.11.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Mar 1 19:15:58 2021 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.7.8a+dfsg-2.dsc dpkg-source: info: extracting rna-star in /<>/rna-star-2.7.8a+dfsg dpkg-source: info: unpacking rna-star_2.7.8a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.8a+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying mathRoutinesNotInScope.patch dpkg-source: info: applying simde.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-21143309 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-21143309 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-21143309 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 2.7.8a+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=source debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/rna-star-2.7.8a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/rna-star-2.7.8a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/rna-star-2.7.8a+dfsg/source' make[1]: Leaving directory '/<>/rna-star-2.7.8a+dfsg' dh_autoreconf_clean -O--sourcedirectory=source dh_clean -O--sourcedirectory=source debian/rules binary-arch dh binary-arch --sourcedirectory=source dh_update_autotools_config -a -O--sourcedirectory=source dh_autoreconf -a -O--sourcedirectory=source dh_auto_configure -a -O--sourcedirectory=source debian/rules override_dh_auto_build make[1]: Entering directory '/<>/rna-star-2.7.8a+dfsg' dh_auto_build -- CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" STAR STARlong cd source && make -j4 "INSTALL=install --strip-program=true" "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" STAR STARlong make[2]: Entering directory '/<>/rna-star-2.7.8a+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_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 ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_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="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_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="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_collapseUMI_Graph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_collapseUMIall.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersClip_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_clip.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipCR4.cpp cd opal && \ g++ -c -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 opal.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_clipChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ClipMate_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_loadRawMatrix.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_emptyDrops_CR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' soloInputFeatureUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_statsOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bamSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloBarcode_extractBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_processRecords.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:41:17: warning: ignoring return value of ‘int symlink(const char*, const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 41 | symlink("../../../SJ.out.tab", (outputPrefixMat+pSolo.outFileNames[1]).c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SoloFeature_addBAMtags.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_swScoreSpliced.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjAlignSplit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' GTF_superTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SuperTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' STAR.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_samAttributes.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:187:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 187 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:191:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 191 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ParametersChimeric_initialize.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericBAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' bam_cat.c g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' serviceFuns.cpp bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMfunctions.