https://launchpad.net/ubuntu/+source/samtools/1.11-1/+build/20209976 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-016 4.15.0-121-generic #123-Ubuntu SMP Mon Oct 5 16:19:23 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 29 Oct 07:05:38 ntpdate[1643]: adjust time server 10.211.37.1 offset -0.000672 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20209976 --image-type chroot /home/buildd/filecache-default/d1fb963478283f19fe8f83381d93195a7691df38 Creating target for build PACKAGEBUILD-20209976 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20209976 Starting target for build PACKAGEBUILD-20209976 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20209976 '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-20209976 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20209976 Updating target for build PACKAGEBUILD-20209976 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 [114 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main arm64 Packages [1350 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe arm64 Packages [12.3 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5262 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 Packages [177 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [73.6 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe arm64 Packages [892 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [585 kB] Fetched 21.7 MB in 7s (3160 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-aarch64-linux-gnu binutils-common cpp-10 g++-10 gcc-10 gcc-10-base libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libaudit-common libaudit1 libbinutils libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdebconfclient0 libgcc-10-dev libgcc-s1 libgomp1 libitm1 liblsan0 libmpc3 libncurses6 libncursesw6 libnpth0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-10-dev libstdc++6 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 ncurses-base ncurses-bin sysvinit-utils tzdata 49 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 158 MB of archives. After this operation, 569 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libcrypt-dev arm64 1:4.4.17-1ubuntu1 [109 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libcrypt1 arm64 1:4.4.17-1ubuntu1 [80.8 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main arm64 base-files arm64 11ubuntu16 [60.4 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libncursesw6 arm64 6.2+20200918-1 [120 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libncurses6 arm64 6.2+20200918-1 [92.4 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libtinfo6 arm64 6.2+20200918-1 [81.9 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 ncurses-bin arm64 6.2+20200918-1 [168 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libdebconfclient0 arm64 0.254ubuntu1 [6124 B] Get:9 http://ftpmaster.internal/ubuntu hirsute/main arm64 base-passwd arm64 3.5.48 [46.6 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 ncurses-base all 6.2+20200918-1 [18.7 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main arm64 sysvinit-utils arm64 2.96-5ubuntu1 [20.4 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcc1-0 arm64 10.2.0-15ubuntu1 [37.2 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main arm64 gcc-10-base arm64 10.2.0-15ubuntu1 [19.5 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcc-s1 arm64 10.2.0-15ubuntu1 [34.6 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgomp1 arm64 10.2.0-15ubuntu1 [93.7 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main arm64 libitm1 arm64 10.2.0-15ubuntu1 [24.1 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main arm64 libatomic1 arm64 10.2.0-15ubuntu1 [9844 B] Get:18 http://ftpmaster.internal/ubuntu hirsute/main arm64 libasan6 arm64 10.2.0-15ubuntu1 [317 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblsan0 arm64 10.2.0-15ubuntu1 [130 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtsan0 arm64 10.2.0-15ubuntu1 [302 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main arm64 libubsan1 arm64 10.2.0-15ubuntu1 [126 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main arm64 g++-10 arm64 10.2.0-15ubuntu1 [49.4 MB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main arm64 libstdc++-10-dev arm64 10.2.0-15ubuntu1 [1694 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcc-10-dev arm64 10.2.0-15ubuntu1 [909 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main arm64 gcc-10 arm64 10.2.0-15ubuntu1 [52.3 MB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main arm64 cpp-10 arm64 10.2.0-15ubuntu1 [46.0 MB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main arm64 libstdc++6 arm64 10.2.0-15ubuntu1 [462 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libmpc3 arm64 1.2.0-1 [42.3 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libctf-nobfd0 arm64 2.35.1-2ubuntu1 [44.9 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libctf0 arm64 2.35.1-2ubuntu1 [43.9 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libbinutils arm64 2.35.1-2ubuntu1 [483 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils-common arm64 2.35.1-2ubuntu1 [212 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils arm64 2.35.1-2ubuntu1 [3372 B] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.35.1-2ubuntu1 [2027 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libapt-pkg6.0 arm64 2.1.11 [764 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libseccomp2 arm64 2.4.3-1ubuntu5 [42.7 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 apt arm64 2.1.11 [1247 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main arm64 libaudit-common all 1:2.8.5-3ubuntu2 [4092 B] Get:39 http://ftpmaster.internal/ubuntu hirsute/main arm64 libaudit1 arm64 1:2.8.5-3ubuntu2 [38.2 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main arm64 libselinux1 arm64 3.1-2build1 [65.5 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsemanage-common all 3.1-1build1 [10.1 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsemanage1 arm64 3.1-1build1 [80.8 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libtirpc-common all 1.2.6-3 [7444 B] Get:44 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libtirpc-dev arm64 1.2.6-3 [185 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libtirpc3 arm64 1.2.6-3 [73.4 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libapparmor1 arm64 3.0.0-0ubuntu2 [35.2 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libcap2 arm64 1:2.44-1 [16.7 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main arm64 tzdata all 2020d-1ubuntu1 [293 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libnpth0 arm64 1.6-3 [7824 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 158 MB in 7s (24.0 MB/s) (Reading database ... 12970 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu1_arm64.deb ... Unpacking libcrypt-dev:arm64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu1_arm64.deb ... Unpacking libcrypt1:arm64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:arm64 (1:4.4.17-1ubuntu1) ... (Reading database ... 12970 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu16_arm64.deb ... Unpacking base-files (11ubuntu16) over (11ubuntu14) ... Setting up base-files (11ubuntu16) ... 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 ... 12970 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.2+20200918-1_arm64.deb ... Unpacking libncursesw6:arm64 (6.2+20200918-1) over (6.2-1) ... 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Setting up base-passwd (3.5.48) ... 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 ... 12970 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.2+20200918-1_all.deb ... Unpacking ncurses-base (6.2+20200918-1) over (6.2-1) ... Setting up ncurses-base (6.2+20200918-1) ... (Reading database ... 12970 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) ... (Reading database ... 12970 files and directories currently installed.) Preparing to unpack .../libcc1-0_10.2.0-15ubuntu1_arm64.deb ... Unpacking libcc1-0:arm64 (10.2.0-15ubuntu1) over (10.2.0-13ubuntu1) ... 