https://launchpad.net/ubuntu/+source/trnascan-se/2.0.7+ds-1/+build/20254811 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-026 4.15.0-122-generic #124-Ubuntu SMP Thu Oct 15 13:03:05 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 6 Nov 05:13:33 ntpdate[1695]: adjust time server 10.211.37.1 offset -0.013078 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20254811 --image-type chroot /home/buildd/filecache-default/720a8366e1260e086c1691fe6381a3f2b1c21d81 Creating target for build PACKAGEBUILD-20254811 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20254811 Starting target for build PACKAGEBUILD-20254811 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20254811 'deb http://ftpmaster.internal/ubuntu hirsute main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu hirsute-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-20254811 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20254811 Updating target for build PACKAGEBUILD-20254811 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [88.4 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [88.4 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main amd64 Packages [1383 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/restricted amd64 Packages [61.2 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/restricted Translation-en [9564 B] Get:9 http://ftpmaster.internal/ubuntu hirsute/universe amd64 Packages [12.8 MB] Get:10 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5329 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/multiverse amd64 Packages [202 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/multiverse Translation-en [106 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 Packages [211 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [68.8 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/restricted amd64 Packages [36.2 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/restricted Translation-en [7088 B] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 Packages [1583 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [520 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/multiverse amd64 Packages [7628 B] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/multiverse Translation-en [6256 B] Fetched 23.4 MB in 3s (7079 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files base-passwd binutils binutils-common binutils-x86-64-linux-gnu cpp-10 fakeroot g++-10 gcc-10 gcc-10-base libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdebconfclient0 libfakeroot libgcc-10-dev libgcc-s1 libgomp1 libidn2-0 libip4tc2 libitm1 liblsan0 libmpc3 libncurses6 libncursesw6 libnpth0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 linux-libc-dev ncurses-base ncurses-bin systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata 64 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 229 MB of archives. After this operation, 885 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcrypt-dev amd64 1:4.4.17-1ubuntu1 [105 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcrypt1 amd64 1:4.4.17-1ubuntu1 [78.8 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6-dev amd64 2.32-0ubuntu4 [2128 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-dev-bin amd64 2.32-0ubuntu4 [30.9 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 linux-libc-dev amd64 5.8.0-26.27 [1165 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc-common all 1.2.6-3 [7444 B] Get:7 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc-dev amd64 1.2.6-3 [184 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc3 amd64 1.2.6-3 [77.2 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcc1-0 amd64 10.2.0-16ubuntu1 [41.3 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10-base amd64 10.2.0-16ubuntu1 [19.6 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-s1 amd64 10.2.0-16ubuntu1 [41.7 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgomp1 amd64 10.2.0-16ubuntu1 [102 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libitm1 amd64 10.2.0-16ubuntu1 [26.4 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libatomic1 amd64 10.2.0-16ubuntu1 [9284 B] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libasan6 amd64 10.2.0-16ubuntu1 [344 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 liblsan0 amd64 10.2.0-16ubuntu1 [144 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtsan0 amd64 10.2.0-16ubuntu1 [320 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libubsan1 amd64 10.2.0-16ubuntu1 [136 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libquadmath0 amd64 10.2.0-16ubuntu1 [146 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 g++-10 amd64 10.2.0-16ubuntu1 [70.1 MB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++-10-dev amd64 10.2.0-16ubuntu1 [1750 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-10-dev amd64 10.2.0-16ubuntu1 [2341 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10 amd64 10.2.0-16ubuntu1 [72.0 MB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 cpp-10 amd64 10.2.0-16ubuntu1 [63.5 MB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++6 amd64 10.2.0-16ubuntu1 [501 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libmpc3 amd64 1.2.0-1 [44.3 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf-nobfd0 amd64 2.35.1-2ubuntu1 [48.2 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf0 amd64 2.35.1-2ubuntu1 [47.6 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libbinutils amd64 2.35.1-2ubuntu1 [481 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-common amd64 2.35.1-2ubuntu1 [212 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils amd64 2.35.1-2ubuntu1 [3376 B] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.35.1-2ubuntu1 [1646 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6 amd64 2.32-0ubuntu4 [2684 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-files amd64 11ubuntu16 [60.5 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libncursesw6 amd64 6.2+20200918-1 [132 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libncurses6 amd64 6.2+20200918-1 [102 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtinfo6 amd64 6.2+20200918-1 [87.3 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 ncurses-bin amd64 6.2+20200918-1 [173 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libdebconfclient0 amd64 0.255ubuntu1 [6184 B] Get:40 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-passwd amd64 3.5.48 [47.5 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-bin amd64 2.32-0ubuntu4 [625 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 ncurses-base all 6.2+20200918-1 [18.7 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main amd64 sysvinit-utils amd64 2.96-5ubuntu1 [20.8 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-timesyncd amd64 246.6-2ubuntu1 [28.2 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-sysv