https://launchpad.net/ubuntu/+source/bedtools/2.27.1+dfsg-2/+build/14925124 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-ppc64el-013 4.4.0-124-generic #148-Ubuntu SMP Wed May 2 13:02:22 UTC 2018 ppc64le Buildd toolchain package versions: launchpad-buildd_161 python-lpbuildd_161 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 23 May 05:11:09 ntpdate[1782]: adjust time server 10.211.37.1 offset 0.001688 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=ppc64el PACKAGEBUILD-14925124 /home/buildd/filecache-default/eae3490d19bb2e30261b695511cfc7c4419ff6fc Creating target for build PACKAGEBUILD-14925124 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=ppc64el PACKAGEBUILD-14925124 Starting target for build PACKAGEBUILD-14925124 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=ppc64el PACKAGEBUILD-14925124 'deb http://ftpmaster.internal/ubuntu cosmic main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-security main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-updates main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-14925124 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=ppc64el PACKAGEBUILD-14925124 Updating target for build PACKAGEBUILD-14925124 Get:1 http://ftpmaster.internal/ubuntu cosmic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic-proposed InRelease [92.5 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main ppc64el Packages [971 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe ppc64el Packages [8320 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [4983 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el Packages [77.1 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [49.0 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe ppc64el Packages [767 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [352 kB] Fetched 16.5 MB in 3s (4718 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libncursesw5 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libncurses6 libncursesw6 libtinfo6 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils build-essential cpp cpp-7 debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base libapt-pkg5.0 libargon2-0 libasan4 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libcomerr2 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgmp10 libgomp1 libgpg-error0 libitm1 liblsan0 libmount1 libncurses5 libncursesw5 libp11-kit0 libperl5.26 libprocps6 libreadline7 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libtsan0 libubsan0 libudev1 libusb-0.1-4 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common systemd systemd-sysv tar tzdata util-linux 84 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 50.3 MB of archives. After this operation, 2498 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main ppc64el base-files ppc64el 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libtinfo6 ppc64el 6.1+20180210-2ubuntu2 [95.6 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main ppc64el debianutils ppc64el 4.8.6 [85.8 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main ppc64el bash ppc64el 4.4.18-2ubuntu2 [680 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el bsdutils ppc64el 1:2.32-0.1ubuntu1 [62.0 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main ppc64el tar ppc64el 1.30+dfsg-2 [268 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main ppc64el dpkg ppc64el 1.19.0.5ubuntu3 [1147 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libext2fs2 ppc64el 1.44.2-1 [173 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main ppc64el e2fsprogs ppc64el 1.44.2-1 [402 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main ppc64el ncurses-bin ppc64el 6.1+20180210-2ubuntu2 [171 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el perl-modules-5.26 all 5.26.2-5 [2762 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libperl5.26 ppc64el 5.26.2-5 [3401 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el perl ppc64el 5.26.2-5 [202 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el perl-base ppc64el 5.26.2-5 [1306 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libuuid1 ppc64el 2.32-0.1ubuntu1 [20.9 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libblkid1 ppc64el 2.32-0.1ubuntu1 [137 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libfdisk1 ppc64el 2.32-0.1ubuntu1 [170 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libncursesw6 ppc64el 6.1+20180210-2ubuntu2 [134 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libmount1 ppc64el 2.32-0.1ubuntu1 [147 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libsmartcols1 ppc64el 2.32-0.1ubuntu1 [91.4 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el fdisk ppc64el 2.32-0.1ubuntu1 [112 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el util-linux ppc64el 2.32-0.1ubuntu1 [917 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main ppc64el base-passwd ppc64el 3.5.45 [50.2 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main ppc64el ncurses-base all 6.1+20180210-2ubuntu2 [17.8 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libgomp1 ppc64el 8.1.0-3ubuntu2 [79.8 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libitm1 ppc64el 8.1.0-3ubuntu2 [29.3 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el gcc-8-base ppc64el 8.1.0-3ubuntu2 [18.4 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libgcc1 ppc64el 1:8.1.0-3ubuntu2 [30.3 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el liblsan0 ppc64el 8.1.0-3ubuntu2 [144 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libtsan0 ppc64el 8.1.0-3ubuntu2 [295 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libcc1-0 ppc64el 8.1.0-3ubuntu2 [40.8 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libatomic1 ppc64el 8.1.0-3ubuntu2 [9896 B] Get:33 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libstdc++6 ppc64el 8.1.0-3ubuntu2 [444 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libudev1 ppc64el 237-3ubuntu11 [59.9 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libapt-pkg5.0 ppc64el 1.7.0~alpha0ubuntu1 [903 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main ppc64el adduser all 3.117ubuntu1 [163 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main ppc64el apt ppc64el 1.7.0~alpha0ubuntu1 [1214 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libaudit-common all 1:2.8.3-1ubuntu1 [4052 B] Get:39 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libcap-ng0 ppc64el 0.7.9-1 [11.7 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libaudit1 ppc64el 1:2.8.3-1ubuntu1 [41.8 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libgpg-error0 ppc64el 1.31-1 [65.6 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el mount ppc64el 2.32-0.1ubuntu1 [105 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libncurses6 ppc64el 6.1+20180210-2ubuntu2 [109 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libprocps6 ppc64el 2:3.3.12-3ubuntu2 [32.9 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main ppc64el procps ppc64el 2:3.3.12-3ubuntu2 [238 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el systemd ppc64el 237-3ubuntu11 [3110 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libsystemd0 ppc64el 237-3ubuntu11 [222 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el systemd-sysv ppc64el 237-3ubuntu11 [11.6 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libcom-err2 ppc64el 1.44.2-1 [9368 B] Get:50 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libsepol1 ppc64el 2.7-2 [253 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libss2 ppc64el 1.44.2-1 [11.5 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libncurses5 ppc64el 6.1+20180210-2ubuntu2 [101 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libncursesw5 ppc64el 6.1+20180210-2ubuntu2 [120 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libtinfo5 ppc64el 6.1+20180210-2ubuntu2 [90.6 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libgmp10 ppc64el 2:6.1.2+dfsg-3 [218 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libp11-kit0 ppc64el 0.23.10-2 [165 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libtasn1-6 ppc64el 4.13-3 [40.0 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libargon2-0 ppc64el 0~20161029-2 [20.4 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main ppc64el readline-common all 7.0-5 [52.2 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libreadline7 ppc64el 7.0-5 [125 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libslang2 ppc64el 2.3.2-1ubuntu1 [385 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libsqlite3-0 ppc64el 3.23.1-1 [472 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main ppc64el tzdata all 2018e-1 [188 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libbinutils ppc64el 2.30-20ubuntu2 [469 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main ppc64el binutils-common ppc64el 2.30-20ubuntu2 [193 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main ppc64el binutils ppc64el 2.30-20ubuntu2 [3384 B] Get:67 http://ftpmaster.internal/ubuntu cosmic/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.30-20ubuntu2 [2003 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libasan4 ppc64el 7.3.0-19ubuntu2 [366 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libubsan0 ppc64el 7.3.0-19ubuntu2 [136 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el g++-7 ppc64el 7.3.0-19ubuntu2 [7124 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el gcc-7 ppc64el 7.3.0-19ubuntu2 [6937 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libstdc++-7-dev ppc64el 7.3.0-19ubuntu2 [1532 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libgcc-7-dev ppc64el 7.3.0-19ubuntu2 [984 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el cpp-7 ppc64el 7.3.0-19ubuntu2 [6275 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el gcc-7-base ppc64el 7.3.0-19ubuntu2 [18.9 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main ppc64el cpp ppc64el 4:7.3.0-3ubuntu3 [27.6 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main ppc64el gcc ppc64el 4:7.3.0-3ubuntu3 [5228 B] Get:78 http://ftpmaster.internal/ubuntu cosmic/main ppc64el g++ ppc64el 4:7.3.0-3ubuntu3 [1584 B] Get:79 http://ftpmaster.internal/ubuntu cosmic/main ppc64el dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main ppc64el build-essential ppc64el 12.5ubuntu2 [4740 B] Get:82 http://ftpmaster.internal/ubuntu cosmic/main ppc64el e2fslibs ppc64el 1.44.2-1 [2700 B] Get:83 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libcomerr2 ppc64el 1.44.2-1 [2700 B] Get:84 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libusb-0.1-4 ppc64el 2:0.1.12-32 [17.0 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el linux-libc-dev ppc64el 4.15.0-22.24 [994 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el pinentry-curses ppc64el 1.1.0-1build1 [38.7 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic/main ppc64el pkgbinarymangler all 139 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 50.3 MB in 1s (63.0 MB/s) (Reading database ... 12528 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_ppc64el.deb ... Unpacking base-files (10.1ubuntu4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu4) ... 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 ... Selecting previously unselected package libtinfo6:ppc64el. (Reading database ... 12528 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-2ubuntu2_ppc64el.deb ... Unpacking libtinfo6:ppc64el (6.1+20180210-2ubuntu2) ... Setting up libtinfo6:ppc64el (6.1+20180210-2ubuntu2) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_ppc64el.