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Setting up tzdata (2020d-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Oct 29 07:06:46 UTC 2020. Universal Time is now: Thu Oct 29 07:06:46 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libtirpc-dev:arm64 (1.2.6-3) ... Setting up libncurses6:arm64 (6.2+20200918-1) ... Setting up libmpc3:arm64 (1.2.0-1) ... Setting up libatomic1:arm64 (10.2.0-15ubuntu1) ... Setting up libncursesw6:arm64 (6.2+20200918-1) ... Setting up libubsan1:arm64 (10.2.0-15ubuntu1) ... Setting up libcrypt-dev:arm64 (1:4.4.17-1ubuntu1) ... Setting up libbinutils:arm64 (2.35.1-2ubuntu1) ... Setting up libcc1-0:arm64 (10.2.0-15ubuntu1) ... Setting up liblsan0:arm64 (10.2.0-15ubuntu1) ... Setting up cpp-10 (10.2.0-15ubuntu1) ... Setting up libitm1:arm64 (10.2.0-15ubuntu1) ... Setting up libtsan0:arm64 (10.2.0-15ubuntu1) ... Setting up libctf0:arm64 (2.35.1-2ubuntu1) ... Setting up libgcc-10-dev:arm64 (10.2.0-15ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.35.1-2ubuntu1) ... Setting up binutils (2.35.1-2ubuntu1) ... Setting up gcc-10 (10.2.0-15ubuntu1) ... Setting up libstdc++-10-dev:arm64 (10.2.0-15ubuntu1) ... Setting up g++-10 (10.2.0-15ubuntu1) ... Processing triggers for libc-bin (2.32-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20209976 arm64 hirsute-proposed -c chroot:build-PACKAGEBUILD-20209976 --arch=arm64 --dist=hirsute-proposed --nolog samtools_1.11-1.dsc Initiating build PACKAGEBUILD-20209976 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-121-generic #123-Ubuntu SMP Mon Oct 5 16:19:23 UTC 2020 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-016.buildd +==============================================================================+ | samtools 1.11-1 (arm64) Thu, 29 Oct 2020 07:06:48 +0000 | +==============================================================================+ Package: samtools Version: 1.11-1 Source Version: 1.11-1 Distribution: hirsute-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20209976/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools_1.11-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/samtools-Da6F3x/samtools-1.11' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-Da6F3x' 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-zAL3J3/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-zAL3J3/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zAL3J3/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-zAL3J3/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zAL3J3/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-zAL3J3/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (48.6 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 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-zAL3J3/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 (63.0 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12968 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 any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.11), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.11), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<>/resolver-zAL3J3/apt_archive/sbuild-build-depends-samtools-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-samtools-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-zAL3J3/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zAL3J3/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-zAL3J3/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zAL3J3/apt_archive ./ Sources [592 B] Get:5 copy:/<>/resolver-zAL3J3/apt_archive ./ Packages [661 B] Fetched 2216 B in 0s (47.1 kB/s) Reading package lists... Reading package lists... Install samtools 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 bash-completion bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libio-pty-perl libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db pkg-config po-debconf tabix zlib1g-dev Suggested packages: 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 liblzma-doc ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libio-pty-perl libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 25.0 MB of archives. After this operation, 93.2 MB of additional disk space will be used. Get:1 copy:/<>/resolver-zAL3J3/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [952 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main arm64 bsdextrautils arm64 2.36-3ubuntu1 [74.2 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main arm64 libuchardet0 arm64 0.0.7-1 [68.0 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main arm64 groff-base arm64 1.22.4-5 [797 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpipeline1 arm64 1.5.3-1 [26.1 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main arm64 man-db arm64 2.9.3-2 [1100 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe arm64 autoconf-archive all 20190106-2.1ubuntu1 [665 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmagic-mgc arm64 1:5.38-5 [218 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmagic1 arm64 1:5.38-5 [71.6 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main arm64 file arm64 1:5.38-5 [23.3 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main arm64 libelf1 arm64 0.181-1 [43.4 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main arm64 libglib2.0-0 arm64 2.66.1-2 [1214 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main arm64 libicu67 arm64 67.1-4 [8461 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libxml2 arm64 2.9.10+dfsg-6.1 [558 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main arm64 bash-completion all 1:2.11-2ubuntu1 [179 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main arm64 gettext-base arm64 0.19.8.1-10build1 [48.2 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpsl5 arm64 0.21.0-1.1ubuntu1 [52.0 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsigsegv2 arm64 2.12-2build1 [13.7 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main arm64 m4 arm64 1.4.18-4 [194 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main arm64 autoconf all 2.69-11.1 [321 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main arm64 automake all 1:1.16.2-4ubuntu1 [548 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main arm64 autopoint all 0.19.8.1-10build1 [412 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtool all 2.4.6-14 [161 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main arm64 dh-autoreconf all 19 [16.1 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdebhelper-perl all 13.2.1ubuntu1 [63.6 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:29 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main arm64 dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:31 http://ftpmaster.internal/ubuntu hirsute/main arm64 dwz arm64 0.13-5 [134 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcroco3 arm64 0.6.13-1 [77.1 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main arm64 gettext arm64 0.19.8.1-10build1 [850 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main arm64 po-debconf all 1.0.21 [233 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main arm64 debhelper all 13.2.1ubuntu1 [879 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-2 [39.4 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-2 [150 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main arm64 libbrotli1 arm64 1.0.9-2build1 [276 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main arm64 libbz2-dev arm64 1.0.8-4ubuntu2 [31.6 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-2 [27.9 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-2 [84.8 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-2 [47.2 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-2 [98.6 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-2 [192 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-2 [14.8 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-2 [88.4 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2ubuntu1 [14.9 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2ubuntu1 [48.4 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main arm64 libldap-2.4-2 arm64 2.4.53+dfsg-1ubuntu1 [148 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main arm64 libnghttp2-14 arm64 1.41.0-3 [64.6 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build2 [53.1 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main arm64 libssh-4 arm64 0.9.4-1ubuntu3 [161 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcurl3-gnutls arm64 7.68.0-1ubuntu4 [211 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcurl4-gnutls-dev arm64 7.68.0-1ubuntu4 [307 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdeflate0 arm64 1.6-1 [51.1 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdeflate-dev arm64 1.6-1 [43.0 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute-proposed/universe arm64 libhts3 arm64 1.11-2 [314 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblzma-dev arm64 5.2.4-1ubuntu1 [144 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu4 [154 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute-proposed/universe arm64 libhts-dev arm64 1.11-2 [3832 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main arm64 libio-pty-perl arm64 1:1.12-1 [31.5 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libncurses-dev arm64 6.2+20200918-1 [335 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute-proposed/main arm64 libncurses5-dev arm64 6.2+20200918-1 [988 B] Get:65 http://ftpmaster.internal/ubuntu hirsute/main arm64 pkg-config arm64 0.29.2-1ubuntu1 [44.5 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute-proposed/universe arm64 tabix arm64 1.11-2 [291 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.0 MB in 1s (19.8 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12968 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36-3ubuntu1_arm64.deb ... Unpacking bsdextrautils (2.36-3ubuntu1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_arm64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_arm64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package autoconf-archive. Preparing to unpack .../05-autoconf-archive_20190106-2.1ubuntu1_all.deb ... Unpacking autoconf-archive (20190106-2.1ubuntu1) ... 