https://launchpad.net/ubuntu/+source/r-bioc-rsamtools/1.32.2-1/+build/15094779 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-017 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:52:48 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_163 python-lpbuildd_163 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_1:2.7.4-0ubuntu1.4 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 7 Jul 07:54:09 ntpdate[1858]: adjust time server 10.211.37.1 offset 0.000303 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15094779 /home/buildd/filecache-default/fc6c56f66744d62233b3c844f67cb7d83d839bbc Creating target for build PACKAGEBUILD-15094779 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15094779 Starting target for build PACKAGEBUILD-15094779 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15094779 '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-15094779 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15094779 Updating target for build PACKAGEBUILD-15094779 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 armhf Packages [970 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe armhf Packages [8376 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [5013 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf Packages [51.5 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [31.3 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe armhf Packages [128 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [86.6 kB] Fetched 15.6 MB in 7s (2353 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libncursesw5 libprocps6 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libargon2-1 libncurses6 libncursesw6 libprocps7 libtinfo6 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils build-essential cpp cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv libapparmor1 libapt-pkg5.0 libargon2-0 libasan4 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libkmod2 liblz4-1 libmount1 libncurses5 libncursesw5 libnpth0 libp11-kit0 libperl5.26 libreadline7 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libusb-0.1-4 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common systemd systemd-sysv tar tzdata util-linux 98 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 47.5 MB of archives. After this operation, 1721 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main armhf base-files armhf 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main armhf libtinfo6 armhf 6.1+20180210-4ubuntu1 [71.2 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main armhf debianutils armhf 4.8.6 [84.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main armhf bash armhf 4.4.18-2ubuntu2 [552 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main armhf bsdutils armhf 1:2.32-0.1ubuntu1 [55.5 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main armhf tar armhf 1.30+dfsg-2 [218 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main armhf dpkg armhf 1.19.0.5ubuntu3 [1096 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main armhf libext2fs2 armhf 1.44.2-1 [144 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main armhf e2fsprogs armhf 1.44.2-1 [369 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main armhf ncurses-bin armhf 6.1+20180210-4ubuntu1 [155 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main armhf perl-modules-5.26 all 5.26.2-6 [2762 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main armhf libperl5.26 armhf 5.26.2-6 [2870 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main armhf perl armhf 5.26.2-6 [202 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main armhf perl-base armhf 5.26.2-6 [1291 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main armhf libuuid1 armhf 2.32-0.1ubuntu1 [19.2 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main armhf libblkid1 armhf 2.32-0.1ubuntu1 [115 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main armhf libfdisk1 armhf 2.32-0.1ubuntu1 [155 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main armhf libncursesw6 armhf 6.1+20180210-4ubuntu1 [104 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libselinux1 armhf 2.8-1build1 [59.2 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main armhf libmount1 armhf 2.32-0.1ubuntu1 [125 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main armhf libsmartcols1 armhf 2.32-0.1ubuntu1 [76.2 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main armhf fdisk armhf 2.32-0.1ubuntu1 [98.7 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main armhf util-linux armhf 2.32-0.1ubuntu1 [858 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main armhf base-passwd armhf 3.5.45 [46.0 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main armhf ncurses-base all 6.1+20180210-4ubuntu1 [18.4 