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_ppc64el.deb ... Unpacking bash (4.4.18-2ubuntu2) over (4.4.18-2ubuntu1) ... Setting up bash (4.4.18-2ubuntu2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.32-0.1ubuntu1_ppc64el.deb ... Unpacking bsdutils (1:2.32-0.1ubuntu1) over (1:2.31.1-0.4ubuntu3) ... Setting up bsdutils (1:2.32-0.1ubuntu1) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-2_ppc64el.deb ... Unpacking tar (1.30+dfsg-2) over (1.29b-2) ... Setting up tar (1.30+dfsg-2) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.5ubuntu3_ppc64el.deb ... Unpacking dpkg (1.19.0.5ubuntu3) over (1.19.0.5ubuntu2) ... Setting up dpkg (1.19.0.5ubuntu3) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../libext2fs2_1.44.2-1_ppc64el.deb ... Unpacking libext2fs2:ppc64el (1.44.2-1) over (1.44.1-1) ... Setting up libext2fs2:ppc64el (1.44.2-1) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.44.2-1_ppc64el.deb ... Unpacking e2fsprogs (1.44.2-1) over (1.44.1-1) ... Setting up e2fsprogs (1.44.2-1) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.1+20180210-2ubuntu2_ppc64el.deb ... Unpacking ncurses-bin (6.1+20180210-2ubuntu2) over (6.1-1ubuntu1) ... Setting up ncurses-bin (6.1+20180210-2ubuntu2) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../perl_5.26.2-5_ppc64el.deb ... Unpacking perl (5.26.2-5) over (5.26.1-6) ... Preparing to unpack .../perl-modules-5.26_5.26.2-5_all.deb ... 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Unpacking libfdisk1:ppc64el (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up libfdisk1:ppc64el (2.32-0.1ubuntu1) ... Selecting previously unselected package libncursesw6:ppc64el. (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20180210-2ubuntu2_ppc64el.deb ... Unpacking libncursesw6:ppc64el (6.1+20180210-2ubuntu2) ... Setting up libncursesw6:ppc64el (6.1+20180210-2ubuntu2) ... (Reading database ... 12546 files and directories currently installed.) Preparing to unpack .../libmount1_2.32-0.1ubuntu1_ppc64el.deb ... Unpacking libmount1:ppc64el (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up libmount1:ppc64el (2.32-0.1ubuntu1) ... (Reading database ... 12546 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.32-0.1ubuntu1_ppc64el.deb ... Unpacking libsmartcols1:ppc64el (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up libsmartcols1:ppc64el (2.32-0.1ubuntu1) ... (Reading database ... 12546 files and directories currently installed.) Preparing to unpack .../fdisk_2.32-0.1ubuntu1_ppc64el.deb ... Unpacking fdisk (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up fdisk (2.32-0.1ubuntu1) ... (Reading database ... 12546 files and directories currently installed.) Preparing to unpack .../util-linux_2.32-0.1ubuntu1_ppc64el.deb ... Unpacking util-linux (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up util-linux (2.32-0.1ubuntu1) ... (Reading database ... 12546 files and directories currently installed.) Preparing to unpack .../base-passwd_3.5.45_ppc64el.deb ... Unpacking base-passwd (3.5.45) over (3.5.44) ... Setting up base-passwd (3.5.45) ... (Reading database ... 12546 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20180210-2ubuntu2_all.deb ... Unpacking ncurses-base (6.1+20180210-2ubuntu2) over (6.1-1ubuntu1) ... Setting up ncurses-base (6.1+20180210-2ubuntu2) ... 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Current default time zone: 'Etc/UTC' Local time is now: Wed May 23 05:11:32 UTC 2018. Universal Time is now: Wed May 23 05:11:32 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (237-3ubuntu11) ... Setting up libtsan0:ppc64el (8.1.0-3ubuntu2) ... Setting up linux-libc-dev:ppc64el (4.15.0-22.24) ... Setting up perl-modules-5.26 (5.26.2-5) ... Setting up liblsan0:ppc64el (8.1.0-3ubuntu2) ... Setting up libargon2-0:ppc64el (0~20161029-2) ... Setting up gcc-7-base:ppc64el (7.3.0-19ubuntu2) ... Setting up binutils-common:ppc64el (2.30-20ubuntu2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up libperl5.26:ppc64el (5.26.2-5) ... Setting up libsqlite3-0:ppc64el (3.23.1-1) ... Setting up pinentry-curses (1.1.0-1build1) ... Setting up libcomerr2:ppc64el (1.44.2-1) ... Setting up libslang2:ppc64el (2.3.2-1ubuntu1) ... Setting up libusb-0.1-4:ppc64el (2:0.1.12-32) ... Setting up libitm1:ppc64el (8.1.0-3ubuntu2) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14925124 ppc64el cosmic-proposed -c chroot:build-PACKAGEBUILD-14925124 --arch=ppc64el --dist=cosmic-proposed --nolog bedtools_2.27.1+dfsg-2.dsc Initiating build PACKAGEBUILD-14925124 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-124-generic #148-Ubuntu SMP Wed May 2 13:02:22 UTC 2018 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-ppc64el-013.buildd +==============================================================================+ | bedtools 2.27.1+dfsg-2 (ppc64el) 23 May 2018 05:11 | +==============================================================================+ Package: bedtools Version: 2.27.1+dfsg-2 Source Version: 2.27.1+dfsg-2 Distribution: cosmic-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/bedtools-xCI9oJ/bedtools-2.27.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedtools-xCI9oJ' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14925124/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bedtools_2.27.1+dfsg-2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-jaMP1S/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-jaMP1S/apt_archive ./ InRelease Get:2 copy:/<>/resolver-jaMP1S/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-jaMP1S/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-jaMP1S/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-jaMP1S/apt_archive ./ Packages [529 B] Fetched 2862 B in 0s (152 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-jaMP1S/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12552 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), python, zlib1g-dev, samtools Filtered Build-Depends: debhelper (>= 11~), python, zlib1g-dev, samtools dpkg-deb: building package 'sbuild-build-depends-bedtools-dummy' in '/<>/resolver-8qOf66/apt_archive/sbuild-build-depends-bedtools-dummy.deb'. Ign:1 copy:/<>/resolver-8qOf66/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8qOf66/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-8qOf66/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8qOf66/apt_archive ./ Sources [229 B] Get:5 copy:/<>/resolver-8qOf66/apt_archive ./ Packages [550 B] Fetched 2898 B in 0s (93.2 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install bedtools 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 automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts2 libhx509-5-heimdal libicu60 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts2 libhx509-5-heimdal libicu60 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal samtools sbuild-build-depends-bedtools-dummy zlib1g-dev 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 24.6 MB of archives. After this operation, 102 MB of additional disk space will be used. Get:1 copy:/<>/resolver-8qOf66/apt_archive ./ sbuild-build-depends-bedtools-dummy 0.invalid.0 [876 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libbsd0 ppc64el 0.9.1-1 [53.6 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main ppc64el bsdmainutils ppc64el 11.1.2ubuntu2 [185 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main ppc64el groff-base ppc64el 1.22.3-10 [1468 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libpipeline1 ppc64el 1.5.0-1 [24.7 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main ppc64el man-db ppc64el 2.8.3-2 [1034 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libpython2.7-minimal ppc64el 2.7.15-1 [334 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main ppc64el python2.7-minimal ppc64el 2.7.15-1 [1445 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main ppc64el python-minimal ppc64el 2.7.15~rc1-1 [28.1 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main ppc64el mime-support all 3.60ubuntu1 [30.1 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libexpat1 ppc64el 2.2.5-3 [89.5 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libpython2.7-stdlib ppc64el 2.7.15-1 [2005 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main ppc64el python2.7 ppc64el 2.7.15-1 [239 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libpython-stdlib ppc64el 2.7.15~rc1-1 [7624 B] Get:15 http://ftpmaster.internal/ubuntu cosmic/main ppc64el python ppc64el 2.7.15~rc1-1 [140 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libmagic-mgc ppc64el 1:5.33-2 [193 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libmagic1 ppc64el 1:5.33-2 [78.0 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main ppc64el file ppc64el 1:5.33-2 [23.5 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libglib2.0-0 ppc64el 2.56.1-2ubuntu1 [1160 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libicu60 ppc64el 60.2-6ubuntu1 [8350 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libxml2 ppc64el 2.9.4+dfsg1-6.1ubuntu1 [615 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main ppc64el gettext-base ppc64el 0.19.8.1-6build1 [50.1 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libkrb5support0 ppc64el 1.16-2build1 [32.3 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libk5crypto3 ppc64el 1.16-2build1 [106 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libkeyutils1 ppc64el 1.5.9-9.2ubuntu3 [9092 B] Get:26 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libkrb5-3 ppc64el 1.16-2build1 [309 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libgssapi-krb5-2 ppc64el 1.16-2build1 [123 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libpsl5 ppc64el 0.20.1-1 [51.2 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libsigsegv2 ppc64el 2.12-2 [13.9 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main ppc64el m4 ppc64el 1.4.18-1 [202 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main ppc64el autoconf all 2.69-11 [322 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main ppc64el autotools-dev all 20180224.1 [39.6 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main ppc64el automake all 1:1.15.1-3ubuntu2 [509 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main ppc64el autopoint all 0.19.8.1-6build1 [412 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libtool all 2.4.6-2.1 [195 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main ppc64el dh-autoreconf all 19 [16.1 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libarchive-zip-perl all 1.60-1 [83.9 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libfile-stripnondeterminism-perl all 0.041-1 [15.3 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libtimedate-perl all 2.3000-2 [37.5 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main ppc64el dh-strip-nondeterminism all 0.041-1 [5188 B] Get:41 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libcroco3 ppc64el 0.6.12-2 [82.5 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main ppc64el gettext ppc64el 0.19.8.1-6build1 [953 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main ppc64el intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main ppc64el po-debconf all 1.0.20 [232 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main ppc64el debhelper all 11.2.1ubuntu1 [906 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libroken18-heimdal ppc64el 7.5.0+dfsg-1 [42.2 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libasn1-8-heimdal ppc64el 7.5.0+dfsg-1 [140 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libheimbase1-heimdal ppc64el 7.5.0+dfsg-1 [30.5 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libhcrypto4-heimdal ppc64el 7.5.0+dfsg-1 [100 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libwind0-heimdal ppc64el 7.5.0+dfsg-1 [48.0 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libhx509-5-heimdal ppc64el 7.5.0+dfsg-1 [108 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libkrb5-26-heimdal ppc64el 7.5.0+dfsg-1 [216 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libheimntlm0-heimdal ppc64el 7.5.0+dfsg-1 [16.4 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libgssapi3-heimdal ppc64el 7.5.0+dfsg-1 [92.6 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libsasl2-modules-db ppc64el 2.1.27~101-g0780600+dfsg-3ubuntu2 [15.0 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libsasl2-2 ppc64el 2.1.27~101-g0780600+dfsg-3ubuntu2 [53.8 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libldap-common all 2.4.46+dfsg-5ubuntu1 [16.6 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libldap-2.4-2 ppc64el 2.4.46+dfsg-5ubuntu1 [158 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main ppc64el libnghttp2-14 ppc64el 1.30.0-1ubuntu1 [84.6 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2 [54.5 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic-proposed/main ppc64el libcurl3-gnutls ppc64el 7.58.0-2ubuntu4 [217 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/universe ppc64el libhts2 ppc64el 1.7-2 [332 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/universe ppc64el samtools ppc64el 1.7-2 [459 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-0ubuntu2 [178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.6 MB in 1s (20.9 MB/s) Selecting previously unselected package libbsd0:ppc64el. (Reading database ... 