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Unpacking libwind0-heimdal:arm64 (7.7.0+dfsg-2) ... Selecting previously unselected package libhx509-5-heimdal:arm64. Preparing to unpack .../42-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 .../43-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 .../44-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 .../45-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 .../46-libsasl2-modules-db_2.1.27+dfsg-2ubuntu1_arm64.deb ... 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Setting up libdebhelper-perl (13.2.1ubuntu1) ... Setting up libbrotli1:arm64 (1.0.9-2build1) ... Setting up libnghttp2-14:arm64 (1.41.0-3) ... Setting up libmagic1:arm64 (1:5.38-5) ... Setting up libdeflate0:arm64 (1.6-1) ... 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 libsasl2-modules-db:arm64 (2.1.27+dfsg-2ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build2) ... Setting up bash-completion (1:2.11-2ubuntu1) ... Setting up libsigsegv2:arm64 (2.12-2build1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:arm64 (0.9.4-1ubuntu3) ... Setting up libroken18-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up liblzma-dev:arm64 (5.2.4-1ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu4) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libncurses5-dev:arm64 (6.2+20200918-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:arm64 (1.6-1) ... Setting up tabix (1.11-2) ... Setting up libelf1:arm64 (0.181-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.1) ... Setting up libheimbase1-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libbz2-dev:arm64 (1.0.8-4ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-4) ... Setting up libhcrypto4-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libwind0-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libcroco3:arm64 (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 libhx509-5-heimdal:arm64 (7.7.0+dfsg-2) ... 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 libkrb5-26-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21) ... 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 (2.4.53+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.68.0-1ubuntu4) ... Setting up libcurl4-gnutls-dev:arm64 (7.68.0-1ubuntu4) ... Setting up libhts3:arm64 (1.11-2) ... Setting up libhts-dev:arm64 (1.11-2) ... Setting up debhelper (13.2.1ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-121-generic arm64 (aarch64) Toolchain package versions: binutils_2.35.1-2ubuntu1 dpkg-dev_1.20.5ubuntu2 g++-10_10.2.0-15ubuntu1 gcc-10_10.2.0-15ubuntu1 libc6-dev_2.32-0ubuntu3 libstdc++-10-dev_10.2.0-15ubuntu1 libstdc++6_10.2.0-15ubuntu1 linux-libc-dev_5.8.0-25.26 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 bash-completion_1:2.11-2ubuntu1 binutils_2.35.1-2ubuntu1 binutils-aarch64-linux-gnu_2.35.1-2ubuntu1 binutils-common_2.35.1-2ubuntu1 bsdextrautils_2.36-3ubuntu1 bsdutils_1:2.36-3ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.32-3ubuntu1 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.0-15ubuntu1 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 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.2-1 file_1:5.38-5 findutils_4.7.0-1ubuntu2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.0-15ubuntu1 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.0-15ubuntu1 gcc-10-base_10.2.0-15ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_3.0.0-0ubuntu2 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.0-15ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.2.0-15ubuntu1 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 libbrotli1_1.0.9-2build1 libbz2-1.0_1.0.8-4ubuntu2 libbz2-dev_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu3 libc-dev-bin_2.32-0ubuntu3 libc6_2.32-0ubuntu3 libc6-dev_2.32-0ubuntu3 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcc1-0_10.2.0-15ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.3-1ubuntu6 libctf-nobfd0_2.35.1-2ubuntu1 libctf0_2.35.1-2ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu4 libcurl4-gnutls-dev_7.68.0-1ubuntu4 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.254ubuntu1 libdebhelper-perl_13.2.1ubuntu1 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.20.5ubuntu2 libelf1_0.181-1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.2-1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-15ubuntu1 libgcc-s1_10.2.0-15ubuntu1 libgcrypt20_1.8.5-5ubuntu2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.1-2 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.6.15-4ubuntu2 libgomp1_10.2.0-15ubuntu1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libhx509-5-heimdal_7.7.0+dfsg-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libio-pty-perl_1:1.12-1 libip4tc2_1.8.5-3ubuntu1 libisl22_0.22.1-1 libitm1_10.2.0-15ubuntu1 libjson-c5_0.15-1 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libldap-2.4-2_2.4.53+dfsg-1ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.2.0-15ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1ubuntu1 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 libncurses-dev_6.2+20200918-1 libncurses5-dev_6.2+20200918-1 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 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_0.23.21-2build1 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 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpsl5_0.21.0-1.1ubuntu1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27+dfsg-2ubuntu1 libseccomp2_2.4.3-1ubuntu5 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 libssh-4_0.9.4-1ubuntu3 libssl1.1_1.1.1f-1ubuntu4 libstdc++-10-dev_10.2.0-15ubuntu1 libstdc++6_10.2.0-15ubuntu1 libsub-override-perl_0.09-2 libsystemd0_246.6-1ubuntu1 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_10.2.0-15ubuntu1 libubsan1_10.2.0-15ubuntu1 libuchardet0_0.0.7-1 libudev1_246.6-1ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36-3ubuntu1 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-6.1 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.0-25.26 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 pkg-config_0.29.2-1ubuntu1 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-samtools-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 systemd_246.6-1ubuntu1 systemd-sysv_246.6-1ubuntu1 systemd-timesyncd_246.6-1ubuntu1 sysvinit-utils_2.96-5ubuntu1 tabix_1.11-2 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 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Oct 1 14:52:01 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./samtools_1.11-1.dsc dpkg-source: info: extracting samtools in /<> dpkg-source: info: unpacking samtools_1.11.orig.tar.gz dpkg-source: info: unpacking samtools_1.11-1.debian.tar.xz 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-20209976 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20209976 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20209976 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.11-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from samtools-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f config.mk touch config.mk dh_auto_clean -- install -d /<>/debian/.debhelper/generated/_source/home make -j4 distclean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS rm -rf autom4te.cache make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level autoconf configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system install -d /<>/debian/.debhelper/generated/_source/home ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk 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 for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.11"' > version.h gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j4 test VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/<>' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} /usr/bin/bgzip -c -b 65272 -s 5 /tmp/f1U6ZuMHoO/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/f1U6ZuMHoO/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/f1U6ZuMHoO/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/f1U6ZuMHoO/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/f1U6ZuMHoO/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/f1U6ZuMHoO/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/f1U6ZuMHoO/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/f1U6ZuMHoO/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/f1U6ZuMHoO/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/f1U6ZuMHoO/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/f1U6ZuMHoO/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /<>/samtools fqidx /tmp/f1U6ZuMHoO/fqidx.fq 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/f1U6ZuMHoO/fqidx.fq.gz 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/f1U6ZuMHoO/fqidx.fq 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/f1U6ZuMHoO/fqidx.fq.gz 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/f1U6ZuMHoO/fqidx.fq 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/f1U6ZuMHoO/fqidx.fq.gz 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/f1U6ZuMHoO/fqidx.fq 1:99998-100007 .. ok .. ok /<>/samtools fqidx /tmp/f1U6ZuMHoO/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /<>/test/dat/dict.fa .