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main armhf libgomp1 armhf 8.1.0-9ubuntu1 [66.6 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc-8-base armhf 8.1.0-9ubuntu1 [18.9 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main armhf libgcc1 armhf 1:8.1.0-9ubuntu1 [37.1 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main armhf libcc1-0 armhf 8.1.0-9ubuntu1 [32.7 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main armhf libatomic1 armhf 8.1.0-9ubuntu1 [7052 B] Get:31 http://ftpmaster.internal/ubuntu cosmic/main armhf libstdc++6 armhf 8.1.0-9ubuntu1 [350 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main armhf liblz4-1 armhf 1.8.2-1ubuntu1 [76.1 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libudev1 armhf 238-5ubuntu2 [50.7 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main armhf libapt-pkg5.0 armhf 1.7.0~alpha1 [732 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf debconf all 1.5.67 [124 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main armhf adduser all 3.117ubuntu1 [163 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main armhf libgpg-error0 armhf 1.31-1 [48.5 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main armhf libgcrypt20 armhf 1.8.2-2ubuntu1 [364 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gpgv armhf 2.2.8-1ubuntu1 [167 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main armhf libseccomp2 armhf 2.3.3-3ubuntu1 [30.4 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main armhf apt armhf 1.7.0~alpha1 [1128 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libapparmor1 armhf 2.12-4ubuntu6 [27.1 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libaudit-common all 1:2.8.3-1ubuntu2 [4064 B] Get:44 http://ftpmaster.internal/ubuntu cosmic/main armhf libcap-ng0 armhf 0.7.9-1 [10.1 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libaudit1 armhf 1:2.8.3-1ubuntu2 [35.5 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libargon2-1 armhf 0~20171227-0.1 [20.7 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libargon2-0 armhf 0~20171227-0.1 [4536 B] Get:48 http://ftpmaster.internal/ubuntu cosmic/main armhf libcryptsetup12 armhf 2:2.0.2-1ubuntu2 [119 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main armhf libkmod2 armhf 25-1ubuntu1 [35.7 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main armhf mount armhf 2.32-0.1ubuntu1 [97.4 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses6 armhf 6.1+20180210-4ubuntu1 [78.5 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main armhf libprocps7 armhf 2:3.3.15-2ubuntu1 [29.6 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main armhf procps armhf 2:3.3.15-2ubuntu1 [219 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf systemd armhf 238-5ubuntu2 [2783 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libsystemd0 armhf 238-5ubuntu2 [189 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf systemd-sysv armhf 238-5ubuntu2 [13.7 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main armhf libcom-err2 armhf 1.44.2-1 [8404 B] Get:58 http://ftpmaster.internal/ubuntu cosmic/main armhf libsepol1 armhf 2.8-1 [219 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main armhf libsemanage-common all 2.8-1build1 [7000 B] Get:60 http://ftpmaster.internal/ubuntu cosmic/main armhf libsemanage1 armhf 2.8-1build1 [73.0 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main armhf libss2 armhf 1.44.2-1 [9392 B] Get:62 http://ftpmaster.internal/ubuntu cosmic/main armhf libgmp10 armhf 2:6.1.2+dfsg-3 [182 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main armhf libp11-kit0 armhf 0.23.12-2 [163 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main armhf libtasn1-6 armhf 4.13-3 [31.1 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses5 armhf 6.1+20180210-4ubuntu1 [74.9 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main armhf libncursesw5 armhf 6.1+20180210-4ubuntu1 [95.3 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main armhf libtinfo5 armhf 6.1+20180210-4ubuntu1 [67.6 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main armhf readline-common all 7.0-5 [52.2 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main armhf libreadline7 armhf 7.0-5 [102 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/main armhf libslang2 armhf 2.3.2-1ubuntu1 [383 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libsqlite3-0 armhf 3.24.0-1 [429 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main armhf libssl1.1 armhf 1.1.0g-2ubuntu5 [912 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main armhf openssl armhf 1.1.0g-2ubuntu5 [510 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main armhf tzdata all 2018e-1 [188 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main armhf libbinutils armhf 2.30-22ubuntu1 [309 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils-common armhf 2.30-22ubuntu1 [193 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils armhf 2.30-22ubuntu1 [3352 B] Get:78 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils-arm-linux-gnueabihf armhf 2.30-22ubuntu1 [2175 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main armhf libasan4 armhf 7.3.0-24ubuntu1 [328 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main armhf libubsan0 armhf 7.3.0-24ubuntu1 [108 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main armhf libcilkrts5 armhf 7.3.0-24ubuntu1 [35.9 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic/main armhf g++-7 armhf 7.3.0-24ubuntu1 [6051 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc-7 armhf 7.3.0-24ubuntu1 [5952 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic/main armhf libstdc++-7-dev armhf 7.3.0-24ubuntu1 [1537 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic/main armhf libgcc-7-dev armhf 7.3.0-24ubuntu1 [706 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic/main armhf cpp-7 armhf 7.3.0-24ubuntu1 [5294 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc-7-base armhf 7.3.0-24ubuntu1 [19.0 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic/main armhf cpp armhf 4:7.3.0-3ubuntu3 [27.6 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc armhf 4:7.3.0-3ubuntu3 [5228 B] Get:90 http://ftpmaster.internal/ubuntu cosmic/main armhf g++ armhf 4:7.3.0-3ubuntu3 [1600 B] Get:91 http://ftpmaster.internal/ubuntu cosmic/main armhf dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main armhf libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main armhf build-essential armhf 12.5ubuntu2 [4732 B] Get:94 http://ftpmaster.internal/ubuntu cosmic/main armhf e2fslibs armhf 1.44.2-1 [2700 B] Get:95 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf pinentry-curses armhf 1.1.0-1build2 [31.4 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main armhf libnpth0 armhf 1.5-4 [6648 B] Get:97 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gpg armhf 2.2.8-1ubuntu1 [411 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gpgconf armhf 2.2.8-1ubuntu1 [105 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gpg-agent armhf 2.2.8-1ubuntu1 [189 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic/main armhf libcomerr2 armhf 1.44.2-1 [2700 B] Get:101 http://ftpmaster.internal/ubuntu cosmic/main armhf libusb-0.1-4 armhf 2:0.1.12-32 [15.6 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf linux-libc-dev armhf 4.17.0-4.5 [978 kB] Get:103 http://ftpmaster.internal/ubuntu cosmic/main armhf pkgbinarymangler all 139 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.5 MB in 4s (12.3 MB/s) (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_armhf.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:armhf. (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-4ubuntu1_armhf.deb ... Unpacking libtinfo6:armhf (6.1+20180210-4ubuntu1) ... Setting up libtinfo6:armhf (6.1+20180210-4ubuntu1) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_armhf.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_armhf.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 ... 12387 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.32-0.1ubuntu1_armhf.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 ... 12387 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-2_armhf.deb ... Unpacking tar (1.30+dfsg-2) over (1.29b-2) ... Setting up tar (1.30+dfsg-2) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.5ubuntu3_armhf.deb ... Unpacking dpkg (1.19.0.5ubuntu3) over (1.19.0.5ubuntu2) ... Setting up dpkg (1.19.0.5ubuntu3) ... (Reading database ... 12387 files and directories currently installed.) 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Unpacking libperl5.26:armhf (5.26.2-6) over (5.26.1-6) ... Preparing to unpack .../perl-base_5.26.2-6_armhf.deb ... Unpacking perl-base (5.26.2-6) over (5.26.1-6) ... Setting up perl-base (5.26.2-6) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../libuuid1_2.32-0.1ubuntu1_armhf.deb ... Unpacking libuuid1:armhf (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up libuuid1:armhf (2.32-0.1ubuntu1) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../libblkid1_2.32-0.1ubuntu1_armhf.deb ... Unpacking libblkid1:armhf (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up libblkid1:armhf (2.32-0.1ubuntu1) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.32-0.1ubuntu1_armhf.deb ... Unpacking libfdisk1:armhf (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up libfdisk1:armhf (2.32-0.1ubuntu1) ... Selecting previously unselected package libncursesw6:armhf. (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20180210-4ubuntu1_armhf.deb ... Unpacking libncursesw6:armhf (6.1+20180210-4ubuntu1) ... Setting up libncursesw6:armhf (6.1+20180210-4ubuntu1) ... (Reading database ... 