12552 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.9.1-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_ppc64el.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_ppc64el.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../03-libpipeline1_1.5.0-1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.3-2_ppc64el.deb ... Unpacking man-db (2.8.3-2) ... Selecting previously unselected package libpython2.7-minimal:ppc64el. Preparing to unpack .../05-libpython2.7-minimal_2.7.15-1_ppc64el.deb ... Unpacking libpython2.7-minimal:ppc64el (2.7.15-1) ... 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Unpacking python2.7 (2.7.15-1) ... Selecting previously unselected package libpython-stdlib:ppc64el. Preparing to unpack .../12-libpython-stdlib_2.7.15~rc1-1_ppc64el.deb ... Unpacking libpython-stdlib:ppc64el (2.7.15~rc1-1) ... Setting up libpython2.7-minimal:ppc64el (2.7.15-1) ... Setting up python2.7-minimal (2.7.15-1) ... Setting up python-minimal (2.7.15~rc1-1) ... Selecting previously unselected package python. (Reading database ... 13884 files and directories currently installed.) Preparing to unpack .../00-python_2.7.15~rc1-1_ppc64el.deb ... Unpacking python (2.7.15~rc1-1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.33-2_ppc64el.deb ... Unpacking libmagic-mgc (1:5.33-2) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../02-libmagic1_1%3a5.33-2_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.33-2) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.33-2_ppc64el.deb ... Unpacking file (1:5.33-2) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../04-libglib2.0-0_2.56.1-2ubuntu1_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.56.1-2ubuntu1) ... Selecting previously unselected package libicu60:ppc64el. Preparing to unpack .../05-libicu60_60.2-6ubuntu1_ppc64el.deb ... Unpacking libicu60:ppc64el (60.2-6ubuntu1) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../06-libxml2_2.9.4+dfsg1-6.1ubuntu1_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.4+dfsg1-6.1ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.19.8.1-6build1_ppc64el.deb ... Unpacking gettext-base (0.19.8.1-6build1) ... Selecting previously unselected package libkrb5support0:ppc64el. Preparing to unpack .../08-libkrb5support0_1.16-2build1_ppc64el.deb ... Unpacking libkrb5support0:ppc64el (1.16-2build1) ... 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Selecting previously unselected package libhts2:ppc64el. Preparing to unpack .../47-libhts2_1.7-2_ppc64el.deb ... Unpacking libhts2:ppc64el (1.7-2) ... Selecting previously unselected package samtools. Preparing to unpack .../48-samtools_1.7-2_ppc64el.deb ... Unpacking samtools (1.7-2) ... Selecting previously unselected package zlib1g-dev:ppc64el. Preparing to unpack .../49-zlib1g-dev_1%3a1.2.11.dfsg-0ubuntu2_ppc64el.deb ... Unpacking zlib1g-dev:ppc64el (1:1.2.11.dfsg-0ubuntu2) ... Selecting previously unselected package sbuild-build-depends-bedtools-dummy. Preparing to unpack .../50-sbuild-build-depends-bedtools-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-bedtools-dummy (0.invalid.0) ... Setting up libexpat1:ppc64el (2.2.5-3) ... Setting up libicu60:ppc64el (60.2-6ubuntu1) ... Setting up libarchive-zip-perl (1.60-1) ... Setting up libnghttp2-14:ppc64el (1.30.0-1ubuntu1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:ppc64el (2.12-2) ... Setting up libldap-common (2.4.46+dfsg-5ubuntu1) ... Setting up libpsl5:ppc64el (0.20.1-1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:ppc64el (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:ppc64el (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libsasl2-2:ppc64el (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-6build1) ... Setting up libpipeline1:ppc64el (1.5.0-1) ... Setting up libroken18-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:ppc64el (0.9.1-1) ... Setting up libkrb5support0:ppc64el (1.16-2build1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-6.1ubuntu1) ... Setting up libmagic-mgc (1:5.33-2) ... Setting up libmagic1:ppc64el (1:5.33-2) ... Setting up libcroco3:ppc64el (0.6.12-2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up libkeyutils1:ppc64el (1.5.9-9.2ubuntu3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpython2.7-stdlib:ppc64el (2.7.15-1) ... Setting up autopoint (0.19.8.1-6build1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.041-1) ... Setting up libk5crypto3:ppc64el (1.16-2build1) ... Setting up libwind0-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up gettext (0.19.8.1-6build1) ... Setting up libasn1-8-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up libhcrypto4-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up python2.7 (2.7.15-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.33-2) ... Setting up libhx509-5-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up libpython-stdlib:ppc64el (2.7.15~rc1-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:ppc64el (1.16-2build1) ... Setting up libkrb5-26-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up libheimntlm0-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up python (2.7.15~rc1-1) ... Setting up libtool (2.4.6-2.1) ... Setting up po-debconf (1.0.20) ... Setting up libgssapi-krb5-2:ppc64el (1.16-2build1) ... Setting up libgssapi3-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up libldap-2.4-2:ppc64el (2.4.46+dfsg-5ubuntu1) ... Setting up libcurl3-gnutls:ppc64el (7.58.0-2ubuntu4) ... Setting up libhts2:ppc64el (1.7-2) ... Setting up samtools (1.7-2) ... Setting up dh-autoreconf (19) ... Setting up debhelper (11.2.1ubuntu1) ... Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.041-1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-124-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.30-20ubuntu2 dpkg-dev_1.19.0.5ubuntu3 g++-7_7.3.0-19ubuntu2 gcc-7_7.3.0-19ubuntu2 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-19ubuntu2 libstdc++6_8.1.0-3ubuntu2 linux-libc-dev_4.15.0-22.24 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0~alpha0ubuntu1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6build1 autotools-dev_20180224.1 base-files_10.1ubuntu4 base-passwd_3.5.45 bash_4.4.18-2ubuntu2 binutils_2.30-20ubuntu2 binutils-common_2.30-20ubuntu2 binutils-powerpc64le-linux-gnu_2.30-20ubuntu2 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu3 cpp-7_7.3.0-19ubuntu2 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.2.1ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu3 dpkg-dev_1.19.0.5ubuntu3 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu1 file_1:5.33-2 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu3 g++-7_7.3.0-19ubuntu2 gcc_4:7.3.0-3ubuntu3 gcc-7_7.3.0-19ubuntu2 gcc-7-base_7.3.0-19ubuntu2 gcc-8-base_8.1.0-3ubuntu2 gettext_0.19.8.1-6build1 gettext-base_0.19.8.1-6build1 gpg_2.2.4-1ubuntu1 gpg-agent_2.2.4-1ubuntu1 gpgconf_2.2.4-1ubuntu1 gpgv_2.2.4-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5 libapt-pkg5.0_1.7.0~alpha0ubuntu1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19ubuntu2 libasn1-8-heimdal_7.5.0+dfsg-1 libassuan0_2.5.1-2 libatomic1_8.1.0-3ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu1 libaudit1_1:2.8.3-1ubuntu1 libbinutils_2.30-20ubuntu2 libblkid1_2.32-0.1ubuntu1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-3ubuntu2 libcom-err2_1.44.2-1 libcomerr2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1 libcurl3-gnutls_7.58.0-2ubuntu4 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu3 libexpat1_2.2.5-3 libext2fs2_1.44.2-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgcc-7-dev_7.3.0-19ubuntu2 libgcc1_1:8.1.0-3ubuntu2 libgcrypt20_1.8.1-4ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.1.0-3ubuntu2 libgpg-error0_1.31-1 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-1 libhcrypto4-heimdal_7.5.0+dfsg-1 libheimbase1-heimdal_7.5.0+dfsg-1 libheimntlm0-heimdal_7.5.0+dfsg-1 libhogweed4_3.4-1 libhts2_1.7-2 libhx509-5-heimdal_7.5.0+dfsg-1 libicu60_60.2-6ubuntu1 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libitm1_8.1.0-3ubuntu2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.2ubuntu3 libkmod2_24-1ubuntu3 libkrb5-26-heimdal_7.5.0+dfsg-1 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 libldap-2.4-2_2.4.46+dfsg-5ubuntu1 libldap-common_2.4.46+dfsg-5ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.1.0-3ubuntu2 liblz4-1_0.0~r131-2ubuntu3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.32-0.1ubuntu1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-2ubuntu2 libncurses6_6.1+20180210-2ubuntu2 libncursesw5_6.1+20180210-2ubuntu2 libncursesw6_6.1+20180210-2ubuntu2 libnettle6_3.4-1 libnghttp2-14_1.30.0-1ubuntu1 libnpth0_1.5-3 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-9 libperl5.26_5.26.2-5 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3ubuntu2 libpsl5_0.20.1-1 libpython-stdlib_2.7.15~rc1-1 libpython2.7-minimal_2.7.15-1 libpython2.7-stdlib_2.7.15-1 libreadline7_7.0-5 libroken18-heimdal_7.5.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-2 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu1 libsqlite3-0_3.23.1-1 libss2_1.44.2-1 libssl1.1_1.1.0g-2ubuntu4 libstdc++-7-dev_7.3.0-19ubuntu2 libstdc++6_8.1.0-3ubuntu2 libsystemd0_237-3ubuntu11 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-2ubuntu2 libtinfo6_6.1+20180210-2ubuntu2 libtool_2.4.6-2.1 libtsan0_8.1.0-3ubuntu2 libubsan0_7.3.0-19ubuntu2 libudev1_237-3ubuntu11 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-32 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1ubuntu1 libwind0-heimdal_7.5.0+dfsg-1 libxml2_2.9.4+dfsg1-6.1ubuntu1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-22.24 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu1 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1+20180210-2ubuntu2 ncurses-bin_6.1+20180210-2ubuntu2 openssl_1.1.0g-2ubuntu4 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.2-5 perl-base_5.26.2-5 perl-modules-5.26_5.26.2-5 pinentry-curses_1.1.0-1build1 pkgbinarymangler_139 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu2 python_2.7.15~rc1-1 python-minimal_2.7.15~rc1-1 python2.7_2.7.15-1 python2.7-minimal_2.7.15-1 readline-common_7.0-5 samtools_1.7-2 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu11 systemd-sysv_237-3ubuntu11 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.30+dfsg-2 tzdata_2018e-1 ubuntu-keyring_2018.02.28 util-linux_2.32-0.1ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue May 22 19:48:05 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedtools_2.27.1+dfsg-2.dsc dpkg-source: info: extracting bedtools in bedtools-2.27.1+dfsg dpkg-source: info: unpacking bedtools_2.27.1+dfsg.orig.tar.xz dpkg-source: info: unpacking bedtools_2.27.1+dfsg-2.debian.tar.xz dpkg-source: info: applying gzstream.h.patch dpkg-source: info: applying fix_test_script.patch dpkg-source: info: applying remove_barski_binding_site.png.patch dpkg-source: info: applying reproducible_build.patch Check disc 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-14925124 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14925124 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14925124 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bedtools dpkg-buildpackage: info: source version 2.27.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build bedtools-2.27.1+dfsg dpkg-buildpackage: info: host architecture ppc64el dpkg-source: info: using options from bedtools-2.27.1+dfsg/debian/source/options: --single-debian-patch fakeroot debian/rules clean dh clean dh_auto_clean make -j4 -Oline clean * Cleaning-up BamTools API make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' * Cleaning up. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/bedtools.substvars debian/bedtools-test.substvars debian/files rm -fr -- debian/bedtools/ debian/tmp/ debian/bedtools-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 build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 -Oline "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' $CXXFLAGS is [-Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11] Building BEDTools: make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' ========================================================= make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * Creating BamTools API make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' DETECTED_VERSION = v2.27.1 CURRENT_VERSION = Updating version file. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/FileReaders make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/Records make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling Record.cpp * compiling FileReader.cpp * compiling FileRecordMgr.cpp * compiling bedFile.cpp * compiling SingleLineDelimTextFileReader.cpp * compiling EmptyRecord.cpp * compiling FileRecordMergeMgr.cpp * compiling Bed3Interval.cpp * compiling BamFileReader.cpp * compiling FileRecordMgr.cpp * compiling Bed4Interval.cpp * compiling BufferedStreamMgr.cpp * compiling FileRecordMergeMgr.cpp * compiling BedGraphInterval.cpp * compiling InputStreamMgr.cpp - Building in FileReaders * compiling InputStreamMgr.cpp * compiling Bed5Interval.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BinTree make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BinTree.cpp * compiling Bed6Interval.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/version make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' - Building in Records * compiling version.cpp * compiling Bed6Interval.cpp * compiling PlusFields.cpp * compiling PlusFields.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedGraphFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bedGraphFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/chromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling chromsweep.cpp * compiling BedPlusInterval.cpp * compiling BedPlusInterval.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Contexts make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling ContextBase.cpp * compiling Bed12Interval.cpp * compiling Bed12Interval.cpp * compiling BamRecord.cpp * compiling BamRecord.cpp * compiling ContextIntersect.cpp * compiling GffRecord.cpp * compiling GffRecord.cpp * compiling ContextFisher.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/general make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling ParseTools.cpp * compiling GffPlusRecord.cpp * compiling GffPlusRecord.cpp * compiling ContextMap.cpp * compiling PushBackStreamBuf.cpp * compiling VcfRecord.cpp * compiling CompressionTools.cpp * compiling VcfRecord.cpp * compiling ContextSample.cpp * compiling Tokenizer.cpp * compiling NoPosPlusRecord.cpp * compiling NoPosPlusRecord.cpp * compiling CommonHelp.cpp * compiling ContextSpacing.cpp * compiling BlockMgr.cpp * compiling BlockMgr.cpp * compiling ContextMerge.cpp * compiling StrandQueue.cpp * compiling StrandQueue.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/gzstream make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling RecordMgr.cpp * compiling ContextJaccard.cpp g++ -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ../../../obj//gzstream.o gzstream.C -I. * compiling RecordList.cpp * compiling RecordMgr.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/fileType make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling fileType.cpp * compiling ContextClosest.cpp * compiling FileRecordTypeChecker.cpp * compiling ContextSubtract.cpp * compiling RecordKeyList.cpp FileRecordTypeChecker.cpp: In member function ‘bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)’: FileRecordTypeChecker.cpp:365:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; j < len; j++) { ~~^~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFilePE make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bedFilePE.cpp * compiling ContextCoverage.cpp * compiling RecordList.cpp * compiling RecordKeyVector.cpp * compiling RecordKeyList.cpp * compiling ContextComplement.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/KeyListOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling KeyListOps.cpp * compiling RecordKeyVector.cpp * compiling ContextGroupBy.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/NewChromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling NewChromsweep.cpp * compiling CloseSweep.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/sequenceUtilities make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling sequenceUtils.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/tabFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling tabFile.cpp * compiling KeyListOpsMethods.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamAlignment.cpp * compiling BamMultiReader.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools-Ancillary make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamAncillary.cpp * compiling BamReader.cpp * compiling BamWriter.cpp * compiling BamAncillary.cpp * compiling SamHeader.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BlockedIntervals make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BlockedIntervals.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Fasta make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling Fasta.cpp * compiling SamProgram.cpp * compiling SamProgramChain.cpp * compiling split.cpp * compiling SamReadGroup.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/VectorOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling VectorOps.cpp * compiling SamReadGroupDictionary.cpp Fasta.cpp: In member function ‘std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)’: Fasta.cpp:290:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), seqlen, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp: In member function ‘std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)’: Fasta.cpp:332:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), (off_t) seqlen, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling SamSequence.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/GenomeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling GenomeFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/RecordOutputMgr make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling RecordOutputMgr.cpp * compiling SamSequenceDictionary.cpp GenomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: GenomeFile.cpp:60:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] long c2; ^~ * compiling NewGenomeFile.cpp * compiling BamHeader_p.cpp * compiling BamMultiReader_p.cpp * compiling BamRandomAccessController_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/ToolBase make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling ToolBase.cpp * compiling BamReader_p.cpp * compiling BamWriter_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/driver make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BedtoolsDriver.cpp * compiling BamIndexFactory_p.cpp * compiling BamStandardIndex_p.cpp * compiling BamToolsIndex_p.cpp * compiling BamDeviceFactory_p.cpp * compiling BamFile_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/annotateBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling annotateMain.cpp * compiling BamFtp_p.cpp * compiling BamHttp_p.cpp annotateMain.cpp: In function ‘int annotate_main(int, char**)’: annotateMain.cpp:39:10: warning: variable ‘haveTitles’ set but not used [-Wunused-but-set-variable] bool haveTitles = false; ^~~~~~~~~~ * compiling annotateBed.cpp src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’: src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) ) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling BamPipe_p.cpp * compiling BgzfStream_p.cpp src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendRequest(size_t)’: src/api/internal/io/BamHttp_p.cpp:396:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize ); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ * compiling ByteArray_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bamToBed.cpp * compiling HostAddress_p.cpp * compiling HostInfo_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToFastq make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bamToFastqMain.cpp src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’: src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if ( i != 0 ) ^~ src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | ^~ * compiling bamToFastq.cpp * compiling HttpHeader_p.cpp bamToFastqMain.cpp: In function ‘int bamtofastq_main(int, char**)’: bamToFastqMain.cpp:38:10: warning: variable ‘haveFastq2’ set but not used [-Wunused-but-set-variable] bool haveFastq2 = false; ^~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bedToBam.cpp bamToBed.cpp: In function ‘int bamtobed_main(int, char**)’: bamToBed.cpp:88:10: warning: variable ‘useAlignmentScore’ set but not used [-Wunused-but-set-variable] bool useAlignmentScore = false; ^~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedpeToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bedpeToBam.cpp * compiling ILocalIODevice_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToIgv make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bedToIgv.cpp * compiling RollingBuffer_p.cpp bedToBam.cpp: In function ‘int bedtobam_main(int, char**)’: bedToBam.cpp:60:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bed12ToBed6 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bed12ToBed6.cpp * compiling TcpSocketEngine_p.cpp * compiling TcpSocketEngine_unix_p.cpp bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’: bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/closestFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling closestHelp.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/clusterBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling clusterMain.cpp * compiling TcpSocket_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/complementFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling complementHelp.cpp * compiling closestFile.cpp * compiling complementFile.cpp clusterMain.cpp: In function ‘int cluster_main(int, char**)’: clusterMain.cpp:38:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable] bool haveMaxDistance = false; ^~~~~~~~~~~~~~~ * compiling clusterBed.cpp * compiling SamFormatParser_p.cpp * compiling SamFormatPrinter_p.cpp * compiling SamHeaderValidator_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/coverageFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling coverageHelp.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/expand make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling expand.cpp * compiling coverageFile.cpp * compiling BamException_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling fastaFromBedMain.cpp * linking lib/libbamtools.a ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o ranlib lib/libbamtools.a * compiling fastaFromBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/flankBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling flankBedMain.cpp * compiling flankBed.cpp coverageFile.cpp: In member function ‘virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)’: coverageFile.cpp:100:11: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] asprintf(&depthPctString, "%0.7f", depthPct); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coverageFile.cpp: In member function ‘void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)’: coverageFile.cpp:181:10: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] asprintf(&meanString, "%0.7f", mean); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coverageFile.cpp: In member function ‘void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)’: coverageFile.cpp:210:11: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] asprintf(&coveredFractionString, "%0.7f", coveredFraction); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coverageFile.cpp: In member function ‘void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)’: coverageFile.cpp:230:10: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] asprintf(&coveredFractionString, "%0.7f", coveredFraction); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/genomeCoverageBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling genomeCoverageMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/getOverlap make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling getOverlap.cpp * compiling genomeCoverageBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/groupBy make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling groupBy.cpp getOverlap.cpp: In function ‘int getoverlap_main(int, char**)’: getOverlap.cpp:44:10: warning: variable ‘haveColumns’ set but not used [-Wunused-but-set-variable] bool haveColumns = false; ^~~~~~~~~~~ * compiling groupByHelp.