amd64 246.6-2ubuntu1 [10.3 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapparmor1 amd64 3.0.0-0ubuntu2 [36.3 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit-common all 1:2.8.5-3ubuntu2 [4092 B] Get:48 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit1 amd64 1:2.8.5-3ubuntu2 [39.5 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap2 amd64 1:2.44-1 [17.2 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main amd64 libidn2-0 amd64 2.3.0-2 [52.5 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libip4tc2 amd64 1.8.5-3ubuntu3 [18.7 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main amd64 libseccomp2 amd64 2.4.3-1ubuntu5 [42.0 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd amd64 246.6-2ubuntu1 [4165 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libsystemd0 amd64 246.6-2ubuntu1 [273 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libudev1 amd64 246.6-2ubuntu1 [67.6 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapt-pkg6.0 amd64 2.1.11 [848 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main amd64 apt amd64 2.1.11 [1305 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main amd64 libselinux1 amd64 3.1-2build1 [69.4 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage-common all 3.1-1build1 [10.1 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage1 amd64 3.1-1build1 [87.2 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main amd64 tzdata all 2020d-1ubuntu1 [293 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libfakeroot amd64 1.25.3-1 [26.6 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 fakeroot amd64 1.25.3-1 [62.9 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnpth0 amd64 1.6-3 [8220 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 229 MB in 7s (31.7 MB/s) (Reading database ... 12980 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu1_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:amd64 (1:4.4.17-1ubuntu1) ... (Reading database ... 12980 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.32-0ubuntu4_amd64.deb ... Unpacking libc6-dev:amd64 (2.32-0ubuntu4) over (2.32-0ubuntu3) ... Preparing to unpack .../1-libc-dev-bin_2.32-0ubuntu4_amd64.deb ... Unpacking libc-dev-bin (2.32-0ubuntu4) over (2.32-0ubuntu3) ... Preparing to unpack .../2-linux-libc-dev_5.8.0-26.27_amd64.deb ... Unpacking linux-libc-dev:amd64 (5.8.0-26.27) over (5.8.0-25.26) ... Preparing to unpack .../3-libtirpc-common_1.2.6-3_all.deb ... Unpacking libtirpc-common (1.2.6-3) over (1.2.6-1build1) ... Preparing to unpack .../4-libtirpc-dev_1.2.6-3_amd64.deb ... 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Setting up gcc-10 (10.2.0-16ubuntu1) ... Setting up g++-10 (10.2.0-16ubuntu1) ... Setting up systemd (246.6-2ubuntu1) ... Initializing machine ID from random generator. Setting up systemd-timesyncd (246.6-2ubuntu1) ... Setting up systemd-sysv (246.6-2ubuntu1) ... Processing triggers for libc-bin (2.32-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20254811 amd64 hirsute-proposed -c chroot:build-PACKAGEBUILD-20254811 --arch=amd64 --dist=hirsute-proposed --nolog -A trnascan-se_2.0.7+ds-1.dsc Initiating build PACKAGEBUILD-20254811 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-122-generic #124-Ubuntu SMP Thu Oct 15 13:03:05 UTC 2020 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lgw01-amd64-026.buildd +==============================================================================+ | trnascan-se 2.0.7+ds-1 (amd64) Fri, 06 Nov 2020 05:14:41 +0000 | +==============================================================================+ Package: trnascan-se Version: 2.0.7+ds-1 Source Version: 2.0.7+ds-1 Distribution: hirsute-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20254811/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- trnascan-se_2.0.7+ds-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/trnascan-se-zkM39Y/trnascan-se-2.0.7+ds' with '<>' I: NOTICE: Log filtering will replace 'build/trnascan-se-zkM39Y' 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-9MAVqM/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-9MAVqM/apt_archive ./ InRelease Get:2 copy:/<>/resolver-9MAVqM/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-9MAVqM/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-9MAVqM/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-9MAVqM/apt_archive ./ Packages [434 B] Fetched 1740 B in 0s (119 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 NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-9MAVqM/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12979 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), autoconf-archive, infernal Filtered Build-Depends: debhelper-compat (= 13), autoconf-archive, infernal dpkg-deb: building package 'sbuild-build-depends-trnascan-se-dummy' in '/<>/resolver-9MAVqM/apt_archive/sbuild-build-depends-trnascan-se-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-trnascan-se-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-9MAVqM/apt_archive ./ InRelease Get:2 copy:/<>/resolver-9MAVqM/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-9MAVqM/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-9MAVqM/apt_archive ./ Sources [510 B] Get:5 copy:/<>/resolver-9MAVqM/apt_archive ./ Packages [593 B] Fetched 2066 B in 0s (124 kB/s) Reading package lists... Reading package lists... Install trnascan-se build dependencies (apt-based resolver) ----------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base infernal intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base infernal intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-trnascan-se-dummy 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 23.4 MB of archives. After this operation, 123 MB of additional disk space will be used. Get:1 copy:/<>/resolver-9MAVqM/apt_archive ./ sbuild-build-depends-trnascan-se-dummy 0.invalid.0 [884 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main amd64 bsdextrautils amd64 2.36-3ubuntu1 [77.5 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main amd64 libuchardet0 amd64 0.0.7-1 [68.0 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main amd64 groff-base amd64 1.22.4-5 [847 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpipeline1 amd64 1.5.3-1 [27.8 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main amd64 man-db amd64 2.9.3-2 [1117 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe amd64 autoconf-archive all 20190106-2.1ubuntu1 [665 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmagic-mgc amd64 1:5.38-5 [218 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmagic1 amd64 1:5.38-5 [76.0 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main amd64 file amd64 1:5.38-5 [23.3 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main amd64 libelf1 amd64 0.181-1 [44.3 