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/f1U6ZuMHoO/dict.fa.gz .. ok test_dict: cat /<>/test/dat/dict.fa | /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /<>/samtools dict -AH < /<>/test/dat/dict.alias.fa .. ok test_index: /<>/samtools view /tmp/f1U6ZuMHoO/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/f1U6ZuMHoO/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/f1U6ZuMHoO/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools merge -O sam - -X -cp -R ref2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_a.bam.bai /tmp/f1U6ZuMHoO/test_input_1_b.bam.bai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.bam /tmp/f1U6ZuMHoO/auto_indexed.csi && cat /tmp/f1U6ZuMHoO/auto_indexed.csi .. ok test_index: /<>/samtools index /<>/test/dat/auto_indexed.tmp.cram /tmp/f1U6ZuMHoO/auto_indexed.crai && cat /tmp/f1U6ZuMHoO/auto_indexed.crai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.sam /tmp/f1U6ZuMHoO/auto_indexed.csi && cat /tmp/f1U6ZuMHoO/auto_indexed.csi .. ok test_index: /<>/samtools view -@ 2 /tmp/f1U6ZuMHoO/large_chrom.bam ref2 .. ok test_index: /<>/samtools view -@ 2 /tmp/f1U6ZuMHoO/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/f1U6ZuMHoO/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools merge -@ 2 -O sam - -X -cp -R ref2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_a.bam.bai /tmp/f1U6ZuMHoO/test_input_1_b.bam.bai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.bam /tmp/f1U6ZuMHoO/auto_indexed.csi && cat /tmp/f1U6ZuMHoO/auto_indexed.csi .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/auto_indexed.tmp.cram /tmp/f1U6ZuMHoO/auto_indexed.crai && cat /tmp/f1U6ZuMHoO/auto_indexed.crai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.sam /tmp/f1U6ZuMHoO/auto_indexed.csi && cat /tmp/f1U6ZuMHoO/auto_indexed.csi .. ok test_mpileup: /<>/samtools mpileup -b /tmp/f1U6ZuMHoO/mpileup.bam.list -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/f1U6ZuMHoO/mpileup.cram.list -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/f1U6ZuMHoO/mpileup.bam.urllist -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/f1U6ZuMHoO/mpileup.cram.urllist -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/f1U6ZuMHoO/mpileup.bam.list -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/f1U6ZuMHoO/mpileup.cram.list -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/f1U6ZuMHoO/mpileup.cram.list -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/f1U6ZuMHoO/mpileup.cram.list -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:1050-1060 /tmp/f1U6ZuMHoO/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/f1U6ZuMHoO/mpileup.ref.fa.gz -r17:1050-1060 /tmp/f1U6ZuMHoO/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup /<>/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, tview, view, depad .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/f1U6ZuMHoO/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/f1U6ZuMHoO/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/f1U6ZuMHoO/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/f1U6ZuMHoO/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/f1U6ZuMHoO/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/f1U6ZuMHoO/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/f1U6ZuMHoO/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/f1U6ZuMHoO/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/f1U6ZuMHoO/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/f1U6ZuMHoO/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/f1U6ZuMHoO/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/f1U6ZuMHoO/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/f1U6ZuMHoO/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/f1U6ZuMHoO/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/f1U6ZuMHoO/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/f1U6ZuMHoO/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/f1U6ZuMHoO/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/f1U6ZuMHoO/view.001.fogn (CRAM input).. ok 67: Filter -d BC:TGCA (SAM input) .. ok 68: Count -d BC:TGCA (SAM input) .. ok 69: Filter -d BC:TGCA (BAM input) .. ok 70: Count -d BC:TGCA (BAM input) .. ok 71: Filter -d BC:TGCA (CRAM input) .. ok 72: Count -d BC:TGCA (CRAM input) .. ok 73: Filter -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (SAM input) .. ok 74: Count -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (SAM input) .. ok 75: Filter -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (BAM input) .. ok 76: Count -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (BAM input) .. ok 77: Filter -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (CRAM input) .. ok 78: Count -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (CRAM input) .. ok 79: Filter -D BC:/tmp/f1U6ZuMHoO/view.001.fobc -d BC:TGCA (SAM input).. ok 80: Count -D BC:/tmp/f1U6ZuMHoO/view.001.fobc -d BC:TGCA (SAM input).. ok 81: Filter -D BC:/tmp/f1U6ZuMHoO/view.001.fobc -d BC:TGCA (BAM input).. ok 82: Count -D BC:/tmp/f1U6ZuMHoO/view.001.fobc -d BC:TGCA (BAM input).. ok 83: Filter -D BC:/tmp/f1U6ZuMHoO/view.001.fobc -d BC:TGCA (CRAM input).. ok 84: Count -D BC:/tmp/f1U6ZuMHoO/view.001.fobc -d BC:TGCA (CRAM input).. ok 85: Filter -d BC:TGCA -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (SAM input).. ok 86: Count -d BC:TGCA -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (SAM input).. ok 87: Filter -d BC:TGCA -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (BAM input).. ok 88: Count -d BC:TGCA -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (BAM input).. ok 89: Filter -d BC:TGCA -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (CRAM input).. ok 90: Count -d BC:TGCA -D BC:/tmp/f1U6ZuMHoO/view.001.fobc (CRAM input).. ok 91: Filter -D RG:/tmp/f1U6ZuMHoO/view.001.fogn (SAM input) .. ok 92: Count -D RG:/tmp/f1U6ZuMHoO/view.001.fogn (SAM input) .. ok 93: Filter -D RG:/tmp/f1U6ZuMHoO/view.001.fogn (BAM input) .. ok 94: Count -D RG:/tmp/f1U6ZuMHoO/view.001.fogn (BAM input) .. ok 95: Filter -D RG:/tmp/f1U6ZuMHoO/view.001.fogn (CRAM input) .. ok 96: Count -D RG:/tmp/f1U6ZuMHoO/view.001.fogn (CRAM input) .. ok 97: Filter -d NE:TGCA (SAM input) .. ok 98: Count -d NE:TGCA (SAM input) .. ok 99: Filter -d NE:TGCA (BAM input) .. ok 100: Count -d NE:TGCA (BAM input) .. ok 101: Filter -d NE:TGCA (CRAM input) .. ok 102: Count -d NE:TGCA (CRAM input) .. ok 103: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test103.sam -h -d TGCA /tmp/f1U6ZuMHoO/view.001.sam --no-PG .. expected failure 104: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/f1U6ZuMHoO/view.001.sam --no-PG .. expected failure 105: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test105.sam -h -d TGCA /tmp/f1U6ZuMHoO/view.test001.bam --no-PG .. expected failure 106: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/f1U6ZuMHoO/view.test001.bam --no-PG .. expected failure 107: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test107.sam -h -d TGCA /tmp/f1U6ZuMHoO/view.test006.cram --no-PG .. expected failure 108: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/f1U6ZuMHoO/view.test006.cram --no-PG .. expected failure 109: Filter -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/f1U6ZuMHoO/view.001.fobc" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test109.sam -h -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc /tmp/f1U6ZuMHoO/view.001.sam --no-PG .. expected failure 110: Count -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/f1U6ZuMHoO/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc /tmp/f1U6ZuMHoO/view.001.sam --no-PG .. expected failure 111: Filter -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/f1U6ZuMHoO/view.001.fobc" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test111.sam -h -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc /tmp/f1U6ZuMHoO/view.test001.bam --no-PG .. expected failure 112: Count -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/f1U6ZuMHoO/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc /tmp/f1U6ZuMHoO/view.test001.bam --no-PG .. expected failure 113: Filter -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/f1U6ZuMHoO/view.001.fobc" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test113.sam -h -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc /tmp/f1U6ZuMHoO/view.test006.cram --no-PG .. expected failure 114: Count -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/f1U6ZuMHoO/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/f1U6ZuMHoO/view.001.fobc /tmp/f1U6ZuMHoO/view.test006.cram --no-PG .. expected failure 115: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/f1U6ZuMHoO/view.001.sam --no-PG .. expected failure 116: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/f1U6ZuMHoO/view.001.sam --no-PG .. expected failure 117: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/f1U6ZuMHoO/view.test001.bam --no-PG .. expected failure 118: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/f1U6ZuMHoO/view.test001.bam --no-PG .. expected failure 119: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/f1U6ZuMHoO/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/f1U6ZuMHoO/view.test006.cram --no-PG .. expected failure 120: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/f1U6ZuMHoO/view.test006.cram --no-PG .. expected failure 121: Filter -l Library 2 (SAM input) .. ok 122: Count -l Library 2 (SAM input) .. ok 123: Filter -l Library 2 (BAM input) .. ok 124: Count -l Library 2 (BAM