12396 files and directories currently installed.) Preparing to unpack .../libselinux1_2.8-1build1_armhf.deb ... Unpacking libselinux1:armhf (2.8-1build1) over (2.7-2build2) ... Setting up libselinux1:armhf (2.8-1build1) ... (Reading database ... 12396 files and directories currently installed.) Preparing to unpack .../libmount1_2.32-0.1ubuntu1_armhf.deb ... Unpacking libmount1:armhf (2.32-0.1ubuntu1) over (2.31.1-0.4ubuntu3) ... Setting up libmount1:armhf (2.32-0.1ubuntu1) ... (Reading database ... 12396 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.32-0.1ubuntu1_armhf.deb ... 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Setting up build-essential (12.5ubuntu2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15094779 armhf cosmic-proposed -c chroot:build-PACKAGEBUILD-15094779 --arch=armhf --dist=cosmic-proposed --nolog r-bioc-rsamtools_1.32.2-1.dsc Initiating build PACKAGEBUILD-15094779 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:52:48 UTC 2018 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-017.buildd +==============================================================================+ | r-bioc-rsamtools 1.32.2-1 (armhf) 07 Jul 2018 07:55 | +==============================================================================+ Package: r-bioc-rsamtools Version: 1.32.2-1 Source Version: 1.32.2-1 Distribution: cosmic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-R60naT/r-bioc-rsamtools-1.32.2' with '<>' I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-R60naT' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15094779/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- r-bioc-rsamtools_1.32.2-1.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-KH6Sup/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-KH6Sup/apt_archive ./ InRelease Get:2 copy:/<>/resolver-KH6Sup/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-KH6Sup/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-KH6Sup/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-KH6Sup/apt_archive ./ Packages [525 B] Fetched 2858 B in 49710d 6h 28min 15s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libncursesw5 libprocps6 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-KH6Sup/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 49710d 6h 28min 15s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12440 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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~), dh-r, r-base-dev, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<>/resolver-fAwxEz/apt_archive/sbuild-build-depends-r-bioc-rsamtools-dummy.deb'. Ign:1 copy:/<>/resolver-fAwxEz/apt_archive ./ InRelease Get:2 copy:/<>/resolver-fAwxEz/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-fAwxEz/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-fAwxEz/apt_archive ./ Sources [332 B] Get:5 copy:/<>/resolver-fAwxEz/apt_archive ./ Packages [646 B] Fetched 3097 B in 49710d 6h 28min 15s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install r-bioc-rsamtools build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libncursesw5 libprocps6 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils dctrl-tools debhelper default-libmysqlclient-dev dh-autoreconf dh-r dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gdal-data gettext gettext-base gfortran gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0 libarchive-zip-perl libarmadillo-dev libarmadillo8 libarpack2 libarpack2-dev libasn1-8-heimdal libblas-dev libblas3 libboost-dev libboost1.65-dev libbsd0 libbz2-dev libcairo2 libcharls-dev libcharls1 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdap-dev libdap25 libdapclient6v5 libdapserver7v5 libdatrie1 libelf1 libepsilon-dev libepsilon1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfreetype6 libfreexl-dev libfreexl1 libfribidi0 libfyba-dev libfyba0 libgdal-dev libgdal20 libgeos-3.6.2 libgeos-c1v5 libgeos-dev libgeotiff-dev libgeotiff2 libgfortran-7-dev libgfortran4 libgif-dev libgif7 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libhdf4-0-alt libhdf4-alt-dev libhdf5-100 libhdf5-cpp-100 libhdf5-dev libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libiculx60 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjson-c-dev libk5crypto3 libkeyutils1 libkml-dev libkmlbase1 libkmlconvenience1 libkmldom1 libkmlengine1 libkmlregionator1 libkmlxsd1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libminizip-dev libminizip1 libmpdec2 libmysqlclient-dev libmysqlclient20 libncurses-dev libncurses5-dev libnetcdf-dev libnetcdf13 libnghttp2-14 libnspr4 libnss3 libodbc1 libogdi3.2 libogdi3.2-dev libopenjp2-7 