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libglib2.0-0 amd64 2.66.2-1 [1306 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main amd64 libicu67 amd64 67.1-4 [8620 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libxml2 amd64 2.9.10+dfsg-6.2 [623 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main amd64 gettext-base amd64 0.19.8.1-10build1 [50.2 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsigsegv2 amd64 2.12-2build1 [13.9 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main amd64 m4 amd64 1.4.18-4 [199 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main amd64 autoconf all 2.69-11.1 [321 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main amd64 automake all 1:1.16.2-4ubuntu1 [548 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main amd64 autopoint all 0.19.8.1-10build1 [412 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtool all 2.4.6-14 [161 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main amd64 dh-autoreconf all 19 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdebhelper-perl all 13.2.1ubuntu1 [63.6 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:27 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main amd64 dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:29 http://ftpmaster.internal/ubuntu hirsute/main amd64 dwz amd64 0.13-5 [151 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main amd64 gettext amd64 0.19.8.1-10build1 [895 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main amd64 po-debconf all 1.0.21 [233 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main amd64 debhelper all 13.2.1ubuntu1 [879 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/universe amd64 infernal amd64 1.1.3-5 [5480 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.4 MB in 1s (44.2 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12979 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36-3ubuntu1_amd64.deb ... Unpacking bsdextrautils (2.36-3ubuntu1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_amd64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package autoconf-archive. Preparing to unpack .../05-autoconf-archive_20190106-2.1ubuntu1_all.deb ... Unpacking autoconf-archive (20190106-2.1ubuntu1) ... 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Setting up bsdextrautils (2.36-3ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-4) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.66.2-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.2.1ubuntu1) ... Setting up libmagic1:amd64 (1:5.38-5) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up autoconf-archive (20190106-2.1ubuntu1) ... Setting up file (1:5.38-5) ... Setting up infernal (1.1.3-5) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:amd64 (2.12-2build1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:amd64 (0.181-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.2) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libtool (2.4.6-14) ... Setting up m4 (1.4.18-4) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up automake (1:1.16.2-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10build1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.2.1ubuntu1) ... Setting up sbuild-build-depends-trnascan-se-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu4) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-122-generic amd64 (x86_64) Toolchain package versions: binutils_2.35.1-2ubuntu1 dpkg-dev_1.20.5ubuntu2 g++-10_10.2.0-16ubuntu1 gcc-10_10.2.0-16ubuntu1 libc6-dev_2.32-0ubuntu4 libstdc++-10-dev_10.2.0-16ubuntu1 libstdc++6_10.2.0-16ubuntu1 linux-libc-dev_5.8.0-26.27 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.11 autoconf_2.69-11.1 autoconf-archive_20190106-2.1ubuntu1 automake_1:1.16.2-4ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.0-6ubuntu2 binutils_2.35.1-2ubuntu1 binutils-common_2.35.1-2ubuntu1 binutils-x86-64-linux-gnu_2.35.1-2ubuntu1 bsdextrautils_2.36-3ubuntu1 bsdutils_1:2.36-3ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 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libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libquadmath0_10.2.0-16ubuntu1 libreadline8_8.0-4 libseccomp2_2.4.3-1ubuntu5 libselinux1_3.1-2build1 libsemanage-common_3.1-1build1 libsemanage1_3.1-1build1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.36-3ubuntu1 libsqlite3-0_3.33.0-1 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu4 libstdc++-10-dev_10.2.0-16ubuntu1 libstdc++6_10.2.0-16ubuntu1 libsub-override-perl_0.09-2 libsystemd0_246.6-2ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libtsan0_10.2.0-16ubuntu1 libubsan1_10.2.0-16ubuntu1 libuchardet0_0.0.7-1 libudev1_246.6-2ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36-3ubuntu1 libxml2_2.9.10+dfsg-6.2 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.0-26.27 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3ubuntu1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 openssl_1.1.1f-1ubuntu4 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 readline-common_8.0-4 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-trnascan-se-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 systemd_246.6-2ubuntu1 systemd-sysv_246.6-2ubuntu1 systemd-timesyncd_246.6-2ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.30+dfsg-7 tzdata_2020d-1ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.36-3ubuntu1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Nov 5 08:37:48 2020 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./trnascan-se_2.0.7+ds-1.dsc dpkg-source: info: extracting trnascan-se in /<>/trnascan-se-2.0.7+ds dpkg-source: info: unpacking trnascan-se_2.0.7+ds.orig.tar.gz dpkg-source: info: unpacking trnascan-se_2.0.7+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pkg-data.patch dpkg-source: info: applying confdir.patch dpkg-source: info: applying chmod_only_if_exists.patch dpkg-source: info: applying configure_debugging.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-20254811 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20254811 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20254811 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package trnascan-se dpkg-buildpackage: info: source version 2.0.7+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel configure.ac:21: installing './compile' configure.ac:31: installing './install-sh' configure.ac:56: installing './missing' Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/trnascan-se-2.0.7+ds' dh_auto_configure -- --enable-debugging ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-debugging checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for a BSD-compatible install... /usr/bin/install -c checking for perl... /usr/bin/perl checking for Perl version 5.0.0 or later... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for memory.h... (cached) yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for size_t... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for bzero... yes checking for memset... yes checking for re_comp... yes checking for regcomp... yes checking for sqrt... no checking for strcasecmp... yes checking for strchr... yes checking for strstr... yes checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/<>/trnascan-se-2.0.7+ds' dh_auto_build -O--no-parallel make -j1 make[1]: Entering directory '/<>/trnascan-se-2.0.7+ds' make all-am make[2]: Entering directory '/<>/trnascan-se-2.0.7+ds' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/alignio.o src/alignio.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/sqerror.o src/sqerror.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/sqio.o src/sqio.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/iupac.o src/iupac.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/msf.o src/msf.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/revcomp.o src/revcomp.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/selex.o src/selex.c src/selex.c: In function ‘ReadSELEX’: src/selex.c:451:3: warning: ‘blocks’ may be used uninitialized in this function [-Wmaybe-uninitialized] 451 | free(blocks); | ^~~~~~~~~~~~ src/selex.c:456:14: warning: ‘num’ may be used uninitialized in this function [-Wmaybe-uninitialized] 456 | *ret_num = num; | ~~~~~~~~~~~^~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/sre_ctype.o src/sre_ctype.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/sre_math.o src/sre_math.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/sre_string.o src/sre_string.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/stack.o src/stack.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/types.o src/types.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/gnuregex.o src/gnuregex.c src/gnuregex.c: In function ‘regex_compile’: src/gnuregex.c:1613:18: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1613 | if (COMPILE_STACK_EMPTY) | ^ src/gnuregex.c:1633:18: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1633 | if (COMPILE_STACK_EMPTY) | ^ src/gnuregex.c: In function ‘re_match_2’: src/gnuregex.c:2341:11: warning: unused variable ‘destination’ [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ src/gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ src/gnuregex.c:2341:11: warning: unused variable ‘destination’ [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ src/gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ src/gnuregex.c:2341:11: warning: unused variable ‘destination’ [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ src/gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ src/gnuregex.c:4061:19: warning: variable ‘sdummy’ set but not used [-Wunused-but-set-variable] 4061 | char *sdummy; | ^~~~~~ src/gnuregex.c:4060:28: warning: variable ‘pdummy’ set but not used [-Wunused-but-set-variable] 4060 | unsigned char *pdummy; | ^~~~~~ src/gnuregex.c:2341:11: warning: unused variable ‘destination’ [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ src/gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ src/gnuregex.c:2341:11: warning: unused variable ‘destination’ [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ src/gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/interleaved.o src/interleaved.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/getopt.o src/getopt.c src/getopt.c: In function ‘Getopt’: src/getopt.c:110:25: warning: ‘opti’ may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | *ret_optname = opt[opti].name; | ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/eufind_main.o src/eufind_main.c In file included from src/eufind_main.c:27: src/eufind_const.h:16:9: warning: "/*" within comment [-Wcomment] 16 | /* AB_BOX_DIST_RANGE used */ | src/eufind_const.h:19:11: warning: "/*" within comment [-Wcomment] 19 | /* distance for A-B box pairs */ | src/eufind_main.c: In function ‘main’: src/eufind_main.c:66:5: warning: "/*" within comment [-Wcomment] 66 | /* changing seqs to DNA & upper case */ | src/eufind_main.c:106:21: warning: implicit declaration of function ‘getopt’; did you mean ‘Getopt’? [-Wimplicit-function-declaration] 106 | while ((optchar = getopt(argc, argv, OPTIONS)) != -1) | ^~~~~~ | Getopt src/eufind_main.c:168:17: warning: implicit declaration of function ‘IntEncodeSeq’ [-Wimplicit-function-declaration] 168 | if (errno = IntEncodeSeq(iseq,seq,sqinfo.len)) | ^~~~~~~~~~~~ src/eufind_main.c:168:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 168 | if (errno = IntEncodeSeq(iseq,seq,sqinfo.len)) | ^~~~~ src/eufind_main.c:175:7: warning: implicit declaration of function ‘Init_tRNA’ [-Wimplicit-function-declaration] 175 | Init_tRNA(prev_tRNA); /* clear previous tRNA */ | ^~~~~~~~~ src/eufind_main.c:194:14: warning: implicit declaration of function ‘GetBbox’ [-Wimplicit-function-declaration] 194 | while (GetBbox(&FirstScore,&seqidx,iseq,sqinfo.len,strand, | ^~~~~~~ src/eufind_main.c:204:10: warning: implicit declaration of function ‘GetSecABox’ [-Wimplicit-function-declaration] 204 | && (GetSecABox(tRNA,seq))){ | ^~~~~~~~~~ src/eufind_main.c:206:9: warning: implicit declaration of function ‘GetBestTrxTerm’ [-Wimplicit-function-declaration] 206 | if (!GetBestTrxTerm(tRNA,seq,sqinfo.len,NoTermPenalty) && | ^~~~~~~~~~~~~~ src/eufind_main.c:218:4: warning: implicit declaration of function ‘GetBestABox’ [-Wimplicit-function-declaration] 218 | GetBestABox(tRNA,seq,iseq,sqinfo.len,strand,ShowScores, | ^~~~~~~~~~~ src/eufind_main.c:239:2: warning: implicit declaration of function ‘Get_tRNA_stats’ [-Wimplicit-function-declaration] 239 | Get_tRNA_stats(tRNA,seq,sqinfo.len,strand); | ^~~~~~~~~~~~~~ src/eufind_main.c:241:6: warning: implicit declaration of function ‘tRNAOverlap’ [-Wimplicit-function-declaration] 241 | if (tRNAOverlap(tRNA,prev_tRNA,strand)) { | ^~~~~~~~~~~ src/eufind_main.c:258:6: warning: implicit declaration of function ‘Save_tRNA’ [-Wimplicit-function-declaration] 258 | Save_tRNA(prev_tRNA,&sqinfo,seq,strand,ShowScores,sqoffset); | ^~~~~~~~~ src/eufind_main.c:74:13: warning: unused variable ‘reviseq’ [-Wunused-variable] 74 | *iseq, *reviseq; /* encoded seq & encoded reverse comp */ | ^~~~~~~ src/eufind_main.c:58:13: warning: unused variable ‘i’ [-Wunused-variable] 58 | int i, errno, | ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/pavesi.o src/pavesi.c In file included from src/pavesi.c:26: src/eufind_const.h:16:9: warning: "/*" within comment [-Wcomment] 16 | /* AB_BOX_DIST_RANGE used */ | src/eufind_const.h:19:11: warning: "/*" within comment [-Wcomment] 19 | /* distance for A-B box pairs */ | src/pavesi.c: In function ‘GetBbox’: src/pavesi.c:138:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 138 | if (verbose) | ^ src/pavesi.c: In function ‘GetBestABox’: src/pavesi.c:320:5: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 