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/intersectFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling intersectHelp.cpp * compiling intersectFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fisher make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling fisherHelp.cpp * compiling fisher.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/jaccard make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling jaccardHelp.cpp genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::CoverageBam(std::__cxx11::string)’: genomeCoverageBed.cpp:322:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(end<_fragmentSize) { //sometimes fragmentSize is bigger :( ~~~^~~~~~~~~~~~~~ * compiling kfunc.cpp * compiling jaccard.cpp intersectFile.cpp: In member function ‘virtual void IntersectFile::processHits(RecordOutputMgr*, RecordKeyVector&)’: intersectFile.cpp:70:33: warning: variable ‘hitListIter’ set but not used [-Wunused-but-set-variable] RecordKeyVector::iterator_type hitListIter = hits.begin(); ^~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/linksBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling linksMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/maskFastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling maskFastaFromBedMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mapFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling mapHelp.cpp * compiling linksBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mergeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling mergeHelp.cpp * compiling maskFastaFromBed.cpp * compiling mapFile.cpp * compiling mergeFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiBamCov make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling multiBamCovMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiIntersectBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling multiIntersectBedMain.cpp * compiling multiBamCov.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/nucBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling nucBedMain.cpp multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’: multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable] bool haveBed = false; ^~~~~~~ multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable] bool haveBams = false; ^~~~~~~~ multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling pairToBedMain.cpp multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’: multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ * compiling multiIntersectBed.cpp * compiling nucBed.cpp * compiling pairToBed.cpp pairToBedMain.cpp: In function ‘int pairtobed_main(int, char**)’: pairToBedMain.cpp:43:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToPair make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling pairToPairMain.cpp * compiling pairToPair.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/randomBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling randomBedMain.cpp pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’: pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ * compiling randomBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/regressTest make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' compiling RegressTest.cpp pairToBed.cpp: In member function ‘void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)’: pairToBed.cpp:257:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable] CHRPOS spanLength = 0; ^~~~~~~~~~ pairToBed.cpp: In member function ‘bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)’: pairToBed.cpp:310:9: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable] int spanLength = 0; ^~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/reldist make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling reldistMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sampleFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling sampleHelp.cpp pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’: pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable] bool found1 = false; ^~~~~~ pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable] bool found2 = false; ^~~~~~ * compiling sampleFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shiftBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling shiftBedMain.cpp * compiling reldist.cpp * compiling shiftBed.cpp RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’: RegressTest.cpp:431:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’: RegressTest.cpp:573:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’: RegressTest.cpp:622:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ compiling regressTestMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shuffleBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling shuffleBedMain.cpp * compiling shuffleBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/slopBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling slopBedMain.cpp * compiling slopBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sortBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling sortMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/spacingFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling spacingHelp.cpp * compiling spacingFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/split make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling splitBed.cpp * compiling sortBed.cpp * compiling splitBedMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/subtractFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling subtractHelp.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/tagBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling subtractFile.cpp * compiling tagBamMain.cpp * compiling tagBam.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/unionBedGraphs make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling unionBedGraphsMain.cpp * compiling unionBedGraphs.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling windowMain.cpp unionBedGraphsMain.cpp: In function ‘int unionbedgraphs_main(int, char**)’: unionBedGraphsMain.cpp:46:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ unionBedGraphsMain.cpp:48:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ unionBedGraphsMain.cpp:49:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ * compiling windowBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowMaker make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling windowMakerMain.cpp * compiling windowMaker.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building main bedtools binary. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Creating executables for old CLI. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_auto_test -a make -j4 -Oline test make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' $CXXFLAGS is [-Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11] Building BEDTools: make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' ========================================================= make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * Creating BamTools API make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' DETECTED_VERSION = v2.27.1 CURRENT_VERSION = v2.27.1 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/FileReaders make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/Records make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//bedFile.o' is up to date. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BinTree make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/version make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' - Building in FileReaders make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedGraphFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//BinTree.o' is up to date. make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//bedGraphFile.o' is up to date. make[3]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Contexts make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' - Building in Records make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/chromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/general make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[3]: Nothing to be done for 'all'. make[2]: '../../../obj//chromsweep.o' is up to date. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/gzstream make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFilePE make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/fileType make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//gzstream.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/KeyListOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//bedFilePE.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. - Building in src/utils/NewChromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/sequenceUtilities make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/tabFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools-Ancillary make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//sequenceUtils.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BlockedIntervals make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//tabFile.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Fasta make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/VectorOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/GenomeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//VectorOps.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/RecordOutputMgr make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//NewGenomeFile.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/driver make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/ToolBase make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/annotateBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//RecordOutputMgr.o' is up to date. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//ToolBase.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToFastq make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedpeToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToIgv make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bed12ToBed6 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/closestFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/complementFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/coverageFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/clusterBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/expand make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/genomeCoverageBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/flankBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/getOverlap make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/groupBy make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/intersectFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/jaccard make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fisher make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/linksBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/maskFastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mapFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mergeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiBamCov make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiIntersectBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/nucBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToPair make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/randomBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/regressTest make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/reldist make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sampleFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shiftBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shuffleBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. compiling RegressTest.