input) .. ok 125: Filter -l Library 2 (CRAM input) .. ok 126: Count -l Library 2 (CRAM input) .. ok 127: Filter -l Library 3 (SAM input) .. ok 128: Count -l Library 3 (SAM input) .. ok 129: Filter -l Library 3 (BAM input) .. ok 130: Count -l Library 3 (BAM input) .. ok 131: Filter -l Library 3 (CRAM input) .. ok 132: Count -l Library 3 (CRAM input) .. ok 133: Filter -q 50 (SAM input) .. ok 134: Count -q 50 (SAM input) .. ok 135: Filter -q 50 (BAM input) .. ok 136: Count -q 50 (BAM input) .. ok 137: Filter -q 50 (CRAM input) .. ok 138: Count -q 50 (CRAM input) .. ok 139: Filter -q 99 (SAM input) .. ok 140: Count -q 99 (SAM input) .. ok 141: Filter -q 99 (BAM input) .. ok 142: Count -q 99 (BAM input) .. ok 143: Filter -q 99 (CRAM input) .. ok 144: Count -q 99 (CRAM input) .. ok 145: Filter -q 100 (SAM input) .. ok 146: Count -q 100 (SAM input) .. ok 147: Filter -q 100 (BAM input) .. ok 148: Count -q 100 (BAM input) .. ok 149: Filter -q 100 (CRAM input) .. ok 150: Count -q 100 (CRAM input) .. ok 151: Filter -x fa (SAM input) .. ok 152: Count -x fa (SAM input) .. ok 153: Filter -x fa (BAM input) .. ok 154: Count -x fa (BAM input) .. ok 155: Filter -x fa (CRAM input) .. ok 156: Count -x fa (CRAM input) .. ok 157: Filter -x fa -x ha (SAM input) .. ok 158: Count -x fa -x ha (SAM input) .. ok 159: Filter -x fa -x ha (BAM input) .. ok 160: Count -x fa -x ha (BAM input) .. ok 161: Filter -x fa -x ha (CRAM input) .. ok 162: Count -x fa -x ha (CRAM input) .. ok 163: Filter -x fa -r grp2 (SAM input) .. ok 164: Count -x fa -r grp2 (SAM input) .. ok 165: Filter -x fa -r grp2 (BAM input) .. ok 166: Count -x fa -r grp2 (BAM input) .. ok 167: Filter -x fa -r grp2 (CRAM input) .. ok 168: Count -x fa -r grp2 (CRAM input) .. ok 169: Filter -x RG -r grp2 (SAM input) .. ok 170: Count -x RG -r grp2 (SAM input) .. ok 171: Filter -x RG -r grp2 (BAM input) .. ok 172: Count -x RG -r grp2 (BAM input) .. ok 173: Filter -x RG -r grp2 (CRAM input) .. ok 174: Count -x RG -r grp2 (CRAM input) .. ok 175: Filter -m 10 (SAM input) .. ok 176: Count -m 10 (SAM input) .. ok 177: Filter -m 10 (BAM input) .. ok 178: Count -m 10 (BAM input) .. ok 179: Filter -m 10 (CRAM input) .. ok 180: Count -m 10 (CRAM input) .. ok 181: Filter -m 11 (SAM input) .. ok 182: Count -m 11 (SAM input) .. ok 183: Filter -m 11 (BAM input) .. ok 184: Count -m 11 (BAM input) .. ok 185: Filter -m 11 (CRAM input) .. ok 186: Count -m 11 (CRAM input) .. ok 187: Filter -m 15 (SAM input) .. ok 188: Count -m 15 (SAM input) .. ok 189: Filter -m 15 (BAM input) .. ok 190: Count -m 15 (BAM input) .. ok 191: Filter -m 15 (CRAM input) .. ok 192: Count -m 15 (CRAM input) .. ok 193: Filter -m 16 (SAM input) .. ok 194: Count -m 16 (SAM input) .. ok 195: Filter -m 16 (BAM input) .. ok 196: Count -m 16 (BAM input) .. ok 197: Filter -m 16 (CRAM input) .. ok 198: Count -m 16 (CRAM input) .. ok 199: 1bp reads file SAM -> BAM -> SAM .. ok 200: 1bp reads file SAM -> CRAM -> SAM .. ok 200: Region Z (BAM input) .. ok 201: Count Z (BAM input) .. ok 202: Region Z (CRAM input) .. ok 203: Count Z (CRAM input) .. ok 204: Region Z:30 (BAM input) .. ok 205: Count Z:30 (BAM input) .. ok 206: Region Z:30 (CRAM input) .. ok 207: Count Z:30 (CRAM input) .. ok 208: Region Z:20-40 (BAM input) .. ok 209: Count Z:20-40 (BAM input) .. ok 210: Region Z:20-40 (CRAM input) .. ok 211: Count Z:20-40 (CRAM input) .. ok 212: Region ref1 (BAM input) .. ok 213: Count ref1 (BAM input) .. ok 214: Region ref1 (CRAM input) .. ok 215: Count ref1 (CRAM input) .. ok 216: Region ref1:15 (BAM input) .. ok 217: Count ref1:15 (BAM input) .. ok 218: Region ref1:15 (CRAM input) .. ok 219: Count ref1:15 (CRAM input) .. ok 220: Region ref1:15-45 (BAM input) .. ok 221: Count ref1:15-45 (BAM input) .. ok 222: Region ref1:15-45 (CRAM input) .. ok 223: Count ref1:15-45 (CRAM input) .. ok 224: Region ref1:15-45 ref2 (BAM input) .. ok 225: Count ref1:15-45 ref2 (BAM input) .. ok 226: Region ref1:15-45 ref2 (CRAM input) .. ok 227: Count ref1:15-45 ref2 (CRAM input) .. ok 228: Region ref1:15-45 ref2:16 (BAM input) .. ok 229: Count ref1:15-45 ref2:16 (BAM input) .. ok 230: Region ref1:15-45 ref2:16 (CRAM input) .. ok 231: Count ref1:15-45 ref2:16 (CRAM input) .. ok 232: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 233: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 234: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 235: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 236: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 237: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 238: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 239: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 240: Region -f 128 ref1 (BAM input) .. ok 241: Count -f 128 ref1 (BAM input) .. ok 242: Region -f 128 ref1 (CRAM input) .. ok 243: Count -f 128 ref1 (CRAM input) .. ok 244: Region -q 50 ref1:15-45 (BAM input) .. ok 245: Count -q 50 ref1:15-45 (BAM input) .. ok 246: Region -q 50 ref1:15-45 (CRAM input) .. ok 247: Count -q 50 ref1:15-45 (CRAM input) .. ok 248: Region -r grp2 ref1:15-45 (BAM input) .. ok 249: Count -r grp2 ref1:15-45 (BAM input) .. ok 250: Region -r grp2 ref1:15-45 (CRAM input) .. ok 251: Count -r grp2 ref1:15-45 (CRAM input) .. ok 252: Region * (BAM input) .. ok 253: Count * (BAM input) .. ok 254: Region * (CRAM input) .. ok 255: Count * (CRAM input) .. ok 256: Region -L /<>/test/dat/view.002.01.bed (BAM input).. ok 257: Count -L /<>/test/dat/view.002.01.bed (BAM input).. ok 258: Region -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 259: Count -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 260: Region -L /<>/test/dat/view.002.02.bed (BAM input).. ok 261: Count -L /<>/test/dat/view.002.02.bed (BAM input).. ok 262: Region -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 263: Count -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 264: Region -L /<>/test/dat/view.001.01.bed (BAM input).. ok 265: Count -L /<>/test/dat/view.001.01.bed (BAM input).. ok 266: Region -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 267: Count -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 268: Region -L /<>/test/dat/view.001.02.bed (BAM input).. ok 269: Count -L /<>/test/dat/view.001.02.bed (BAM input).. ok 270: Region -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 271: Count -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 272: Region -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 273: Count -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 274: Region -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 275: Count -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 276: Region -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 277: Count -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 278: Region -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 279: Count -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 280: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 281: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 282: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 283: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 284: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 285: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 286: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 287: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 288: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 289: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 290: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 291: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 292: Region -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 293: Count -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 294: Region -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 295: Count -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 296: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 297: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 298: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 299: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 300: Region -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 301: Count -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 302: Region -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 303: Count -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 304: Region -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 305: Count -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 306: Region -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 307: Count -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 308: Region -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 309: Count -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 310: Region -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 311: Count -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 312: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 313: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 314: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 315: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 316: Make BAM with no M5/UR tags .. ok 317: Add @SQ with -t (SAM -> SAM) .. ok 318: Add @SQ with -T (SAM -> SAM) .. ok 319: Add @SQ with -t (BAM -> SAM) .. ok 320: Add @SQ with -T (BAM -> SAM) .. ok 321: Add @SQ with -t (SAM -> BAM) .. ok 322: Add @SQ with -T (SAM -> BAM) .. ok 323: Add @SQ with -t (BAM -> BAM) .. ok 324: Add @SQ with -T (BAM -> BAM) .. ok 325: Add @SQ with -t (SAM -> CRAM) .. ok 326: Add @SQ with -T (SAM -> CRAM) .. ok 327: Add @SQ with -t (BAM -> CRAM) .. ok 328: Add @SQ with -T (BAM -> CRAM) .. ok 329: Make CRAM with no UR field .. ok 330: Decoding CRAM with no UR field via -T .. ok 331: CIGAR B-operator removal .. ok 332: Big SAM -> BAM .. ok 333: Big SAM -> BAM (2 threads) .. ok 334: Big SAM -> BAM (4 threads) .. ok 335: Big SAM -> CRAM .. ok 336: Big SAM -> CRAM (2 threads) .. ok 337: Big SAM -> CRAM (4 threads) .. ok 338: Subsample 0.2 (SAM input) ............ ok 339: Subsample 0.5 (SAM input) ............ ok 340: Subsample 0.8 (SAM input) ............ ok 341: Subsample 0.2 (BAM input) ............ ok 342: Subsample 0.5 (BAM input) ............ ok 343: Subsample 0.8 (BAM input) ............ ok 344: Subsample 0.2 (CRAM input) ............ ok 345: Subsample 0.5 (CRAM input) ............ ok 346: Subsample 0.8 (CRAM input) ............ ok 347: SAM add PG .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.010.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -T MD,ia -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -i --index-format 'i*i*' -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.703.sam .. ok test_bam2fq: /<>/samtools fastq -N -1 /<>/test/o.fq -2 /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -s /tmp/f1U6ZuMHoO/bam2fq.discard.s.fq -0 /tmp/f1U6ZuMHoO/bam2fq.discard.0.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -T ba,bb,bc,bd,be,bf,bg /<>/test/dat/bam2fq.013.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.010.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -T MD,ia -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -i --index-format 'i*i*' -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.703.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -1 /<>/test/o.fq -2 /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -s /tmp/f1U6ZuMHoO/bam2fq.discard.s.fq -0 /tmp/f1U6ZuMHoO/bam2fq.discard.0.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /<>/test/dat/bam2fq.013.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa -i 0 /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -t /<>/test/stat/11.stats.targets /<>/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /<>/samtools stats -g 4 -t /<>/test/stat/11.stats.targets /<>/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -g 4 /<>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -t /<>/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -p -t /<>/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -t /<>/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -p -t /<>/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -s 1 -O sam -b /tmp/4X3ALDRzBI - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -r -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -cp -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/f1U6ZuMHoO/merge.tag.1.bam /tmp/f1U6ZuMHoO/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/f1U6ZuMHoO/merge.tag.3.bam /tmp/f1U6ZuMHoO/merge.tag.4.bam .. ok test_merge: /<>/samtools merge --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge --no-PG -O SAM -L /<>/test/merge/merge.bed - /tmp/f1U6ZuMHoO/merge.bed.1.bam /tmp/f1U6ZuMHoO/merge.bed.2.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam -b /tmp/mPt4cmyWR2 - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -@ 2 -r -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -cp -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/f1U6ZuMHoO/merge.tag.1.bam /tmp/f1U6ZuMHoO/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/f1U6ZuMHoO/merge.tag.3.bam /tmp/f1U6ZuMHoO/merge.tag.4.bam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM -L /<>/test/merge/merge.bed - /tmp/f1U6ZuMHoO/merge.bed.1.bam /tmp/f1U6ZuMHoO/merge.bed.2.bam .. ok test_sort: /<>/samtools sort /<>/test/dat/test_input_1_a.bam /tmp/f1U6ZuMHoO/sortout .. ok test_sort: /<>/samtools sort -f /<>/test/dat/test_input_1_a.bam /tmp/f1U6ZuMHoO/sortout.bam .. ok test_sort: /<>/samtools sort -o /<>/test/dat/test_input_1_a.bam /tmp/f1U6ZuMHoO/sorttmp .. ok test_sort: /<>/samtools sort -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t AS -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -t FI -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 /<>/test/dat/test_input_1_a.bam /tmp/f1U6ZuMHoO/sortout .. ok test_sort: /<>/samtools sort -@ 2 -f /<>/test/dat/test_input_1_a.bam /tmp/f1U6ZuMHoO/sortout.bam .. ok test_sort: /<>/samtools sort -@ 2 -o /<>/test/dat/test_input_1_a.bam /tmp/f1U6ZuMHoO/sorttmp .. ok test_sort: /<>/samtools sort -@ 2 -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t AS -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t FI -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /<>/samtools collate --output-fmt=sam -O /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -o /<>/test/collate/collate1.tmp.sam /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -o /<>/test/collate/collate2.tmp.sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate2.tmp .. ok test_collate: /<>/samtools collate --output-fmt=sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate3.tmp .. ok test_collate: /<>/samtools collate --output-fmt=sam -f /<>/test/collate/fast_collate.sam -o /<>/test/collate/1_fast_collate.sam .. ok test_collate: /<>/samtools collate --output-fmt=sam -f -r 4 /<>/test/collate/fast_collate.sam -o /<>/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -O /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -@ 2 -o /<>/test/collate/collate1.tmp.sam /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -@ 2 -o /<>/test/collate/collate2.tmp.sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate2.tmp .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate3.tmp .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -f /<>/test/collate/fast_collate.sam -o /<>/test/collate/1_fast_collate.sam .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -f -r 4 /<>/test/collate/fast_collate.sam -o /<>/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/8_isize_overflow_64bit.sam - .. ok /<>/samtools calmd -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok /<>/samtools calmd -@ 2 -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.bam .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.cram .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.sam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /<>/samtools quickcheck -v /<>/test/quickcheck/1.quickcheck.badeof.bam /<>/test/quickcheck/2.quickcheck.badheader.bam /<>/test/quickcheck/3.quickcheck.ok.bam /<>/test/quickcheck/4.quickcheck.ok.bam /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<>/test/quickcheck/6.quickcheck.cram21.ok.cram /<>/test/quickcheck/7.quickcheck.cram30.ok.cram /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram /<>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /<>/samtools quickcheck -uv /<>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram && /<>/samtools view -h --no-PG /<>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram && /<>/samtools view -h --no-PG /<>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -R '1#9' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -R '1#9' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/5_markdup.sam - .. ok test_markdup: /<>/samtools markdup -O sam -r --no-PG /<>/test/markdup/6_remove_dups.sam - .. ok test_markdup: /<>/samtools markdup -S -O sam --no-PG /<>/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /<>/test/markdup/8_optical_dup.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<>/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/5_markdup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -O sam -r --no-PG /<>/test/markdup/6_remove_dups.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -O sam --no-PG /<>/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /<>/test/markdup/8_optical_dup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<>/test/markdup/9_optical_dup_qcfail.sam - .. ok test_bedcov: /<>/samtools bedcov /<>/test/bedcov/bedcov.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -j /<>/test/bedcov/bedcov.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -g512 -G2048 /<>/test/bedcov/bedcov_gG.bed /<>/test/bedcov/bedcov.bam .. ok test_split: /<>/samtools split --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/f1U6ZuMHoO/longref.sam.gz .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/f1U6ZuMHoO/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /<>/samtools view -h --no-PG -L /<>/test/large_pos/test.bed /tmp/f1U6ZuMHoO/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -m 10M /<>/test/large_pos/longref_name.sam .. ok test_large_positions: /<>/samtools merge -O sam --no-PG - /<>/test/large_pos/longref.sam /<>/test/large_pos/longref2.sam .. ok test_large_positions: /<>/samtools depth /<>/test/large_pos/longref.sam .. ok test_large_positions: /<>/samtools depth -b /<>/test/large_pos/test.bed /<>/test/large_pos/longref.sam .. ok test_large_positions: /<>/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/f1U6ZuMHoO/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /<>/samtools fixmate -O sam --no-PG - - | /<>/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -t 50 -d 1,20,100 /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_hard_clipped.expected.sam /<>/test/ampliconclip/1_soft_clipped.expected.sam /<>/test/ampliconclip/1_soft_clipped_strand.expected.sam /<>/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' | tee /tmp/out.txt .. ok Number of tests: total .. 