320 | if (verbose) | ^ src/pavesi.c:239:5: warning: unused variable ‘bestsc’ [-Wunused-variable] 239 | bestsc, /* best score so far */ | ^~~~~~ src/pavesi.c:236:5: warning: variable ‘best_offset1’ set but not used [-Wunused-but-set-variable] 236 | best_offset1; | ^~~~~~~~~~~~ src/pavesi.c:235:5: warning: variable ‘best_gap’ set but not used [-Wunused-but-set-variable] 235 | best_gap, /* gapct & offset1 vals for best score so far */ | ^~~~~~~~ src/pavesi.c: In function ‘GetBestTrxTerm’: src/pavesi.c:347:9: warning: unused variable ‘score’ [-Wunused-variable] 347 | float score; /* current score */ | ^~~~~ src/pavesi.c: In function ‘Init_tRNA’: src/pavesi.c:102:1: warning: control reaches end of non-void function [-Wreturn-type] 102 | } | ^ src/pavesi.c: In function ‘GetBestABox’: src/pavesi.c:336:1: warning: control reaches end of non-void function [-Wreturn-type] 336 | } | ^ gcc -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bin/eufindtRNA src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/eufind_main.o src/pavesi.o -lm gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTSCANDIR=\"/usr/share/trnascan-se\/models\" -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/bin_trnascan_1_4-trnascan.o `test -f 'src/trnascan.c' || echo './'`src/trnascan.c src/trnascan.c:335:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 335 | main(int argc, char **argv) | ^~~~ src/trnascan.c: In function ‘main’: src/trnascan.c:433:16: warning: implicit declaration of function ‘getopt’; did you mean ‘getsubopt’? [-Wimplicit-function-declaration] 433 | while ((optc = getopt(argc, argv, "csraho:v:i:")) != -1) | ^~~~~~ | getsubopt src/trnascan.c: In function ‘lectval’: src/trnascan.c:1152:5: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1152 | int ret = 0; | ^~~ src/trnascan.c: In function ‘fgetseq’: src/trnascan.c:1208:7: warning: variable ‘ptrRet’ set but not used [-Wunused-but-set-variable] 1208 | char *ptrRet; | ^~~~~~ src/trnascan.c: In function ‘getseqsize’: src/trnascan.c:1335:7: warning: variable ‘ptrRet’ set but not used [-Wunused-but-set-variable] 1335 | char* ptrRet; | ^~~~~~ src/trnascan.c: At top level: src/trnascan.c:1421:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 1421 | myindex (char *s, char *t) | ^~~~~~~ src/trnascan.c: In function ‘basepairing’: src/trnascan.c:1643:22: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1643 | case 'g': case 'r': if ((*(ptr+lpair-n) == 'c') || (*(ptr+lpair-n) == 't')) | ^~ src/trnascan.c:1644:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1644 | (*ncomp)++; break; | ^~~~~ src/trnascan.c:1645:22: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1645 | case 't': case 'y': if ((*(ptr+lpair-n) == 'a') || (*(ptr+lpair-n) == 'g')) | ^~ src/trnascan.c:1646:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1646 | (*ncomp)++; break; | ^~~~~ src/trnascan.c: In function ‘main’: src/trnascan.c:792:25: warning: ‘fpverb’ may be used uninitialized in this function [-Wmaybe-uninitialized] 792 | following_search(pos,pos1,ptr1,ptr3,lpair,nloop, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 793 | sequence,seqlen,fpo,fpverb,name,score,match2,&ntrna,&npred,&match,sqoffset); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DTSCANDIR=\"/usr/share/trnascan-se\/models\" -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bin/trnascan-1.4 src/bin_trnascan_1_4-trnascan.o -lm gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/align.o src/align.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/dbviterbi.o src/dbviterbi.c src/dbviterbi.c: In function ‘ViterbiScan’: src/dbviterbi.c:421:10: warning: ‘emitsc’ may be used uninitialized in this function [-Wmaybe-uninitialized] 421 | *scp += emitsc; | ^~ src/dbviterbi.c:348:8: note: ‘emitsc’ was declared here 348 | int emitsc; | ^~~~~~ src/dbviterbi.c:397:11: warning: ‘beam’ may be used uninitialized in this function [-Wmaybe-uninitialized] 397 | beam += y + st->offset; | ~~~~~~^~~~~~~~~~~~~~~~~ src/dbviterbi.c:340:8: note: ‘beam’ was declared here 340 | int *beam; /* ptr to a beam (z-axis vector) */ | ^~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/debug.o src/debug.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/emit.o src/emit.c src/emit.c: In function ‘pick_best_single’: src/emit.c:559:22: warning: ‘besti’ may be used uninitialized in this function [-Wmaybe-uninitialized] 559 | *ret_sym = ALPHABET[besti]; | ^ src/emit.c:554:13: warning: ‘emit’ may be used uninitialized in this function [-Wmaybe-uninitialized] 554 | if (emit[i] > best) | ~~~~^~~ src/emit.c: In function ‘pick_single_emit’: src/emit.c:441:18: warning: ‘emit’ may be used uninitialized in this function [-Wmaybe-uninitialized] 441 | sum += emit[i]; | ~~~~^~~ src/emit.c: In function ‘pick_best_transit.isra’: src/emit.c:486:18: warning: ‘newtype’ may be used uninitialized in this function [-Wmaybe-uninitialized] 486 | *ret_newtype = UniqueStatetype(cm->nd[newidx].type, newtype); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/emit.c: In function ‘EmitBestSequence’: src/emit.c:519:23: warning: ‘bestj’ may be used uninitialized in this function [-Wmaybe-uninitialized] 519 | *ret_symr = ALPHABET[bestj]; | ^ src/emit.c:507:19: note: ‘bestj’ was declared here 507 | int besti, bestj; | ^~~~~ src/emit.c:518:23: warning: ‘besti’ may be used uninitialized in this function [-Wmaybe-uninitialized] 518 | *ret_syml = ALPHABET[besti]; | ^ src/emit.c:507:12: note: ‘besti’ was declared here 507 | int besti, bestj; | ^~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/fast-dbviterbi.o src/fast-dbviterbi.c src/fast-dbviterbi.c: In function ‘FastViterbiScan’: src/fast-dbviterbi.c:433:10: warning: ‘emitsc’ may be used uninitialized in this function [-Wmaybe-uninitialized] 433 | *scp += emitsc; | ^~ src/fast-dbviterbi.c:362:8: note: ‘emitsc’ was declared here 362 | int emitsc; | ^~~~~~ src/fast-dbviterbi.c:410:11: warning: ‘beam’ may be used uninitialized in this function [-Wmaybe-uninitialized] 410 | beam += y + st->offset; | ~~~~~~^~~~~~~~~~~~~~~~~ src/fast-dbviterbi.c:354:8: note: ‘beam’ was declared here 354 | int *beam; /* ptr to a beam (z-axis vector) */ | ^~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/fastmodelmaker.o src/fastmodelmaker.c src/fastmodelmaker.c: In function ‘mixy’: src/fastmodelmaker.c:188:11: warning: variable ‘test’ set but not used [-Wunused-but-set-variable] 188 | long test; | ^~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/konings.o src/konings.