libopenjp2-7-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpoppler-dev libpoppler-private-dev libpoppler73 libpq-dev libpq5 libproj-dev libproj13 libpsl5 libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libqhull-dev libqhull-r7 libqhull7 libreadline-dev libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libspatialite-dev libspatialite7 libsqlite3-dev libsuperlu-dev libsuperlu5 libsz2 libtcl8.6 libthai-data libthai0 libtiff-dev libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtk8.6 libtool liburiparser-dev liburiparser1 libwebp-dev libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxerces-c-dev libxerces-c3.2 libxext6 libxft2 libxml2 libxml2-dev libxmuu1 libxrender1 libxss1 libxt6 libzstd-dev m4 man-db mime-support mysql-common odbcinst odbcinst1debian2 pkg-config po-debconf proj-data python3 python3-distutils python3-lib2to3 python3-minimal python3.6 python3.6-minimal r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors r-bioc-xvector r-cran-bitops r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl r-cran-snow ucf unixodbc-dev unzip uuid-dev x11-common xauth xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation debtags dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-7-multilib gfortran-7-doc libgfortran4-dbg libcoarrays-dev groff libitpp-dev liblapack-doc libboost-doc libboost1.65-doc libboost-atomic1.65-dev libboost-chrono1.65-dev libboost-container1.65-dev libboost-context1.65-dev libboost-coroutine1.65-dev libboost-date-time1.65-dev libboost-exception1.65-dev libboost-fiber1.65-dev libboost-filesystem1.65-dev libboost-graph1.65-dev libboost-graph-parallel1.65-dev libboost-iostreams1.65-dev libboost-locale1.65-dev libboost-log1.65-dev libboost-math1.65-dev libboost-mpi1.65-dev libboost-mpi-python1.65-dev libboost-numpy1.65-dev libboost-program-options1.65-dev libboost-python1.65-dev libboost-random1.65-dev libboost-regex1.65-dev libboost-serialization1.65-dev libboost-signals1.65-dev libboost-stacktrace1.65-dev libboost-system1.65-dev libboost-test1.65-dev libboost-thread1.65-dev libboost-timer1.65-dev libboost-type-erasure1.65-dev libboost-wave1.65-dev libboost1.65-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libgdal-doc libgeotiff-epsg geotiff-bin gdal-bin libglib2.0-doc libgraphite2-utils krb5-doc krb5-user libhdf4-doc hdf4-tools libhdf5-doc icu-doc liblcms2-utils libtool-doc liblzma-doc ncurses-doc netcdf-bin netcdf-doc libmyodbc odbc-postgresql tdsodbc unixodbc-bin ogdi-bin libfreetype6-dev postgresql-doc-10 proj-bin readline-doc sqlite3-doc libsuperlu-doc tcl8.6 tk8.6 gcj-jdk libxerces-c-doc m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.6-venv python3.6-doc binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo r-bioc-biobase r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-foreach r-cran-bbmisc r-cran-rmpi r-bioc-variantannotation r-bioc-genomicalignments r-bioc-shortread r-cran-codetools r-cran-knitr r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-summarizedexperiment r-cran-matrix r-bioc-rtracklayer r-bioc-gviz r-bioc-annotationhub r-bioc-delayedarray r-bioc-graph r-cran-data.table r-cran-shiny r-cran-rmarkdown r-cran-jsonlite r-cran-xml r-cran-rsprng r-cran-rlecuyer Recommended packages: devscripts curl | wget | lynx bzip2-doc libarchive-cpio-perl proj-bin shared-mime-info xdg-user-dirs krb5-locales libpng-tools poppler-data publicsuffix libsasl2-modules libmail-sendmail-perl r-recommended r-doc-html r-cran-runit r-cran-batchjobs r-cran-doparallel r-bioc-rsamtools r-cran-digest r-bioc-annotate r-bioc-summarizedexperiment r-cran-testit r-cran-codetools r-cran-survival r-cran-testthat libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils dctrl-tools debhelper default-libmysqlclient-dev dh-autoreconf dh-r dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gdal-data gettext gettext-base gfortran gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0 libarchive-zip-perl libarmadillo-dev libarmadillo8 libarpack2 libarpack2-dev libasn1-8-heimdal libblas-dev libblas3 libboost-dev libboost1.65-dev libbsd0 libbz2-dev libcairo2 libcharls-dev libcharls1 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdap-dev libdap25 libdapclient6v5 libdapserver7v5 libdatrie1 libelf1 libepsilon-dev libepsilon1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfreetype6 libfreexl-dev libfreexl1 libfribidi0 libfyba-dev libfyba0 libgdal-dev libgdal20 libgeos-3.6.2 libgeos-c1v5 libgeos-dev libgeotiff-dev libgeotiff2 libgfortran-7-dev libgfortran4 libgif-dev libgif7 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libhdf4-0-alt libhdf4-alt-dev libhdf5-100 libhdf5-cpp-100 libhdf5-dev libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libiculx60 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjson-c-dev libk5crypto3 libkeyutils1 