700 passed .. 654 failed .. 0 expected failure .. 46 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 163 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ./regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 47 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS make[2]: Leaving directory '/<>' rm -fr -- /tmp/dh-xdg-rundir-9DPwCnSb make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a rm -f -- debian/samtools.substvars rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/ rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- \ prefix=/usr install -d /<>/debian/tmp make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/share/man/man1 install -p samtools /<>/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<>/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl misc/plot-ampliconstats /<>/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /<>/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/<>' make clean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install install -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -d debian/samtools/usr/share/commonwl/ cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl// cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ install -d debian/.debhelper/generated/samtools install -d debian/.debhelper/generated/samtools-test # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/<>' dh_installdocs -a install -d debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools chmod -R u\+rw,go=rX debian/samtools/usr/share/doc install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright rm -f debian/samtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/<>' dh_installexamples -a install -d debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples dh_installman -a rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 dh_lintian -a install -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl -a (grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > debian/samtools.substvars.new mv debian/samtools.substvars.new debian/samtools.substvars dh_link -a rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 dh_strip_nondeterminism -a Using 1601563342 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip dh_compress -a cd debian/samtools chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/<>' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms -a find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -a dh_dwz -a -a install -d debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 661636 new size 684538 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu/samtools.debug dh_strip -a -a install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/1b1cd13462c4963c1091f0677050156b3e32f2.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/1b1cd13462c4963c1091f0677050156b3e32f2.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/1b1cd13462c4963c1091f0677050156b3e32f2.debug debian/samtools/usr/bin/wgsim install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6f objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6f/9b5409f953914dc6e000b775e5080855744449.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6f/9b5409f953914dc6e000b775e5080855744449.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6f/9b5409f953914dc6e000b775e5080855744449.debug debian/samtools/usr/bin/md5fa install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7a/20ee82f67b7ec8652d0cb51511c6c01cf58846.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7a/20ee82f67b7ec8652d0cb51511c6c01cf58846.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7a/20ee82f67b7ec8652d0cb51511c6c01cf58846.debug debian/samtools/usr/bin/samtools install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/e98b0d04030c1727869573841a513b8c47db60.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/e98b0d04030c1727869573841a513b8c47db60.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/e98b0d04030c1727869573841a513b8c47db60.debug debian/samtools/usr/bin/maq2sam-long install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8b objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8b/b4a4483359759c69363aa6bab7292563d31111.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8b/b4a4483359759c69363aa6bab7292563d31111.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8b/b4a4483359759c69363aa6bab7292563d31111.debug debian/samtools/usr/bin/maq2sam-short install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/9e19e60df8164d77b6f6837ffa5a01f56e1359.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/9e19e60df8164d77b6f6837ffa5a01f56e1359.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/9e19e60df8164d77b6f6837ffa5a01f56e1359.debug debian/samtools/usr/bin/ace2sam install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e5/9a63f0912dfcaa55acde4592c3122d7eff200a.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e5/9a63f0912dfcaa55acde4592c3122d7eff200a.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e5/9a63f0912dfcaa55acde4592c3122d7eff200a.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym dh_makeshlibs -a -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a -a install -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=581b1cd13462c4963c1091f0677050156b3e32f2 6f9b5409f953914dc6e000b775e5080855744449 7a20ee82f67b7ec8652d0cb51511c6c01cf58846 8bb4a4483359759c69363aa6bab7292563d31111 ac9e19e60df8164d77b6f6837ffa5a01f56e1359 cde98b0d04030c1727869573841a513b8c47db60 e59a63f0912dfcaa55acde4592c3122d7eff200a" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums -a cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/samtools .. install -d debian/.debhelper/scratch-space/build-samtools dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root debian/.debhelper/scratch-space/build-samtools INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing samtools (in debian/samtools); do_strip: , oemstrip: pkgstriptranslations: processing samtools-dbgsym (in debian/.debhelper/samtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools pkgstripfiles: processing control file: debian/.debhelper/samtools/dbgsym-root/DEBIAN/control, package samtools-dbgsym, directory debian/.debhelper/samtools/dbgsym-root dpkg-deb: building package 'samtools-dbgsym' in 'debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.11-1_arm64.deb'. .. removing usr/share/doc/samtools/changelog.gz pkgstripfiles: Truncating usr/share/doc/samtools/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'samtools' in '../samtools_1.11-1_arm64.deb'. Renaming samtools-dbgsym_1.11-1_arm64.deb to samtools-dbgsym_1.11-1_arm64.ddeb mv debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.11-1_arm64.deb ../samtools-dbgsym_1.11-1_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../samtools_1.11-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-10-29T07:09:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools_1.11-1_arm64.changes: ------------------------------ Format: 1.8 Date: Thu, 01 Oct 2020 16:42:22 +0200 Source: samtools Binary: samtools Architecture: arm64 Version: 1.11-1 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats Changes: samtools (1.11-1) unstable; urgency=medium . * New upstream version * Versioned Build-Depends: libhts-dev (>= 1.11) Checksums-Sha1: 06b3b39f86cb938f0b412e35764c6517d966aa16 812932 samtools-dbgsym_1.11-1_arm64.ddeb 8aaf6089b07d66dd92ca94d5abebfe8a5a758b67 6949 samtools_1.11-1_arm64.buildinfo 9ffd1f5a84ebd93d836a9578dbab6bd3b0917d30 494944 samtools_1.11-1_arm64.deb Checksums-Sha256: aa5effc641487e30c640822d14c04d0c75623659fe29892348460f112cff230b 812932 samtools-dbgsym_1.11-1_arm64.ddeb a03aceffbfea3031ac94e7608714267e737038dfd1eed45f932bf2f18d62f688 6949 samtools_1.11-1_arm64.buildinfo 041bfbfea6490bd4af4ab193824823b2016a0349ebcb5489fdd97ec276133f80 494944 samtools_1.11-1_arm64.deb Files: 772cc7b776720655d00adadfc5fea9f0 812932 debug optional samtools-dbgsym_1.11-1_arm64.ddeb 26170a31685a79cbf1079980f00d0f28 6949 science optional samtools_1.11-1_arm64.buildinfo 933ff53f4cf559d491cbea235bd49bc9 494944 science optional samtools_1.11-1_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: samtools Binary: samtools samtools-dbgsym Architecture: arm64 Version: 1.11-1 Checksums-Md5: 772cc7b776720655d00adadfc5fea9f0 812932 samtools-dbgsym_1.11-1_arm64.ddeb 933ff53f4cf559d491cbea235bd49bc9 494944 samtools_1.11-1_arm64.deb Checksums-Sha1: 06b3b39f86cb938f0b412e35764c6517d966aa16 812932 samtools-dbgsym_1.11-1_arm64.ddeb 9ffd1f5a84ebd93d836a9578dbab6bd3b0917d30 494944 samtools_1.11-1_arm64.deb Checksums-Sha256: aa5effc641487e30c640822d14c04d0c75623659fe29892348460f112cff230b 812932 samtools-dbgsym_1.11-1_arm64.ddeb 041bfbfea6490bd4af4ab193824823b2016a0349ebcb5489fdd97ec276133f80 