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/lengthdist.o src/lengthdist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/maxmodelmaker.o src/maxmodelmaker.c src/maxmodelmaker.c: In function ‘Maxmodelmaker’: src/maxmodelmaker.c:1065:17: warning: ‘mscore’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1065 | mscore[i] += (nseq - gapcount[i]) * (int) (INTPRECISION * log((float) ALPHASIZE)); | ^~ src/maxmodelmaker.c:1019:12: note: ‘mscore’ was declared here 1019 | int *mscore; | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/misc.o src/misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/model.o src/model.c src/model.c: In function ‘RearrangeCM’: src/model.c:283:10: warning: ‘offset’ may be used uninitialized in this function [-Wmaybe-uninitialized] 283 | offset--; | ~~~~~~^~ src/model.c:299:23: warning: ‘fflags’ may be used uninitialized in this function [-Wmaybe-uninitialized] 299 | else if (fflags & uBEGIN_ST) src/model.c:242:9: warning: ‘tflags’ may be used uninitialized in this function [-Wmaybe-uninitialized] 242 | tflags |= uINSL_ST | uINSR_ST; src/model.c: In function ‘MakePCM’: src/model.c:591:10: warning: ‘offset’ may be used uninitialized in this function [-Wmaybe-uninitialized] 591 | offset--; | ~~~~~~^~ src/model.c:601:23: warning: ‘fflags’ may be used uninitialized in this function [-Wmaybe-uninitialized] 601 | else if (fflags & uBEGIN_ST) src/model.c:550:9: warning: ‘tflags’ may be used uninitialized in this function [-Wmaybe-uninitialized] 550 | tflags |= uINSL_ST | uINSR_ST; gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/modelmaking.o src/modelmaking.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/prior.o src/prior.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/probify.o src/probify.c src/probify.c: In function ‘ProbifySingletEmission’: src/probify.c:189:81: warning: ‘em_prior’ may be used uninitialized in this function [-Wmaybe-uninitialized] 189 | emvec[x] = emvec[x] + prior->emalpha[StatetypeIndex(statetype)] * em_prior[x]; | ~~~~~~~~^~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/save.o src/save.c src/save.c: In function ‘read_cm20’: src/save.c:213:11: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 213 | int ret = 0; | ^~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/smallviterbi.o src/smallviterbi.c src/smallviterbi.c: In function ‘SmallViterbiAlign’: src/smallviterbi.c:569:10: warning: ‘emitsc’ may be used uninitialized in this function [-Wmaybe-uninitialized] 569 | *scp += emitsc; | ^~ src/smallviterbi.c:477:8: note: ‘emitsc’ was declared here 477 | int emitsc; | ^~~~~~ src/smallviterbi.c:540:11: warning: ‘beamt’ may be used uninitialized in this function [-Wmaybe-uninitialized] 540 | beamt += y + st->offset; | ~~~~~~^~~~~~~~~~~~~~~~~ src/smallviterbi.c:468:10: note: ‘beamt’ was declared here 468 | TBACK *beamt; /* ptr into connected traceback beam */ | ^~~~~ src/smallviterbi.c:539:11: warning: ‘beam’ may be used uninitialized in this function [-Wmaybe-uninitialized] 539 | beam += y + st->offset; | ~~~~~~^~~~~~~~~~~~~~~~~ src/smallviterbi.c:467:8: note: ‘beam’ was declared here 467 | int *beam; /* ptr to a beam (z-axis vector) */ | ^~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/scorestack.o src/scorestack.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/structs.o src/structs.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/trace.o src/trace.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/viterbi.o src/viterbi.c src/viterbi.c: In function ‘ViterbiAlign’: src/viterbi.c:603:3: warning: ‘connj’ may be used uninitialized in this function [-Wmaybe-uninitialized] 603 | PushTracestack(dolist, AttachTrace(curr_tr, NULL, conni-1, connj-1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 604 | ynext + y + icm[y].offset, | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 605 | icm[ynext + y + icm[y].offset].statetype)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/viterbi.c:489:15: note: ‘connj’ was declared here 489 | int conni, connj; | ^~~~~ src/viterbi.c:603:3: warning: ‘conni’ may be used uninitialized in this function [-Wmaybe-uninitialized] 603 | PushTracestack(dolist, AttachTrace(curr_tr, NULL, conni-1, connj-1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 604 | ynext + y + icm[y].offset, | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 605 | icm[ynext + y + icm[y].offset].statetype)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/viterbi.c:489:8: note: ‘conni’ was declared here 489 | int conni, connj; | ^~~~~ src/viterbi.c:583:9: warning: ‘beam’ may be used uninitialized in this function [-Wmaybe-uninitialized] 583 | beam += y + icm[y].offset; | ~~~~~^~~~~~~~~~~~~~~~~~~~ src/viterbi.c:488:8: note: ‘beam’ was declared here 488 | int *beam; | ^~~~ src/viterbi.c:593:37: warning: ‘symj’ may be used uninitialized in this function [-Wmaybe-uninitialized] 593 | case uINSR_ST: sc -= icm[y].emit[symj]; break; | ~~~~~~~~~~~^~~~~~ src/viterbi.c:484:13: note: ‘symj’ was declared here 484 | int symi, symj; /* array indices for left, right symbols */ | ^~~~ src/viterbi.c:595:37: warning: ‘symi’ may be used uninitialized in this function [-Wmaybe-uninitialized] 595 | case uINSL_ST: sc -= icm[y].emit[symi]; break; | ~~~~~~~~~~~^~~~~~ src/viterbi.c:484:7: note: ‘symi’ was declared here 484 | int symi, symj; /* array indices for left, right symbols */ | ^~~~ src/viterbi.c:427:12: warning: ‘emitsc’ may be used uninitialized in this function [-Wmaybe-uninitialized] 427 | *scp += emitsc; | ^~ src/viterbi.c:351:8: note: ‘emitsc’ was declared here 351 | int emitsc; | ^~~~~~ src/viterbi.c:403:12: warning: ‘beam’ may be used uninitialized in this function [-Wmaybe-uninitialized] 403 | beam += y + st->offset; | ~~~~~^~~~~~~~~~~~~~~~~ src/viterbi.c:343:8: note: ‘beam’ was declared here 343 | int *beam; /* ptr to a beam (z-axis vector) */ | ^~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/scan_main.o src/scan_main.c src/scan_main.c: In function ‘main’: src/scan_main.c:100:18: warning: implicit declaration of function ‘getopt’; did you mean ‘Getopt’? [-Wimplicit-function-declaration] 100 | while ((optc = getopt(argc, argv, OPTIONS)) != -1) | ^~~~~~ | Getopt gcc -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bin/covels-SE src/align.o src/dbviterbi.o src/debug.o src/emit.o src/fast-dbviterbi.o src/fastmodelmaker.o src/konings.o src/lengthdist.o src/maxmodelmaker.o src/misc.o src/model.o src/modelmaking.o src/prior.o src/probify.o src/save.o src/smallviterbi.o src/scorestack.o src/structs.o src/trace.o src/viterbi.o src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/scan_main.o -lm gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o src/score_main.o src/score_main.c src/score_main.c: In function ‘main’: src/score_main.c:87:18: warning: implicit declaration of function ‘getopt’; did you mean ‘Getopt’? [-Wimplicit-function-declaration] 87 | while ((optc = getopt(argc, argv, OPTIONS)) != -1) | ^~~~~~ | Getopt gcc -O -g -O2 -fdebug-prefix-map=/<>/trnascan-se-2.0.