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/slopBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sortBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/split make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/subtractFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/spacingFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/tagBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/unionBedGraphs make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowMaker make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’: RegressTest.cpp:431:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’: RegressTest.cpp:573:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’: RegressTest.cpp:622:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ compiling regressTestMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building main bedtools binary. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Creating executables for old CLI. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' Testing bedtools bamtobed: bamtobed.t1...ok bamtobed.t2...ok bamtobed.t3...ok bamtobed.t4...ok bamtobed.t5...ok bamtobed.t6...ok bamtobed.t7...ok bamtobed.t8...ok bamtobed.t9...ok bamtobed.t10...ok bamtobed.t9...ok bamtobed.t11...ok Testing bedtools bamtofastq: ok ok Testing bedtools bed12tobed6: bed12tobed6.t1...ok bed12tobed6.t2...ok bed12tobed6.t3...ok bed12tobed6.t4...ok bed12tobed6.t5...ok Testing bedtools closest: closest.t1...ok closest.t2...ok closest.t3...ok closest.t4...ok closest.t5...ok closest.t6...ok closest.t7...ok closest.t8...ok closest.t9...ok closest.t10...ok closest.t11...ok closest.t13...ok closest.t14...ok closest.t15...ok closest.t16...ok closest.t17...ok closest.t18...ok closest.t19...ok closest.t20...ok closest.t21...ok closest.t22...ok closest.t23...ok closest.t24...ok closest.t25...ok closest.t26...ok closest.t27...ok closest.t28...ok closest.t29...ok closest.t30...ok closest.t31...ok closest.t32...ok closest.t33...ok closest.t34...ok closest.t35...ok closest.t36...ok closest.t37...ok closest.t38...ok closest.t39...ok closest.t40...ok closest.t41...ok closest.t42...ok closest.t43...ok closest.t44...ok closest.t45...ok closest.t46...ok closest.t47...ok closest.t48...ok closest.t49...ok closest.t50...ok closest.t51...ok closest.t52...ok closest.t53...ok closest.t54...ok closest.t55...ok closest.t56...ok closest.t57...ok closest.t58...ok closest.t59...ok closest.t60...ok closest.t61...ok closest.t62...ok closest.t63...ok closest.t64...ok closest.t65...ok closest.t66...ok closest.t67...ok closest.t68...ok closest.t69...ok closest.t70...ok closest.t71...ok ########################################################### # # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS # ########################################################### closest.t01...ok closest.t02...ok closest.t03...ok closest.t04...ok closest.t05...ok closest.t06...ok closest.t07...ok closest.t08...ok closest.t09...ok closest.t10...ok closest.t11...ok closest.t12...ok closest.t13...ok closest.t14...ok closest.t15...ok closest.t16...ok closest.t17...ok closest.t18...ok closest.t19...ok closest.20...ok closest.21...ok closest.22...ok closest.23...ok ########################################################### # # K CLOSEST HITS TESTS # ########################################################### kclosest.t1...ok kclosest.t2...ok kclosest.t3...ok kclosest.t4...ok kclosest.t5...ok kclosest.t6...ok kclosest.t7...ok kclosest.t8...ok kclosest.t9...ok kclosest.t10...ok kclosest.t11...ok kclosest.t12...ok kclosest.t13...ok kclosest.t14...ok kclosest.t15...ok kclosest.t16...ok kclosest.t17...ok kclosest.t18...ok kclosest.t19...ok kclosest.t20...ok kclosest.t21...ok kclosest.t22...ok kclosest.t23...ok kclosest.t24...ok kclosest.t25...ok kclosest.t26...ok kclosest.t27...ok kclosest.t28...ok kclosest.t29...ok kclosest.t30...ok kclosest.t31...ok kclosest.t32...ok kclosest.t33...ok kclosest.t34...ok kclosest.t35...ok kclosest.t36...ok kclosest.t37...ok kclosest.t38...ok kclosest.t39...ok kclosest.t40...ok kclosest.t41...ok kclosest.t42...ok kclosest.t43...ok kclosest.t44...ok kclosest.t45...ok Testing bedtools cluster: cluster.t1...ok cluster.t2...ok Testing bedtools complement: complement.t1...ok complement.t2...ok complement.t3...ok complement.t4...ok complement.t5...ok complement.t6...ok complement.t7...ok complement.t8...ok complement.t9...ok Testing bedtools coverage: coverage.t1...ok coverage.t1b...ok coverage.t2...ok coverage.t2b...ok coverage.t3...ok coverage.t3b...ok coverage.t4...ok coverage.t4b...ok coverage.t5...ok coverage.t5b...ok coverage.t6...ok coverage.t6b...ok coverage.t7...ok coverage.t7b...ok coverage.t8...ok coverage.t8b...ok coverage.t9...ok coverage.t9b...ok coverage.t10...ok coverage.t10b...ok coverage.t11...ok coverage.t11b...ok coverage.t12...ok coverage.t12b...ok coverage.t13...ok coverage.t13b...ok coverage.t14...ok coverage.t14b...ok coverage.t15...ok coverage.t15b...ok coverage.t16...ok coverage.t16b...ok coverage.t17...ok coverage.t17b...ok coverage.t18...ok coverage.t18b...ok coverage.t19...ok coverage.t19b...ok coverage.t20...ok Testing bedtools expand: expand.t1...ok expand.t2...ok expand.t3...ok Testing bedtools fisher: fisher.t1...ok fisher.t2...ok fisher.t3...ok fisher.t4...ok Testing bedtools flank: flank.t1...ok flank.t2...ok flank.t3...ok flank.t4...ok flank.t5...ok flank.t6...ok flank.t7...ok flank.t8...ok flank.t9...ok flank.t10...ok flank.t11...ok Testing bedtools general: general.t01...ok general.t02...ok general.t03...ok general.t05...ok general.t06...ok general.t07...ok general.t08...ok general.t09...ok general.t10...ok general.t11...ok general.t12...ok general.t13...ok general.t14...ok general.15...ok general.t16...ok general.t17...ok general.t18...ok general.t19...ok general.t20...ok general.t21...ok general.22...ok general.t23...ok general.t24...ok general.t25...ok general.t26...ok general.t27...ok general.t28...ok general.29...ok general.t30...ok general.t31...ok general.t32...ok general.t33...ok general.t34...ok general.t35...ok general.36...ok general.t37...ok general.t38...ok general.t39...ok general.t40...ok general.t41...ok general.t42...ok general.t43...ok general.t44...ok general.t45...ok general.t46...ok Testing bedtools genomecov: genomecov.t1...ok genomecov.t2...ok genomecov.t3...ok genomecov.t4...ok genomecov.t5...ok genomecov.t6...ok genomecov.t7...ok genomecov.t8...ok genomecov.t9...ok genomecov.t10...ok genomecov.t11...ok genomecov.t12...ok genomecov.t13...ok genomecov.t14...ok genomecov.t15...ok Testing bedtools getfasta: getfasta.t01...ok getfasta.t02...ok getfasta.t03...ok getfasta.t04...ok getfasta.t05...ok getfasta.t06...ok getfasta.t07...ok getfasta.t08...index file test.iupac.fa.fai not found, generating... ok getfasta.t09...index file test.iupac.fa.fai not found, generating... ok getfasta.t10...index file test.fa.fai not found, generating... ok getfasta.t11...ok getfasta.t12...ok getfasta.t13...ok getfasta.t14...ok getfasta.t15...ok getfasta.t134..ok Testing bedtools groupby: groupby.t1...ok groupby.t2...ok groupby.t3...ok groupby.t4...ok groupby.t5...ok groupby.t6...ok groupby.t7...ok groupby.t8...ok groupby.t9...ok groupby.t10...ok groupby.t11...ok groupby.t12...ok groupby.t13...ok groupby.t14...ok groupby.t16...ok groupby.t17...ok groupby.t18...ok groupby.t19...\c ok groupby.t20...\c ok Testing bedtools intersect: intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok intersect.t20...ok intersect.t21...ok intersect.t22...ok intersect.t22.a...ok intersect.t22.b...ok intersect.t22.c...ok intersect.t22.d...ok intersect.t22.e...ok intersect.t22.f...ok intersect.t22.g...ok intersect.t23...ok intersect.t24...ok intersect.t25...ok intersect.t26...ok intersect.t27...ok intersect.t28...ok intersect.t29...ok intersect.t30...ok intersect.t31...ok intersect.t32...ok intersect.t33...ok intersect.t34...ok intersect.t35...ok intersect.t36...ok intersect.t37...ok intersect.t38...ok intersect.t39...ok intersect.t40...ok intersect.t41...ok intersect.t42...ok intersect.t43...ok intersect.t44...ok intersect.t45...ok intersect.t46...ok intersect.t47...ok intersect.t48...ok intersect.t49...ok intersect.t50...ok intersect.t51...ok intersect.t52...ok intersect.t53...ok intersect.t54...ok intersect.t55...ok intersect.t56...ok intersect.t57...ok intersect.t58...ok intersect.t59...ok intersect.t60...ok intersect.t61...ok intersect.t62...ok intersect.t63...ok intersect.t64...ok intersect.t65...ok intersect.t66...ok intersect.t67...ok intersect.t68...ok intersect.t69...ok intersect.t70...ok intersect.t71...ok intersect.t72...ok intersect.t73...ok intersect.t74...ok intersect.t75...ok intersect.t76...ok intersect.t77...ok intersect.t78...ok intersect.t79...ok intersect.t80...ok intersect.t81...ok intersect.t82...ok intersect.new.t01...ok intersect.new.t02...ok intersect.new.t03...ok intersect.new.t04...ok intersect.new.t05...ok intersect.new.t06...ok intersect.new.t07...ok intersect.new.t08...ok intersect.new.t09...ok intersect.new.t10...ok intersect.new.t11...ok intersect.new.t12...ok intersect.new.t13...ok intersect.new.t14...ok intersect.new.t15...ok intersect.new.t16...ok intersect.new.t17...ok intersect.new.t18...ok intersect.new.t19...ok intersect.new.t20...ok intersect.new.t20.b...ok intersect.new.t20.c...ok intersect.new.t21...ok intersect.new.t22...ok intersect.new.t23...ok intersect.new.t24...ok intersect.new.t25...ok intersect.new.t26...ok intersect.new.t27...ok intersect.new.t28...ok intersect.new.t29...ok intersect.new.t30...ok intersect.new.t31...ok intersect.new.t32...ok intersect.new.t33...ok intersect.new.t34...ok intersect.new.t35...ok intersect.new.t36...ok intersect.new.t37...ok intersect.new.t38...ok intersect.new.t39...ok intersect.new.t40...ok intersect.new.t41...ok intersect.new.t42...ok intersect.new.t43...ok intersect.new.t44...ok intersect.new.t45...ok intersect.new.t46...ok intersect.new.t47...ok intersect.new.t48...ok intersect.new.t49...ok intersect.new.t50...ok intersect.new.t51...ok intersect.new.t52...ok intersect.new.t53...ok intersect.new.t54...ok intersect.new.t55...ok intersect.new.t56...ok intersect.new.t57...ok intersect.new.t58...ok intersect.new.t59...ok intersect.new.t60...ok intersect.new.t61...ok intersect.new.t62...ok intersect.new.t63...ok intersect.new.t64...ok intersect.new.t65...ok intersect.new.t66...ok intersect.new.t67a...ok intersect.new.t67b...ok intersect.new.t68a...ok intersect.new.t68b...ok intersect.new.t69...ok intersect.new.t70...ok intersect.new.t71...ok intersect.new.t72...ok ########################################################### # # MULTIPLE DATABASE INTERSECTION # ########################################################### intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok ########################################################### # # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS # ########################################################### intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok intersect.20...ok intersect.21...ok intersect.22...ok intersect.23...ok Testing bedtools jaccard: jaccard.t01...ok jaccard.t02...ok jaccard.t03...ok jaccard.t05...ok jaccard.t06...ok jaccard.t07...ok jaccard.t08...ok jaccard.t09...ok jaccard.t10...ok jaccard.t11...ok jaccard.t12...ok jaccard.t13...ok Testing bedtools makewindows: makewindows.t01...ok makewindows.t02...ok makewindows.t03...ok makewindows.t04...ok makewindows.t05...ok makewindows.t06...ok makewindows.t07...ok