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' BAMbinSortByCoordinate.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' 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="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' 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="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -o STARlong -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-03-01T19:14:32+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -ffile-prefix-map=/<>/rna-star-2.7.8a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -Bdynamic -lz -Wl,-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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Transcript.h:10:7: warning: type ‘struct Transcript’ violates the C++ One Definition Rule [-Wodr] 10 | class Transcript { | ^ Transcript.h:10:7: note: a different type is defined in another translation unit 10 | class Transcript { | ^ Transcript.h:12:10: note: the first difference of corresponding definitions is field ‘exons’ 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:12:10: note: a field of same name but different type is defined in another translation unit 12 | uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length | ^ Transcript.h:10:7: note: array types have different bounds 10 | class Transcript { | ^ ReadAlign.h:22:7: warning: type ‘struct ReadAlign’ violates the C++ One Definition Rule [-Wodr] 22 | class ReadAlign { | ^ ReadAlign.h:22:7: note: a different type is defined in another translation unit 22 | class ReadAlign { | ^ ReadAlign.h:57:20: note: the first difference of corresponding definitions is field ‘trA’ 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ ReadAlign.h:57:20: note: a field of same name but different type is defined in another translation unit 57 | Transcript trA, trA1, *trInit; //transcript, best tr, next best tr, initialized tr | ^ Transcript.h:10:7: note: type ‘struct Transcript’ itself violates the C++ One Definition Rule 10 | class Transcript { | ^ ReadAlign.h:210:14: warning: type of ‘calcCIGAR’ does not match original declaration [-Wlto-type-mismatch] 210 | void calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate); | ^ ReadAlign_calcCIGAR.cpp:3:6: note: ‘calcCIGAR’ was previously declared here 3 | void ReadAlign::calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate) { | ^ make[2]: Leaving directory '/<>/rna-star-2.7.8a+dfsg/source' make[1]: Leaving directory '/<>/rna-star-2.7.8a+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/rna-star-2.7.8a+dfsg' debian/tests/run_test.sh /<>/rna-star-2.7.8a+dfsg/source/STAR Mar 11 02:39:03 ..... started STAR run Mar 11 02:39:03 ... starting to generate Genome files Mar 11 02:39:03 ..... 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 Mar 11 02:39:03 ... starting to sort Suffix Array. This may take a long time... Mar 11 02:39:03 ... sorting Suffix Array chunks and saving them to disk... Mar 11 02:39:03 ... loading chunks from disk, packing SA... Mar 11 02:39:03 ... finished generating suffix array Mar 11 02:39:03 ... generating Suffix Array index Mar 11 02:39:03 ... completed Suffix Array index Mar 11 02:39:03 ... writing Genome to disk ... Mar 11 02:39:03 ... writing Suffix Array to disk ... Mar 11 02:39:03 ... writing SAindex to disk Mar 11 02:39:03 ..... finished successfully Mar 11 02:39:03 ..... started STAR run Mar 11 02:39:03 ..... loading genome Mar 11 02:39:03 ..... started mapping Mar 11 02:39:03 ..... finished mapping Mar 11 02:39:03 ..... finished successfully make[1]: Leaving directory '/<>/rna-star-2.7.8a+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=source dh_prep -a -O--sourcedirectory=source debian/rules override_dh_auto_install make[1]: Entering directory '/<>/rna-star-2.7.8a+dfsg' dh_install source/STAR source/STARlong usr/bin/ make[1]: Leaving directory '/<>/rna-star-2.7.8a+dfsg' dh_installdocs -a -O--sourcedirectory=source dh_installchangelogs -a -O--sourcedirectory=source dh_installman -a -O--sourcedirectory=source dh_installsystemduser -a -O--sourcedirectory=source dh_perl -a -O--sourcedirectory=source dh_link -a -O--sourcedirectory=source dh_strip_nondeterminism -a -O--sourcedirectory=source debian/rules override_dh_compress make[1]: Entering directory '/<>/rna-star-2.7.8a+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>/rna-star-2.7.8a+dfsg' dh_fixperms -a -O--sourcedirectory=source dh_missing -a -O--sourcedirectory=source dh_dwz -a -a -O--sourcedirectory=source dh_strip -a -a -O--sourcedirectory=source dh_makeshlibs -a -a -O--sourcedirectory=source dh_shlibdeps -a -a -O--sourcedirectory=source dh_installdeb -a -O--sourcedirectory=source debian/rules override_dh_gencontrol make[1]: Entering directory '/<>/rna-star-2.7.8a+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/<>/rna-star-2.7.8a+dfsg' dh_md5sums -a -O--sourcedirectory=source dh_builddeb -a -O--sourcedirectory=source INFO: pkgstriptranslations version 147 INFO: pkgstriptranslations version 147 pkgstriptranslations: processing rna-star (in debian/rna-star); do_strip: , oemstrip: pkgstriptranslations: processing rna-star-dbgsym (in debian/.debhelper/rna-star/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/rna-star/DEBIAN/control, package rna-star, directory debian/rna-star pkgstripfiles: processing control file: debian/.debhelper/rna-star/dbgsym-root/DEBIAN/control, package rna-star-dbgsym, directory debian/.debhelper/rna-star/dbgsym-root pkgstripfiles: Truncating usr/share/doc/rna-star/changelog.Debian.gz to topmost ten records dpkg-deb: building package 'rna-star-dbgsym' in 'debian/.debhelper/scratch-space/build-rna-star/rna-star-dbgsym_2.7.8a+dfsg-2_arm64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package rna-star ... pkgstripfiles: No PNG files. dpkg-deb: building package 'rna-star' in '../rna-star_2.7.8a+dfsg-2_arm64.deb'. Renaming rna-star-dbgsym_2.7.8a+dfsg-2_arm64.deb to rna-star-dbgsym_2.7.8a+dfsg-2_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../rna-star_2.7.8a+dfsg-2_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 2021-03-11T02:39:39Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.7.8a+dfsg-2_arm64.changes: ------------------------------------- Format: 1.8 Date: Mon, 01 Mar 2021 20:14:32 +0100 Source: rna-star Binary: rna-star Built-For-Profiles: noudeb Architecture: arm64 Version: 2.7.8a+dfsg-2 Distribution: hirsute-proposed Urgency: high Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: rna-star - ultrafast universal RNA-seq aligner Closes: 983723 Changes: rna-star (2.7.8a+dfsg-2) unstable; urgency=high . * Team upload. . [ Nilesh Patra ] * debian/{rules,control,patches/simde.patch}: use libsimde-dev to enable building on non-x86 systems. Removed "-march=native" architecture baseline violation. Closes: #983723 . [ Michael R. Crusoe ] * debian/{rules,clean: specify the source directory, and simplify * debian/patches/reproducible.patch: Reproducibly include the build time using SOURCE_DATE_EPOCH. Also forwarded upstream * On amd64: build STAR for each SIMD level from AVX2 on down. * Build and ship STARlong as well Checksums-Sha1: eb4271089588c373a3a6af60cacdddc8772d5d0f 9522836 rna-star-dbgsym_2.7.8a+dfsg-2_arm64.ddeb e4be7c0fd4e7e07aa52855b3f4eb633da862693b 6963 rna-star_2.7.8a+dfsg-2_arm64.buildinfo 8baa48d9b4222a7eee5d95821dd58121e9348000 639936 rna-star_2.7.8a+dfsg-2_arm64.deb Checksums-Sha256: ca68b04d01bf6a81aaabed49add949a60178af46567f875a8d7c622fbb0b2c6b 9522836 rna-star-dbgsym_2.7.8a+dfsg-2_arm64.ddeb 5797669edfaab78a05a65a8926ee6862dbf063f3d4ab74ccf6ce9805c29ee6ad 6963 rna-star_2.7.8a+dfsg-2_arm64.buildinfo 6a7003a3aa6034cc39efbdbec754aa18b5e613341de6d815052f5fc8cde42d3b 639936 rna-star_2.7.8a+dfsg-2_arm64.deb Files: 8fc07fb9ee96f0848d977dafd6aadf54 9522836 debug optional rna-star-dbgsym_2.7.8a+dfsg-2_arm64.ddeb b88e5239c06c92ecf562d4689b608aa1 6963 science optional rna-star_2.7.8a+dfsg-2_arm64.buildinfo 41c91cf521f88420ee0f86cfb5f1af27 639936 science optional rna-star_2.7.8a+dfsg-2_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: rna-star Binary: rna-star rna-star-dbgsym Architecture: arm64 Version: 2.7.8a+dfsg-2 Checksums-Md5: 8fc07fb9ee96f0848d977dafd6aadf54 9522836 rna-star-dbgsym_2.7.8a+dfsg-2_arm64.ddeb 41c91cf521f88420ee0f86cfb5f1af27 