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bin/coves-SE src/align.o src/dbviterbi.o src/debug.o src/emit.o src/fast-dbviterbi.o src/fastmodelmaker.o src/konings.o src/lengthdist.o src/maxmodelmaker.o src/misc.o src/model.o src/modelmaking.o src/prior.o src/probify.o src/save.o src/smallviterbi.o src/scorestack.o src/structs.o src/trace.o src/viterbi.o src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/score_main.o -lm sed -e 's,\@bindir\@,/usr/bin,g' -e 's,\@pkgdatadir\@,/usr/share/trnascan-se,g' -e 's,[@]PERL[@],/usr/bin/perl,g' -e 's,\@INFERNAL\@,,g' -e 's,\@sysconfdir\@,/etc,g' < ./src/sstofa.in > bin/sstofa if [ -x bin/sstofa ] ; then chmod +x bin/sstofa ; fi sed -e 's,\@bindir\@,/usr/bin,g' -e 's,\@pkgdatadir\@,/usr/share/trnascan-se,g' -e 's,[@]PERL[@],/usr/bin/perl,g' -e 's,\@INFERNAL\@,,g' -e 's,\@sysconfdir\@,/etc,g' < ./src/fasta2gsi.in > bin/fasta2gsi if [ -x bin/fasta2gsi ] ; then chmod +x bin/fasta2gsi ; fi sed -e 's,\@bindir\@,/usr/bin,g' -e 's,\@pkgdatadir\@,/usr/share/trnascan-se,g' -e 's,[@]PERL[@],/usr/bin/perl,g' -e 's,\@INFERNAL\@,,g' -e 's,\@sysconfdir\@,/etc,g' < ./EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter if [ -x bin/EukHighConfidenceFilter ] ; then chmod +x bin/EukHighConfidenceFilter ; fi sed -e 's,\@bindir\@,/usr/bin,g' -e 's,\@pkgdatadir\@,/usr/share/trnascan-se,g' -e 's,[@]PERL[@],/usr/bin/perl,g' -e 's,\@INFERNAL\@,,g' -e 's,\@sysconfdir\@,/etc,g' < ./tRNAscan-SE.src > tRNAscan-SE chmod +x tRNAscan-SE sed -e 's,\@bindir\@,/usr/bin,g' -e 's,\@pkgdatadir\@,/usr/share/trnascan-se,g' -e 's,[@]PERL[@],/usr/bin/perl,g' -e 's,\@INFERNAL\@,,g' -e 's,\@sysconfdir\@,/etc,g' < ./tRNAscan-SE.conf.src > tRNAscan-SE.conf chmod +x tRNAscan-SE.conf make[2]: Leaving directory '/<>/trnascan-se-2.0.7+ds' make[1]: Leaving directory '/<>/trnascan-se-2.0.7+ds' dh_auto_test -O--no-parallel make -j1 check VERBOSE=1 make[1]: Entering directory '/<>/trnascan-se-2.0.7+ds' make[1]: Leaving directory '/<>/trnascan-se-2.0.7+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel make -j1 install DESTDIR=/<>/trnascan-se-2.0.7\+ds/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>/trnascan-se-2.0.7+ds' make[2]: Entering directory '/<>/trnascan-se-2.0.7+ds' /bin/mkdir -p '/<>/trnascan-se-2.0.7+ds/debian/tmp/usr/bin' /usr/bin/install -c bin/eufindtRNA bin/trnascan-1.4 bin/covels-SE bin/coves-SE '/<>/trnascan-se-2.0.7+ds/debian/tmp/usr/bin' /bin/mkdir -p '/<>/trnascan-se-2.0.7+ds/debian/tmp/usr/bin' /usr/bin/install -c bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE '/<>/trnascan-se-2.0.7+ds/debian/tmp/usr/bin' /bin/mkdir -p '/<>/trnascan-se-2.0.7+ds/debian/tmp/etc' /usr/bin/install -c -m 644 tRNAscan-SE.conf '/<>/trnascan-se-2.0.7+ds/debian/tmp/etc' /bin/mkdir -p '/<>/trnascan-se-2.0.7+ds/debian/tmp/usr/include' /usr/bin/install -c -m 644 ./src/dbmalloc.h ./src/eufind_const.h ./src/funcs.h ./src/gnuregex.h ./src/maspar.h ./src/prior.h ./src/sqfuncs.h ./src/squid.h ./src/structs.h ./src/version.h '/<>/trnascan-se-2.0.7+ds/debian/tmp/usr/include' make install-data-hook make[3]: Entering directory '/<>/trnascan-se-2.0.7+ds' test -d /<>/trnascan-se-2.0.7+ds/debian/tmp//usr/share/trnascan-se || mkdir -p /<>/trnascan-se-2.0.7+ds/debian/tmp//usr/share/trnascan-se chmod u+w /<>/trnascan-se-2.0.7+ds/debian/tmp//usr/share/trnascan-se cp -rf ./lib/* /<>/trnascan-se-2.0.7+ds/debian/tmp//usr/share/trnascan-se make[3]: Leaving directory '/<>/trnascan-se-2.0.7+ds' make[2]: Leaving directory '/<>/trnascan-se-2.0.7+ds' make[1]: Leaving directory '/<>/trnascan-se-2.0.7+ds' dh_install -O--no-parallel dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installexamples -O--no-parallel dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel debian/rules override_dh_compress make[1]: Entering directory '/<>/trnascan-se-2.0.7+ds' dh_compress -X .fa make[1]: Leaving directory '/<>/trnascan-se-2.0.7+ds' dh_fixperms -O--no-parallel debian/rules override_dh_missing make[1]: Entering directory '/<>/trnascan-se-2.0.7+ds' rm -rf debian/*/usr/include dh_missing make[1]: Leaving directory '/<>/trnascan-se-2.0.7+ds' dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dpkg-gencontrol: warning: Depends field of package trnascan-se-common: substitution variable ${perl:Depends} used, but is not defined dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing trnascan-se (in debian/trnascan-se); do_strip: , oemstrip: pkgstriptranslations: processing trnascan-se-common (in debian/trnascan-se-common); do_strip: , oemstrip: pkgstriptranslations: processing trnascan-se-dbgsym (in debian/.debhelper/trnascan-se/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/trnascan-se/dbgsym-root/DEBIAN/control, package trnascan-se-dbgsym, directory debian/.debhelper/trnascan-se/dbgsym-root dpkg-deb: building package 'trnascan-se-dbgsym' in 'debian/.debhelper/scratch-space/build-trnascan-se/trnascan-se-dbgsym_2.0.7+ds-1_amd64.deb'. pkgstripfiles: processing control file: debian/trnascan-se/DEBIAN/control, package trnascan-se, directory debian/trnascan-se Skipping arch: any to arch: all dependency to trnascan-se-common pkgstripfiles: Running PNG optimization (using 4 cpus) for package trnascan-se ... pkgstripfiles: No PNG files. dpkg-deb: building package 'trnascan-se' in '../trnascan-se_2.0.7+ds-1_amd64.deb'. Renaming trnascan-se-dbgsym_2.0.7+ds-1_amd64.deb to trnascan-se-dbgsym_2.0.7+ds-1_amd64.ddeb pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/trnascan-se-common/DEBIAN/control, package trnascan-se-common, directory debian/trnascan-se-common pkgstripfiles: Running PNG optimization (using 4 cpus) for package trnascan-se-common ... pkgstripfiles: No PNG files. dpkg-deb: building package 'trnascan-se-common' in '../trnascan-se-common_2.0.7+ds-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../trnascan-se_2.0.7+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-11-06T05:15:35Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ trnascan-se_2.0.7+ds-1_amd64.changes: ------------------------------------- Format: 1.8 Date: Wed, 04 Nov 2020 22:22:54 +0100 Source: trnascan-se Binary: trnascan-se trnascan-se-common Architecture: all amd64 Version: 2.0.7+ds-1 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: trnascan-se - detection of transfer RNA genes in genomic sequence trnascan-se-common - detection of transfer RNA genes in genomic sequence (common files Changes: trnascan-se (2.0.7+ds-1) unstable; urgency=medium . * New upstream version. * Fixed typo in tRNAscan-SE.1. * Added configure_debugging.patch and build dependency to autoconf-archive to allow the propagation of CFLAGS. * Replaced Afif Elghraoui as Uploader since he is not active anymore. Thanks for having built and maintained this package! 