makewindows.t08...ok makewindows.t09...ok Testing bedtools map: map.t01...ok map.t02...ok map.t03...ok map.t04...ok map.t05...ok map.t06...ok map.t07...ok map.t08...ok map.t09...ok map.t10...ok map.t11...ok map.t12...ok map.t13...ok map.t14...ok map.t15...ok map.t16...ok map.t17...ok map.t18...ok map.t19...ok map.t20...ok map.t21...ok map.t22..ok map.t23..ok map.t24..ok map.t25..ok map.t26..ok map.t27..ok map.t28..ok map.t29..ok map.t30..ok map.t31..ok map.t32..ok map.t33..ok map.t33..ok map.t33..ok map.t34..ok map.t35..ok map.t36..ok map.t37..ok map.t38..ok map.t39..ok map.t40..ok map.t41..ok map.t42..ok map.t43..ok map.t44...ok map.t45...ok map.t46...ok map.t47...ok map.t48...ok map.t49...ok map.t50...ok map.t51...ok map.t52...ok map.t53...ok map.t54...ok map.t55...ok Testing bedtools merge: merge.t1...ok merge.t2...ok merge.t3...ok merge.t4...ok merge.t5...ok merge.t6...ok merge.t7...ok merge.t8...ok merge.t9a...ok merge.t9b...ok merge.t10...ok merge.t11...ok merge.t12...ok merge.t13...ok merge.t14...ok merge.t15...ok merge.t16...ok merge.t17...ok merge.t18...ok merge.t19...ok merge.t20...ok merge.t21...ok merge.t22...ok merge.t23a...ok merge.t23b...ok merge.t24...ok merge.t25...ok merge.t26...ok merge.t27...ok merge.t28...ok merge.t29...ok merge.t30...ok merge.t31...ok merge.t32...ok merge.t33...ok merge.t34...ok merge.t35...ok merge.t36...ok merge.t37...ok merge.t38...ok merge.t39...ok merge.t40...ok merge.t41...ok merge.t42...ok merge.t43...ok merge.t44a...ok merge.t44b...skipped - could not find vcfSVtest.2.vcf merge.t45...ok merge.t46...ok merge.t47...ok merge.t48...ok merge.t49...ok Testing bedtools multicov: multicov.t1...ok multicov.t2...ok multicov.t3...ok multicov.t4...ok multicov.t5...ok multicov.t6...ok multicov.t7...ok multicov.t8...ok multicov.t9...ok Testing bedtools negativecontrol: Testing bedtools reldist: reldist.t01...ok reldist.t02...ok reldist.t03...ok Testing bedtools sample: sample.t01...ok sample.new.t02...ok sample.new.t03...ok sample.new.t04...ok sample.new.t05...ok sample.new.t06...ok sample.new.t07...ok sample.new.t08...ok sample.new.t09...ok Testing bedtools shift: shift.t1...ok shift.t2...ok shift.t3...ok shift.t3...ok shift.t4...ok shift.t5...ok shift.t6...ok shift.t7...ok shift.t8...ok shift.t9...ok shift.t10...ok Testing bedtools shuffle: shuffle.t1...ok shuffle.t2...ok shuffle.t3...ok shuffle.t4...ok shuffle.t5...ok shuffle.t6...ok Testing bedtools slop: slop.t1...ok slop.t2...ok slop.t3...ok slop.t4...ok slop.t5...ok slop.t6...ok slop.t7...ok slop.t8...ok slop.t9...ok slop.t10...ok slop.t11...ok slop.t12...ok slop.t13...ok slop.t14...ok slop.t15...ok slop.t16...ok slop.t17...ok slop.t18...ok slop.t19...ok slop.t20...ok slop.t21...ok slop.t22...ok Testing bedtools sort: sort.t01...ok sort.t02...ok sort.t03...ok sort.t04...ok sort.t05...ok sort.t06...ok sort.t07...ok sort.t08...ok sort.t09...ok sort.t10...ok Testing bedtools spacing: spacing.t01...ok Testing bedtools split: split.01.size...ok split.02.simple...ok spliit.03.simple...ok Testing bedtools subtract: subtract.t1...ok subtract.t2...ok subtract.t3...ok subtract.t4...ok subtract.t5...ok subtract.t6...ok subtract.t7...ok subtract.t8...ok subtract.t9...ok subtract.t10...ok subtract.t11...ok subtract.t12...ok subtract.t13...ok subtract.t14...ok subtract.t15...ok subtract.t16...ok subtract.t17...ok subtract.t18...ok subtract.t19...ok subtract.t20...ok subtract.t21...ok -------------------------- Test Results -------------------------- Tools passing: bamtobed bamtofastq bed12tobed6 closest cluster complement coverage expand fisher flank general genomecov getfasta groupby intersect jaccard makewindows map merge multicov reldist sample shift shuffle slop sort spacing split subtract Tools failing: negativecontrol NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, something went wrong with this test script. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a rm -f -- debian/bedtools.substvars rm -fr -- debian/.debhelper/generated/bedtools/ debian/bedtools/ debian/tmp/ dh_auto_install -a install -d /<>/bedtools-2.27.1\+dfsg/debian/tmp make -j4 -Oline install DESTDIR=/<>/bedtools-2.27.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' $CXXFLAGS is [-Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11] Building BEDTools: make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' ========================================================= make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * Creating BamTools API make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' DETECTED_VERSION = v2.27.1 CURRENT_VERSION = v2.27.1 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/FileReaders make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/Records make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//bedFile.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BinTree make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in FileReaders make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/version make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedGraphFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//BinTree.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/chromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[3]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//bedGraphFile.o' is up to date. - Building in Records make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Contexts make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/general make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//chromsweep.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/gzstream make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[3]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/fileType make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//gzstream.o' is up to date. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFilePE make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/KeyListOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/NewChromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/sequenceUtilities make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//bedFilePE.o' is up to date. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//sequenceUtils.o' is up to date. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/tabFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BlockedIntervals make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools-Ancillary make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//tabFile.o' is up to date. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Fasta make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/VectorOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/GenomeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/RecordOutputMgr make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/ToolBase make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//VectorOps.o' is up to date. make[2]: '../../../obj//RecordOutputMgr.o' is up to date. make[2]: '../../../obj//NewGenomeFile.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/driver make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/annotateBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//ToolBase.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToFastq make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedpeToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToIgv make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bed12ToBed6 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/closestFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/complementFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/clusterBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/coverageFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/expand make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/flankBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/genomeCoverageBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/intersectFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/groupBy make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/getOverlap make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fisher make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/jaccard make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/linksBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/maskFastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mapFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mergeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. - Building in src/multiBamCov make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiIntersectBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/nucBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToPair make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/randomBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/regressTest make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/reldist make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. compiling RegressTest.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sampleFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shiftBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shuffleBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/slopBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/spacingFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/split make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sortBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/tagBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/subtractFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/unionBedGraphs make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowMaker make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’: RegressTest.cpp:431:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’: RegressTest.cpp:573:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’: RegressTest.cpp:622:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ compiling regressTestMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building main bedtools binary. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Creating executables for old CLI. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' mkdir -p /<>/bedtools-2.27.1+dfsg/debian/tmp/usr/local/bin make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' for file in bin/* ; do \ cp -f $file /<>/bedtools-2.27.1+dfsg/debian/tmp/usr/local/bin; \ done make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' dh_install install -d debian/bedtools//usr/share/bash-completion/completions cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools//usr/share/bash-completion/completions/ install -d debian/bedtools/usr/bin cp --reflink=auto -a ./bin/annotateBed ./bin/bamToBed ./bin/bamToFastq ./bin/bed12ToBed6 ./bin/bedToBam ./bin/bedToIgv ./bin/bedpeToBam ./bin/bedtools ./bin/closestBed ./bin/clusterBed ./bin/complementBed ./bin/coverageBed ./bin/expandCols ./bin/fastaFromBed ./bin/flankBed ./bin/genomeCoverageBed ./bin/getOverlap ./bin/groupBy ./bin/intersectBed ./bin/linksBed ./bin/mapBed ./bin/maskFastaFromBed ./bin/mergeBed ./bin/multiBamCov ./bin/multiIntersectBed ./bin/nucBed ./bin/pairToBed ./bin/pairToPair ./bin/randomBed ./bin/shiftBed ./bin/shuffleBed ./bin/slopBed ./bin/sortBed ./bin/subtractBed ./bin/tagBam ./bin/unionBedGraphs ./bin/windowBed ./bin/windowMaker debian/bedtools/usr/bin/ install -d debian/bedtools/usr/share/bedtools cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/ install -d debian/.debhelper/generated/bedtools install -d debian/.debhelper/generated/bedtools-test # make sure all *.sh files are featuring a '#!/bin/bash' as first line # since there are at least two files (test/intersect/{new_test-intersect.sh,performanceTest.sh} # requiring bash this is taken for all scripts instead of checking first via /bin/sh -n for sh in `find /<>/bedtools-2.27.1+dfsg/debian -name "*.sh"` ; do \ if ! head -n1 ${sh} | grep -q '^#! */bin/[ba]*sh' ; then \ sed -i '1 i #!