639936 rna-star_2.7.8a+dfsg-2_arm64.deb Checksums-Sha1: eb4271089588c373a3a6af60cacdddc8772d5d0f 9522836 rna-star-dbgsym_2.7.8a+dfsg-2_arm64.ddeb 8baa48d9b4222a7eee5d95821dd58121e9348000 639936 rna-star_2.7.8a+dfsg-2_arm64.deb Checksums-Sha256: ca68b04d01bf6a81aaabed49add949a60178af46567f875a8d7c622fbb0b2c6b 9522836 rna-star-dbgsym_2.7.8a+dfsg-2_arm64.ddeb 6a7003a3aa6034cc39efbdbec754aa18b5e613341de6d815052f5fc8cde42d3b 639936 rna-star_2.7.8a+dfsg-2_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Thu, 11 Mar 2021 02:39:38 +0000 Build-Path: /<>/rna-star-2.7.8a+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-14), automake (= 1:1.16.3-2ubuntu1), autopoint (= 0.21-3ubuntu2), autotools-dev (= 20180224.1+nmu1), base-files (= 11ubuntu18), base-passwd (= 3.5.49), bash (= 5.1-1ubuntu1), binutils (= 2.36.1-5ubuntu1), binutils-aarch64-linux-gnu (= 2.36.1-5ubuntu1), binutils-common (= 2.36.1-5ubuntu1), bsdextrautils (= 2.36.1-7ubuntu2), bsdutils (= 1:2.36.1-7ubuntu2), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), coreutils (= 8.32-4ubuntu2), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.1-21ubuntu1), dash (= 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1), debconf (= 1.5.74), debhelper (= 13.3.3ubuntu3), debianutils (= 4.11.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.11.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.7.1ubuntu3), dpkg-dev (= 1.20.7.1ubuntu3), dwz (= 0.14-1), file (= 1:5.39-3), findutils (= 4.8.0-1ubuntu1), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.1-21ubuntu1), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.1-21ubuntu1), gcc-10-base (= 10.2.1-21ubuntu1), gcc-11-base (= 11-20210306-1ubuntu1), gettext (= 0.21-3ubuntu2), gettext-base (= 0.21-3ubuntu2), grep (= 3.6-1), groff-base (= 1.22.4-6), gzip (= 1.10-2ubuntu3), hostname (= 3.23), init-system-helpers (= 1.60), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10build1), libarchive-zip-perl (= 1.68-1), libasan6 (= 10.2.1-21ubuntu1), libasn1-8-heimdal (= 7.7.0+dfsg-2), libatomic1 (= 11-20210306-1ubuntu1), libattr1 (= 1:2.4.48-6build1), libaudit-common (= 1:3.0-2ubuntu1), libaudit1 (= 1:3.0-2ubuntu1), libbinutils (= 2.36.1-5ubuntu1), libblkid1 (= 2.36.1-7ubuntu2), libbrotli1 (= 1.0.9-2build2), libbz2-1.0 (= 1.0.8-4ubuntu2), libc-bin (= 2.33-0ubuntu2), libc-dev-bin (= 2.33-0ubuntu2), libc6 (= 2.33-0ubuntu2), libc6-dev (= 2.33-0ubuntu2), libcap-ng0 (= 0.7.9-2.2build1), libcap2 (= 1:2.44-1build1), libcc1-0 (= 11-20210306-1ubuntu1), libcom-err2 (= 1.45.7-1ubuntu2), libcrypt-dev (= 1:4.4.17-1ubuntu2), libcrypt1 (= 1:4.4.17-1ubuntu2), libctf-nobfd0 (= 2.36.1-5ubuntu1), libctf0 (= 2.36.1-5ubuntu1), libcurl3-gnutls (= 7.74.0-1ubuntu1), libcurl4-gnutls-dev (= 7.74.0-1ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu3), libdebconfclient0 (= 0.256ubuntu3), libdebhelper-perl (= 13.3.3ubuntu3), libdeflate-dev (= 1.7-1ubuntu1), libdeflate0 (= 1.7-1ubuntu1), libdpkg-perl (= 1.20.7.1ubuntu3), libelf1 (= 0.183-4), libffi8ubuntu1 (= 3.4~20200819gead65ca871-0ubuntu5), libfile-stripnondeterminism-perl (= 1.11.0-1), libgcc-10-dev (= 10.2.1-21ubuntu1), libgcc-s1 (= 11-20210306-1ubuntu1), libgcrypt20 (= 1.8.7-2ubuntu2), libgdbm-compat4 (= 1.19-2), libgdbm6 (= 1.19-2), libgmp10 (= 2:6.2.1+dfsg-1ubuntu1), libgnutls30 (= 3.7.0-5ubuntu1), libgomp1 (= 11-20210306-1ubuntu1), libgpg-error0 (= 1.38-2build1), libgssapi-krb5-2 (= 1.18.3-4), 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 (= 3.7-2.1), libhts-dev (= 1.11-4), libhts3 (= 1.11-4), libhx509-5-heimdal (= 7.7.0+dfsg-2), libicu67 (= 67.1-6ubuntu1), libidn2-0 (= 2.3.0-5), libisl23 (= 0.23-1), libitm1 (= 11-20210306-1ubuntu1), libk5crypto3 (= 1.18.3-4), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-2), libkrb5-3 (= 1.18.3-4), libkrb5support0 (= 1.18.3-4), libldap-2.4-2 (= 2.4.57+dfsg-2ubuntu1), liblsan0 (= 10.2.1-21ubuntu1), liblz4-1 (= 1.9.3-1build1), liblzma-dev (= 5.2.5-1.0build1), liblzma5 (= 5.2.5-1.0build1), libmagic-mgc (= 1:5.39-3), libmagic1 (= 1:5.39-3), libmount1 (= 2.36.1-7ubuntu2), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libnettle8 (= 3.7-2.1), libnghttp2-14 (= 1.43.0-1), 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 (= 10.36-2ubuntu4), libpcre3 (= 2:8.39-13build2), libperl5.32 (= 5.32.1-2), libpipeline1 (= 1.5.3-1), libpsl5 (= 0.21.0-1.2), 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 (= 2.5.1-1ubuntu1), libselinux1 (= 3.1-3build1), libsigsegv2 (= 2.13-1), libsimde-dev (= 0.7.2-4), libsmartcols1 (= 2.36.1-7ubuntu2), libsqlite3-0 (= 3.34.1-3), libssh-4 (= 0.9.5-1), libssl1.1 (= 1.1.1j-1ubuntu1), libstdc++-10-dev (= 10.2.1-21ubuntu1), libstdc++6 (= 11-20210306-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 247.3-1ubuntu4), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2+20201114-2build1), libtirpc-common (= 1.3.1-1build1), libtirpc-dev (= 1.3.1-1build1), libtirpc3 (= 1.3.1-1build1), libtool (= 2.4.6-15), libtsan0 (= 10.2.1-21ubuntu1), libubsan1 (= 10.2.1-21ubuntu1), libuchardet0 (= 0.0.7-1), libudev1 (= 247.3-1ubuntu4), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36.1-7ubuntu2), libwind0-heimdal (= 7.7.0+dfsg-2), libxml2 (= 2.9.10+dfsg-6.3build1), libzstd1 (= 1.4.8+dfsg-2build1), linux-libc-dev (= 5.11.0-11.12), login (= 1:4.8.1-1ubuntu8), lsb-base (= 11.1.0ubuntu2), lto-disabled-list (= 1), m4 (= 1.4.18-5), make (= 4.3-4ubuntu1), man-db (= 2.9.4-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2+20201114-2build1), ncurses-bin (= 6.2+20201114-2build1), patch (= 2.7.6-7), perl (= 5.32.1-2), perl-base (= 5.32.1-2), perl-modules-5.32 (= 5.32.1-2), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu4), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.14), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.34+dfsg-1build1), util-linux (= 2.36.1-7ubuntu2), vim-common (= 2:8.2.2434-1ubuntu1), xxd (= 2:8.2.2434-1ubuntu1), xz-utils (= 5.2.5-1.0build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu5), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu5) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1614626072" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ rna-star_2.7.8a+dfsg-2_arm64.deb -------------------------------- new Debian package, version 2.0. size 639936 bytes: control archive=1464 bytes. 1478 bytes, 26 lines control 653 bytes, 10 lines md5sums Package: rna-star Version: 2.7.8a+dfsg-2 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2291 Depends: libc6 (>= 2.33), libgcc-s1 (>= 4.2), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 9) Built-Using: simde (= 0.7.2-4) 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 2021-03-01 19:14 ./ drwxr-xr-x root/root 0 2021-03-01 19:14 ./usr/ drwxr-xr-x root/root 0 2021-03-01 19:14 ./usr/bin/ -rwxr-xr-x root/root 1037880 2021-03-01 19:14 ./usr/bin/STAR -rwxr-xr-x root/root 1041976 2021-03-01 19:14 ./usr/bin/STARlong drwxr-xr-x root/root 0 2021-03-01 19:14 ./usr/share/ drwxr-xr-x root/root 0 2021-03-01 19:14 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2019-12-17 15:00 ./usr/share/doc-base/rna-star drwxr-xr-x root/root 0 2021-03-01 19:14 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-03-01 19:14 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2019-12-17 15:00 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3290 2021-02-20 22:30 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 7203 2021-02-20 22:30 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 231796 2021-02-20 22:30 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 1156 2021-03-01 19:14 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 2565 2019-12-17 15:00 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2021-03-01 19:14 ./usr/share/man/ drwxr-xr-x root/root 0 2021-03-01 19:14 ./usr/share/man/man1/ -rw-r--r-- root/root 824 2021-03-01 19:14 ./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: 270 Distribution: hirsute-proposed Host Architecture: arm64 Install-Time: 15 Job: rna-star_2.7.8a+dfsg-2.dsc Machine Architecture: arm64 Package: rna-star Package-Time: 287 Source-Version: 2.7.8a+dfsg-2 Space: n/a Status: successful Version: 2.7.8a+dfsg-2 -------------------------------------------------------------------------------- Finished at 2021-03-11T02:39:39Z Build needed 00:04:47, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-21143309 Scanning for processes to kill in build PACKAGEBUILD-21143309