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90965780726e3045ec0a7980f10dbb403a41e425 157864 trnascan-se_2.0.7+ds-1_amd64.deb Checksums-Sha256: 5915173efb18407b54fd99077e87acc900792ac2503614dc5fd0dbbb5ad42253 2341872 trnascan-se-common_2.0.7+ds-1_all.deb fc79b3c6fa595b68768fedd88fa57df0c862e46eea0ae879b55d5a01ae78a551 500916 trnascan-se-dbgsym_2.0.7+ds-1_amd64.ddeb 54c089a7c1b9d4037abf6d27657285a4e7b097340b60a1e09b41d04c06adb9a4 157864 trnascan-se_2.0.7+ds-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Fri, 06 Nov 2020 05:15:35 +0000 Build-Path: /<>/trnascan-se-2.0.7+ds Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-11.1), autoconf-archive (= 20190106-2.1ubuntu1), automake (= 1:1.16.2-4ubuntu1), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.0-6ubuntu2), binutils (= 2.35.1-2ubuntu1), binutils-common (= 2.35.1-2ubuntu1), binutils-x86-64-linux-gnu (= 2.35.1-2ubuntu1), bsdextrautils (= 2.36-3ubuntu1), bsdutils (= 1:2.36-3ubuntu1), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), coreutils (= 8.32-3ubuntu1), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.0-16ubuntu1), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2.1ubuntu1), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.5ubuntu2), dpkg-dev (= 1.20.5ubuntu2), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1ubuntu2), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.0-16ubuntu1), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.0-16ubuntu1), gcc-10-base (= 10.2.0-16ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), hostname (= 3.23), infernal (= 1.1.3-5), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libasan6 (= 10.2.0-16ubuntu1), libatomic1 (= 10.2.0-16ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3ubuntu2), libaudit1 (= 1:2.8.5-3ubuntu2), libbinutils (= 2.35.1-2ubuntu1), libblkid1 (= 2.36-3ubuntu1), libbz2-1.0 (= 1.0.8-4ubuntu2), libc-bin (= 2.32-0ubuntu4), libc-dev-bin (= 2.32-0ubuntu4), libc6 (= 2.32-0ubuntu4), libc6-dev (= 2.32-0ubuntu4), libcap-ng0 (= 0.7.9-2.2), libcc1-0 (= 10.2.0-16ubuntu1), libcom-err2 (= 1.45.6-1ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.17-1ubuntu1), libcrypt1 (= 1:4.4.17-1ubuntu1), libctf-nobfd0 (= 2.35.1-2ubuntu1), libctf0 (= 2.35.1-2ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu3), libdebconfclient0 (= 0.255ubuntu1), libdebhelper-perl (= 13.2.1ubuntu1), libdpkg-perl (= 1.20.5ubuntu2), libelf1 (= 0.181-1), libffi8ubuntu1 (= 3.4~20200819gead65ca871-0ubuntu3), libfile-stripnondeterminism-perl (= 1.9.0-1), libgcc-10-dev (= 10.2.0-16ubuntu1), libgcc-s1 (= 10.2.0-16ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu2), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libglib2.0-0 (= 2.66.2-1), libgmp10 (= 2:6.2.0+dfsg-6ubuntu1), libgomp1 (= 10.2.0-16ubuntu1), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10), libicu67 (= 67.1-4), libisl22 (= 0.22.1-1), libitm1 (= 10.2.0-16ubuntu1), libk5crypto3 (= 1.17-10), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-3 (= 1.17-10), libkrb5support0 (= 1.17-10), liblsan0 (= 10.2.0-16ubuntu1), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1ubuntu1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.36-3ubuntu1), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), 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 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.30 (= 5.30.3-4), libpipeline1 (= 1.5.3-1), libquadmath0 (= 10.2.0-16ubuntu1), libseccomp2 (= 2.4.3-1ubuntu5), libselinux1 (= 3.1-2build1), libsigsegv2 (= 2.12-2build1), libsmartcols1 (= 2.36-3ubuntu1), libssl1.1 (= 1.1.1f-1ubuntu4), libstdc++-10-dev (= 10.2.0-16ubuntu1), libstdc++6 (= 10.2.0-16ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 246.6-2ubuntu1), libtinfo6 (= 6.2+20200918-1), libtirpc-common (= 1.2.6-3), libtirpc-dev (= 1.2.6-3), libtirpc3 (= 1.2.6-3), libtool (= 2.4.6-14), libtsan0 (= 10.2.0-16ubuntu1), libubsan1 (= 10.2.0-16ubuntu1), libuchardet0 (= 0.0.7-1), libudev1 (= 246.6-2ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36-3ubuntu1), libxml2 (= 2.9.10+dfsg-6.2), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.0-26.27), login (= 1:4.8.1-1ubuntu6), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2+20200918-1), ncurses-bin (= 6.2+20200918-1), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), po-debconf (= 1.0.21), rpcsvc-proto (= 1.4.2-0ubuntu4), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.13), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.30+dfsg-7), util-linux (= 2.36-3ubuntu1), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1604524974" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ trnascan-se-common_2.0.7+ds-1_all.deb ------------------------------------- new Debian package, version 2.0. size 2341872 bytes: control archive=4072 bytes. 1205 bytes, 22 lines control 10951 bytes, 131 lines md5sums Package: trnascan-se-common Source: trnascan-se Version: 2.0.7+ds-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 17859 Section: non-free/science Priority: optional Homepage: http://lowelab.ucsc.edu/tRNAscan-SE Description: detection of transfer RNA genes in genomic sequence (common files) tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes. . This package contains the architecture-independent common files. drwxr-xr-x root/root 0 2020-11-04 21:22 ./ drwxr-xr-x root/root 0 2020-11-04 21:22 ./usr/ drwxr-xr-x root/root 0 2020-11-04 21:22 ./usr/share/ drwxr-xr-x root/root 0 2020-11-04 21:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-11-04 21:22 ./usr/share/doc/trnascan-se-common/ -rw-r--r-- root/root 1366 2020-11-04 21:22 ./usr/share/doc/trnascan-se-common/changelog.Debian.gz -rw-r--r-- root/root 3415 2020-11-04 21:22 ./usr/share/doc/trnascan-se-common/copyright drwxr-xr-x root/root 0 2020-11-04 21:22 ./usr/share/trnascan-se/ drwxr-xr-x root/root 0 2020-11-04 21:22 ./usr/share/trnascan-se/gcode/ -rw-r--r-- root/root 143 2020-11-04 21:22 ./usr/share/trnascan-se/gcode/gcode.cilnuc -rw-r--r-- root/root 143 2020-11-04 21:22 ./usr/share/trnascan-se/gcode/gcode.echdmito -rw-r--r-- root/root 146 2020-11-04 21:22 ./usr/share/trnascan-se/gcode/gcode.invmito -rw-r--r-- root/root 152 2020-11-04 21:22 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-rw-r--r-- root/root 12335 2020-11-04 21:22 ./usr/share/trnascan-se/tRNAscanSE/Tscan.pm -rw-r--r-- root/root 5552 2020-11-04 21:22 ./usr/share/trnascan-se/tRNAscanSE/Utils.pm -rw-r--r-- root/root 34745 2020-11-04 21:22 ./usr/share/trnascan-se/tRNAscanSE/tRNA.pm trnascan-se_2.0.7+ds-1_amd64.deb -------------------------------- new Debian package, version 2.0. size 157864 bytes: control archive=1796 bytes. 22 bytes, 1 lines conffiles 1174 bytes, 20 lines control 2168 bytes, 30 lines md5sums Package: trnascan-se Version: 2.0.7+ds-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 724 Depends: libc6 (>= 2.29), perl:any, trnascan-se-common (= 2.0.7+ds-1), infernal Section: non-free/science Priority: optional Homepage: http://lowelab.ucsc.edu/tRNAscan-SE Description: detection of transfer RNA genes in genomic sequence tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s. 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