/bin/bash' ${sh} ; \ fi ; \ done make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_installdocs -a install -d debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./README.md debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/README.test debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/tests/run-unit-test debian/bedtools/usr/share/doc/bedtools chown -R 0:0 debian/bedtools/usr/share/doc chmod -R u\+rw,go=rX debian/bedtools/usr/share/doc install -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright rm -f debian/bedtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' dh_installchangelogs RELEASE_HISTORY install -p -m0644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian install -p -m0644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/bedtools chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian cd '/<>/bedtools-2.27.1+dfsg' rm -f debian/bedtools.debhelper.log debian/rules override_dh_fixperms-arch make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' dh_fixperms find debian/bedtools -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/bedtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/bedtools/usr/share/doc -type f -a -true -a ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/bedtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x chmod -x /<>/bedtools-2.27.1+dfsg/debian/bedtools/usr/share/bedtools/genomes/*.genome find /<>/bedtools-2.27.1+dfsg/debian -name "*.bed" -executable -exec chmod -x \{\} \; find /<>/bedtools-2.27.1+dfsg/debian -name "*.sh" -not -executable -exec chmod +x \{\} \; make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_missing -a dh_strip -a install -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/b7 objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/b7/562ecb3ee3f04e32e6807f26519f2d73034fba.debug chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/b7/562ecb3ee3f04e32e6807f26519f2d73034fba.debug chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/b7/562ecb3ee3f04e32e6807f26519f2d73034fba.debug strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools objcopy --add-gnu-debuglink debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/b7/562ecb3ee3f04e32e6807f26519f2d73034fba.debug debian/bedtools/usr/bin/bedtools install -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym dh_makeshlibs -a rm -f debian/bedtools/DEBIAN/shlibs dh_shlibdeps -a install -d debian/bedtools/DEBIAN dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/bedtools.substvars echo misc:Pre-Depends= >> debian/bedtools.substvars install -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=b7562ecb3ee3f04e32e6807f26519f2d73034fba -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools -UMulti-Arch chmod 0644 -- debian/bedtools/DEBIAN/control chown 0:0 -- debian/bedtools/DEBIAN/control dh_md5sums -a (cd debian/bedtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null chmod 0644 -- debian/bedtools/DEBIAN/md5sums chown 0:0 -- debian/bedtools/DEBIAN/md5sums (cd debian/.debhelper/bedtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --build debian/bedtools .. install -d debian/.debhelper/scratch-space/build-bedtools dpkg-deb --build debian/.debhelper/bedtools/dbgsym-root debian/.debhelper/scratch-space/build-bedtools INFO: pkgstriptranslations version 139 INFO: pkgstriptranslations version 139 pkgstriptranslations: processing bedtools (in debian/bedtools); do_strip: , oemstrip: pkgstriptranslations: processing bedtools-dbgsym (in debian/.debhelper/bedtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/bedtools/DEBIAN/control, package bedtools, directory debian/bedtools .. removing usr/share/doc/bedtools/changelog.gz pkgstripfiles: processing control file: debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control, package bedtools-dbgsym, directory debian/.debhelper/bedtools/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package bedtools-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'bedtools-dbgsym' in 'debian/.debhelper/scratch-space/build-bedtools/bedtools-dbgsym_2.27.1+dfsg-2_ppc64el.deb'. pkgstripfiles: Truncating usr/share/doc/bedtools/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package bedtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'bedtools' in '../bedtools_2.27.1+dfsg-2_ppc64el.deb'. Renaming bedtools-dbgsym_2.27.1+dfsg-2_ppc64el.deb to bedtools-dbgsym_2.27.1+dfsg-2_ppc64el.ddeb mv debian/.debhelper/scratch-space/build-bedtools/bedtools-dbgsym_2.27.1\+dfsg-2_ppc64el.deb ../bedtools-dbgsym_2.27.1\+dfsg-2_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../bedtools_2.27.1+dfsg-2_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build bedtools-2.27.1+dfsg dpkg-source: info: using options from bedtools-2.27.1+dfsg/debian/source/options: --single-debian-patch dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180523-0513 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedtools_2.27.1+dfsg-2_ppc64el.changes: --------------------------------------- Format: 1.8 Date: Tue, 22 May 2018 21:31:56 +0200 Source: bedtools Binary: bedtools bedtools-test Architecture: ppc64el Version: 2.27.1+dfsg-2 Distribution: cosmic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Liubov Chuprikova Description: bedtools - suite of utilities for comparing genomic features bedtools-test - test data for the bedtools package Closes: 894781 Changes: bedtools (2.27.1+dfsg-2) unstable; urgency=medium . * Team upload . [ Andreas Tille ] * Install autopkgtest script as /usr/share/doc/bedtools/run-unit-test * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * Drop useless get-orig-source target . [ Liubov Chuprikova ] * Fix "autopkgtest fails while it succeeded in the past" updated run-unit-test to match new upstream tests Closes: #894781 Checksums-Sha1: aa6c6ce0ecc387487b18acf4baf499fd7c1f51b1 57080 bedtools-dbgsym_2.27.1+dfsg-2_ppc64el.ddeb ff40ad6c6afbe5effc88c9a0ebfbd8573b6e4a3c 6505 bedtools_2.27.1+dfsg-2_ppc64el.buildinfo ca8c7c818710803fb7c89f414f7a1ffadd56be48 597964 bedtools_2.27.1+dfsg-2_ppc64el.deb Checksums-Sha256: d8eebe2bd6ceb4a01ca0cb0e415b9b845cca3a5262555e69c39bd4b453fd6a33 57080 bedtools-dbgsym_2.27.1+dfsg-2_ppc64el.ddeb 71a9a843d3b4ec1619de2bb71488c3ce76c003df67989907298a6d847c46f7db 6505 bedtools_2.27.1+dfsg-2_ppc64el.buildinfo cbcfa580fcd845c037d7cb2c19a96dcbbeba5a9cd0c8072bdd8d41b63a3f3b81 597964 bedtools_2.27.1+dfsg-2_ppc64el.deb Files: 95b48034f86b79a857173ad2319e2b93 57080 debug optional bedtools-dbgsym_2.27.1+dfsg-2_ppc64el.ddeb 375c078762f88edfdf2d69b385e44883 6505 science optional bedtools_2.27.1+dfsg-2_ppc64el.buildinfo a17aa32d795a240a69dc85ea91b99ad2 597964 science optional bedtools_2.27.1+dfsg-2_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedtools_2.27.1+dfsg-2_ppc64el.deb ---------------------------------- new debian package, version 2.0. size 597964 bytes: control archive=2192 bytes. 952 bytes, 21 lines control 2915 bytes, 50 lines md5sums Package: bedtools Version: 2.27.1+dfsg-2 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2471 Depends: libc6 (>= 2.23), libgcc1 (>= 1:4.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3) Conflicts: filo Replaces: filo Provides: filo Section: science Priority: optional Homepage: https://github.com/arq5x/bedtools2 Description: suite of utilities for comparing genomic features The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together. . The groupBy utility is distributed in the filo package. drwxr-xr-x root/root 0 2018-05-22 19:31 ./ drwxr-xr-x root/root 0 2018-05-22 19:31 ./usr/ drwxr-xr-x root/root 0 2018-05-22 19:31 ./usr/bin/ -rwxr-xr-x root/root 41 2018-05-22 19:31 ./usr/bin/annotateBed -rwxr-xr-x root/root 41 2018-05-22 19:31 ./usr/bin/bamToBed -rwxr-xr-x root/root 43 2018-05-22 19:31 ./usr/bin/bamToFastq -rwxr-xr-x root/root 44 2018-05-22 19:31 ./usr/bin/bed12ToBed6 -rwxr-xr-x root/root 41 2018-05-22 19:31 ./usr/bin/bedToBam -rwxr-xr-x root/root 36 2018-05-22 19:31 ./usr/bin/bedToIgv -rwxr-xr-x root/root 43 2018-05-22 19:31 ./usr/bin/bedpeToBam -rwxr-xr-x root/root 2427360 2018-05-22 19:31 ./usr/bin/bedtools -rwxr-xr-x root/root 40 2018-05-22 19:31 ./usr/bin/closestBed -rwxr-xr-x root/root 40 2018-05-22 19:31 ./usr/bin/clusterBed -rwxr-xr-x root/root 43 2018-05-22 19:31 ./usr/bin/complementBed -rwxr-xr-x root/root 41 2018-05-22 19:31 ./usr/bin/coverageBed -rwxr-xr-x root/root 39 2018-05-22 19:31 ./usr/bin/expandCols -rwxr-xr-x root/root 41 2018-05-22 19:31 ./usr/bin/fastaFromBed -rwxr-xr-x root/root 38 2018-05-22 19:31 ./usr/bin/flankBed -rwxr-xr-x root/root 42 2018-05-22 19:31 ./usr/bin/genomeCoverageBed -rwxr-xr-x root/root 40 2018-05-22 19:31 ./usr/bin/getOverlap -rwxr-xr-x root/root 40 2018-05-22 19:31 ./usr/bin/groupBy -rwxr-xr-x root/root 42 2018-05-22 19:31 ./usr/bin/intersectBed -rwxr-xr-x root/root 38 2018-05-22 19:31 ./usr/bin/linksBed -rwxr-xr-x root/root 36 2018-05-22 19:31 ./usr/bin/mapBed -rwxr-xr-x root/root 42 2018-05-22 19:31 ./usr/bin/maskFastaFromBed -rwxr-xr-x root/root 38 2018-05-22 19:31 ./usr/bin/mergeBed -rwxr-xr-x root/root 41 2018-05-22 19:31 ./usr/bin/multiBamCov -rwxr-xr-x root/root 43 2018-05-22 19:31 ./usr/bin/multiIntersectBed -rwxr-xr-x root/root 36 2018-05-22 19:31 ./usr/bin/nucBed -rwxr-xr-x root/root 42 2018-05-22 19:31 ./usr/bin/pairToBed -rwxr-xr-x root/root 43 2018-05-22 19:31 ./usr/bin/pairToPair -rwxr-xr-x root/root 39 2018-05-22 19:31 ./usr/bin/randomBed -rwxr-xr-x root/root 38 2018-05-22 19:31 ./usr/bin/shiftBed -rwxr-xr-x root/root 40 2018-05-22 19:31 ./usr/bin/shuffleBed -rwxr-xr-x root/root 37 2018-05-22 19:31 ./usr/bin/slopBed -rwxr-xr-x root/root 37 2018-05-22 19:31 ./usr/bin/sortBed -rwxr-xr-x root/root 41 2018-05-22 19:31 ./usr/bin/subtractBed -rwxr-xr-x root/root 36 2018-05-22 19:31 ./usr/bin/tagBam -rwxr-xr-x root/root 42 2018-05-22 19:31 ./usr/bin/unionBedGraphs -rwxr-xr-x root/root 39 2018-05-22 19:31 ./usr/bin/windowBed -rwxr-xr-x root/root 44 2018-05-22 19:31 ./usr/bin/windowMaker drwxr-xr-x root/root 0 2018-05-22 19:31 ./usr/share/ drwxr-xr-x root/root 0 2018-05-22 19:31 ./usr/share/bash-completion/ drwxr-xr-x root/root 0 2018-05-22 19:31 ./usr/share/bash-completion/completions/ -rw-r--r-- root/root 638 2018-05-22 19:31 ./usr/share/bash-completion/completions/bedtools drwxr-xr-x root/root 0 2018-05-22 19:31 ./usr/share/bedtools/ drwxr-xr-x root/root 0 2017-12-14 17:15 ./usr/share/bedtools/genomes/ -rw-r--r-- root/root 868 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg18.genome -rw-r--r-- root/root 1984 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg19.genome -rw-r--r-- root/root 11684 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg38.genome -rw-r--r-- root/root 1417 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm10.genome -rw-r--r-- root/root 577 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm8.genome -rw-r--r-- root/root 596 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm9.genome drwxr-xr-x root/root 0 2018-05-22 19:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-05-22 19:31 ./usr/share/doc/bedtools/ -rw-r--r-- root/root 3244 2017-12-14 17:15 ./usr/share/doc/bedtools/README.md -rw-r--r-- root/root 278 2018-05-22 19:31 ./usr/share/doc/bedtools/README.test -rw-r--r-- root/root 1809 2018-05-22 19:31 ./usr/share/doc/bedtools/changelog.Debian.gz -rw-r--r-- root/root 5343 2018-05-22 19:31 ./usr/share/doc/bedtools/copyright -rw-r--r-- root/root 398 2018-05-22 19:31 ./usr/share/doc/bedtools/run-unit-test +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 72464 Build-Time: 77 Distribution: cosmic-proposed Host Architecture: ppc64el Install-Time: 12 Job: bedtools_2.27.1+dfsg-2.dsc Machine Architecture: ppc64el Package: bedtools Package-Time: 91 Source-Version: 2.27.1+dfsg-2 Space: 72464 Status: successful Version: 2.27.1+dfsg-2 -------------------------------------------------------------------------------- Finished at 20180523-0513 Build needed 00:01:31, 72464k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=ppc64el PACKAGEBUILD-14925124 Scanning for processes to kill in build PACKAGEBUILD-14925124 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=cosmic --arch=ppc64el PACKAGEBUILD-14925124 Stopping target for build PACKAGEBUILD-14925124 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=cosmic --arch=ppc64el PACKAGEBUILD-14925124 Removing build PACKAGEBUILD-14925124