494944 samtools_1.11-1_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Thu, 29 Oct 2020 07:09:50 +0000 Build-Path: /<> 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), bash-completion (= 1:2.11-2ubuntu1), binutils (= 2.35.1-2ubuntu1), binutils-aarch64-linux-gnu (= 2.35.1-2ubuntu1), binutils-common (= 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 (= 10.2.0-15ubuntu1), 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 (= 10.2.0-15ubuntu1), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.0-15ubuntu1), gcc-10-base (= 10.2.0-15ubuntu1), 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), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libasan6 (= 10.2.0-15ubuntu1), libasn1-8-heimdal (= 7.7.0+dfsg-2), libatomic1 (= 10.2.0-15ubuntu1), 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), libbrotli1 (= 1.0.9-2build1), libbz2-1.0 (= 1.0.8-4ubuntu2), libbz2-dev (= 1.0.8-4ubuntu2), libc-bin (= 2.32-0ubuntu3), libc-dev-bin (= 2.32-0ubuntu3), libc6 (= 2.32-0ubuntu3), libc6-dev (= 2.32-0ubuntu3), libcap-ng0 (= 0.7.9-2.2), libcc1-0 (= 10.2.0-15ubuntu1), 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), libcurl3-gnutls (= 7.68.0-1ubuntu4), libcurl4-gnutls-dev (= 7.68.0-1ubuntu4), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu3), libdebconfclient0 (= 0.254ubuntu1), libdebhelper-perl (= 13.2.1ubuntu1), libdeflate-dev (= 1.6-1), libdeflate0 (= 1.6-1), libdpkg-perl (= 1.20.5ubuntu2), libelf1 (= 0.181-1), libffi8ubuntu1 (= 3.4~20200819gead65ca871-0ubuntu3), libfile-stripnondeterminism-perl (= 1.9.0-1), libgcc-10-dev (= 10.2.0-15ubuntu1), libgcc-s1 (= 10.2.0-15ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu2), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libglib2.0-0 (= 2.66.1-2), libgmp10 (= 2:6.2.0+dfsg-6ubuntu1), libgnutls30 (= 3.6.15-4ubuntu2), libgomp1 (= 10.2.0-15ubuntu1), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10), libgssapi3-heimdal (= 7.7.0+dfsg-2), libhcrypto4-heimdal (= 7.7.0+dfsg-2), libheimbase1-heimdal (= 7.7.0+dfsg-2), libheimntlm0-heimdal (= 7.7.0+dfsg-2), libhogweed6 (= 3.6-2), libhts-dev (= 1.11-2), libhts3 (= 1.11-2), libhx509-5-heimdal (= 7.7.0+dfsg-2), libicu67 (= 67.1-4), libidn2-0 (= 2.3.0-1), libio-pty-perl (= 1:1.12-1), libisl22 (= 0.22.1-1), libitm1 (= 10.2.0-15ubuntu1), libk5crypto3 (= 1.17-10), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-2), libkrb5-3 (= 1.17-10), libkrb5support0 (= 1.17-10), libldap-2.4-2 (= 2.4.53+dfsg-1ubuntu1), liblsan0 (= 10.2.0-15ubuntu1), liblz4-1 (= 1.9.2-2), liblzma-dev (= 5.2.4-1ubuntu1), 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), libncurses-dev (= 6.2+20200918-1), libncurses5-dev (= 6.2+20200918-1), libncurses6 (= 6.2+20200918-1), libncursesw6 (= 6.2+20200918-1), libnettle8 (= 3.6-2), libnghttp2-14 (= 1.41.0-3), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), libnss-nis (= 3.1-0ubuntu4), libnss-nisplus (= 1.3-0ubuntu4), libp11-kit0 (= 0.23.21-2build1), 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), libpsl5 (= 0.21.0-1.1ubuntu1), libroken18-heimdal (= 7.7.0+dfsg-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build2), libsasl2-2 (= 2.1.27+dfsg-2ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg-2ubuntu1), libseccomp2 (= 2.4.3-1ubuntu5), libselinux1 (= 3.1-2build1), libsigsegv2 (= 2.12-2build1), libsmartcols1 (= 2.36-3ubuntu1), libsqlite3-0 (= 3.33.0-1), libssh-4 (= 0.9.4-1ubuntu3), libssl1.1 (= 1.1.1f-1ubuntu4), libstdc++-10-dev (= 10.2.0-15ubuntu1), libstdc++6 (= 10.2.0-15ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 246.6-1ubuntu1), 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 (= 10.2.0-15ubuntu1), libubsan1 (= 10.2.0-15ubuntu1), libuchardet0 (= 0.0.7-1), libudev1 (= 246.6-1ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36-3ubuntu1), libwind0-heimdal (= 7.7.0+dfsg-2), libxml2 (= 2.9.10+dfsg-6.1), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.0-25.26), 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), pkg-config (= 0.29.2-1ubuntu1), 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), tabix (= 1.11-2), tar (= 1.30+dfsg-7), util-linux (= 2.36-3ubuntu1), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1601563342" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ samtools_1.11-1_arm64.deb ------------------------- new Debian package, version 2.0. size 494944 bytes: control archive=2796 bytes. 968 bytes, 19 lines control 5020 bytes, 74 lines md5sums Package: samtools Version: 1.11-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1149 Depends: libc6 (>= 2.29), libhts3 (>= 1.11), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.1.4) Suggests: cwltool Breaks: bio-tradis (<= 1.4.5+dfsg-1), iva (<= 1.0.9+ds-6) Section: science Priority: optional Homepage: http://www.htslib.org/ Description: processing sequence alignments in SAM, BAM and CRAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing, and allows one to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP or HTTP server. drwxr-xr-x root/root 0 2020-10-01 14:42 ./ drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/ drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/bin/ -rwxr-xr-x root/root 18520 2020-10-01 14:42 ./usr/bin/ace2sam -rwxr-xr-x root/root 5443 2020-10-01 14:42 ./usr/bin/blast2sam.pl -rwxr-xr-x root/root 3360 2020-10-01 14:42 ./usr/bin/bowtie2sam.pl -rwxr-xr-x root/root 17996 2020-10-01 14:42 ./usr/bin/export2sam.pl -rwxr-xr-x root/root 6121 2020-10-01 14:42 ./usr/bin/interpolate_sam.pl -rwxr-xr-x root/root 10328 2020-10-01 14:42 ./usr/bin/maq2sam-long -rwxr-xr-x root/root 10328 2020-10-01 14:42 ./usr/bin/maq2sam-short -rwxr-xr-x root/root 10328 2020-10-01 14:42 ./usr/bin/md5fa -rwxr-xr-x root/root 10328 2020-10-01 14:42 ./usr/bin/md5sum-lite -rwxr-xr-x root/root 7969 2020-10-01 14:42 ./usr/bin/novo2sam.pl -rwxr-xr-x root/root 42985 2020-10-01 14:42 ./usr/bin/plot-ampliconstats -rwxr-xr-x root/root 50473 2020-10-01 14:42 ./usr/bin/plot-bamstats -rwxr-xr-x root/root 3204 2020-10-01 14:42 ./usr/bin/psl2sam.pl -rwxr-xr-x root/root 8957 2020-10-01 14:42 ./usr/bin/sam2vcf.pl -rwxr-xr-x root/root 571680 2020-10-01 14:42 ./usr/bin/samtools -rwxr-xr-x root/root 16474 2020-10-01 14:42 ./usr/bin/samtools.pl -rwxr-xr-x root/root 11327 2020-10-01 14:42 ./usr/bin/seq_cache_populate.pl -rwxr-xr-x root/root 3905 2020-10-01 14:42 ./usr/bin/soap2sam.pl -rwxr-xr-x root/root 30848 2020-10-01 14:42 ./usr/bin/wgsim -rwxr-xr-x root/root 12542 2020-10-01 14:42 ./usr/bin/wgsim_eval.pl -rwxr-xr-x root/root 3579 2020-10-01 14:42 ./usr/bin/zoom2sam.pl drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/ drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/commonwl/ -rwxr-xr-x root/root 1906 2020-10-01 14:42 ./usr/share/commonwl/samtools-faidx.cwl -rwxr-xr-x root/root 1979 2020-10-01 14:42 ./usr/share/commonwl/samtools-index.cwl -rwxr-xr-x root/root 1627 2020-10-01 14:42 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2020-09-22 12:15 ./usr/share/doc/samtools/examples/ex1.fa -rw-r--r-- root/root 114565 2020-10-01 14:42 ./usr/share/doc/samtools/examples/ex1.sam.gz -rw-r--r-- root/root 98 2020-09-22 12:15 ./usr/share/doc/samtools/examples/toy.fa -rw-r--r-- root/root 786 2020-09-22 12:15 ./usr/share/doc/samtools/examples/toy.sam drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 220 2020-10-01 14:42 ./usr/share/lintian/overrides/samtools drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/man/ drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/man/man1/ -rw-r--r-- root/root 462 2020-10-01 14:42 ./usr/share/man/man1/ace2sam.1.gz -rw-r--r-- root/root 1573 2020-10-01 14:42 ./usr/share/man/man1/samtools-addreplacerg.1.gz -rw-r--r-- root/root 2082 2020-10-01 14:42 ./usr/share/man/man1/samtools-ampliconclip.1.gz -rw-r--r-- root/root 5463 2020-10-01 14:42 ./usr/share/man/man1/samtools-ampliconstats.1.gz 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root/root 1470 2020-10-01 14:42 ./usr/share/man/man1/samtools-rmdup.1.gz -rw-r--r-- root/root 3486 2020-10-01 14:42 ./usr/share/man/man1/samtools-sort.1.gz -rw-r--r-- root/root 1643 2020-10-01 14:42 ./usr/share/man/man1/samtools-split.1.gz -rw-r--r-- root/root 6110 2020-10-01 14:42 ./usr/share/man/man1/samtools-stats.1.gz -rw-r--r-- root/root 1426 2020-10-01 14:42 ./usr/share/man/man1/samtools-targetcut.1.gz -rw-r--r-- root/root 1632 2020-10-01 14:42 ./usr/share/man/man1/samtools-tview.1.gz -rw-r--r-- root/root 4885 2020-10-01 14:42 ./usr/share/man/man1/samtools-view.1.gz -rw-r--r-- root/root 11708 2020-10-01 14:42 ./usr/share/man/man1/samtools.1.gz -rw-r--r-- root/root 410 2020-10-01 14:42 ./usr/share/man/man1/samtools.pl.1.gz -rw-r--r-- root/root 518 2020-10-01 14:42 ./usr/share/man/man1/wgsim.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: 151 Distribution: hirsute-proposed Host Architecture: arm64 Install-Time: 30 Job: samtools_1.11-1.dsc Machine Architecture: arm64 Package: samtools Package-Time: 183 Source-Version: 1.11-1 Space: n/a Status: successful Version: 1.11-1 -------------------------------------------------------------------------------- Finished at 2020-10-29T07:09:51Z Build needed 00:03:03, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20209976 Scanning for processes to kill in build PACKAGEBUILD-20209976