libkml-dev libkmlbase1 libkmlconvenience1 libkmldom1 libkmlengine1 libkmlregionator1 libkmlxsd1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libminizip-dev libminizip1 libmpdec2 libmysqlclient-dev libmysqlclient20 libncurses-dev libncurses5-dev libnetcdf-dev libnetcdf13 libnghttp2-14 libnspr4 libnss3 libodbc1 libogdi3.2 libogdi3.2-dev libopenjp2-7 libopenjp2-7-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpoppler-dev libpoppler-private-dev libpoppler73 libpq-dev libpq5 libproj-dev libproj13 libpsl5 libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libqhull-dev libqhull-r7 libqhull7 libreadline-dev libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libspatialite-dev libspatialite7 libsqlite3-dev libsuperlu-dev libsuperlu5 libsz2 libtcl8.6 libthai-data libthai0 libtiff-dev libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtk8.6 libtool liburiparser-dev liburiparser1 libwebp-dev libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxerces-c-dev libxerces-c3.2 libxext6 libxft2 libxml2 libxml2-dev libxmuu1 libxrender1 libxss1 libxt6 libzstd-dev m4 man-db mime-support mysql-common odbcinst odbcinst1debian2 pkg-config po-debconf proj-data python3 python3-distutils python3-lib2to3 python3-minimal python3.6 python3.6-minimal r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors r-bioc-xvector r-cran-bitops r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl r-cran-snow sbuild-build-depends-r-bioc-rsamtools-dummy ucf unixodbc-dev unzip uuid-dev x11-common xauth xdg-utils zip zlib1g-dev 0 upgraded, 271 newly installed, 0 to remove and 0 not upgraded. Need to get 159 MB of archives. After this operation, 550 MB of additional disk space will be used. Get:1 copy:/<>/resolver-fAwxEz/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [980 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.6-minimal armhf 3.6.6-1 [522 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main armhf libexpat1 armhf 2.2.5-3 [59.7 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main armhf python3.6-minimal armhf 3.6.6-1 [1340 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf python3-minimal armhf 3.6.6-1 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main armhf mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main armhf libmpdec2 armhf 2.4.2-2 [66.4 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.6-stdlib armhf 3.6.6-1 [1632 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main armhf python3.6 armhf 3.6.6-1 [190 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libpython3-stdlib armhf 3.6.6-1 [7144 B] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf python3 armhf 3.6.6-1 [33.5 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main armhf libxau6 armhf 1:1.0.8-1 [7324 B] Get:13 http://ftpmaster.internal/ubuntu cosmic/main armhf libbsd0 armhf 0.9.1-1 [43.1 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main armhf libxdmcp6 armhf 1:1.1.2-3 [9316 B] Get:15 http://ftpmaster.internal/ubuntu cosmic/main armhf libxcb1 armhf 1.13-1 [41.2 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libx11-data all 2:1.6.5-1 [113 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libx11-6 armhf 2:1.6.5-1 [514 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main armhf libxext6 armhf 2:1.3.3-1 [25.1 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main armhf bsdmainutils armhf 11.1.2ubuntu2 [176 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main armhf groff-base armhf 1.22.3-10 [1013 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main armhf libpipeline1 armhf 1.5.0-1 [21.1 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main armhf man-db armhf 2.8.3-2 [993 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main armhf libfreetype6 armhf 2.8.1-2ubuntu2 [280 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main armhf ucf all 3.0038 [50.5 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main armhf fonts-dejavu-core all 2.37-1 [1041 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main armhf fontconfig-config all 2.12.6-0ubuntu2 [55.8 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main armhf libfontconfig1 armhf 2.12.6-0ubuntu2 [120 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main armhf fontconfig armhf 2.12.6-0ubuntu2 [167 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main armhf libjpeg-turbo8 armhf 1.5.2-0ubuntu6 [87.4 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main armhf x11-common all 1:7.7+19ubuntu8 [22.5 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main armhf libice6 armhf 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http://ftpmaster.internal/ubuntu cosmic/main armhf libglib2.0-data all 2.56.1-2ubuntu1 [4220 B] Get:43 http://ftpmaster.internal/ubuntu cosmic/main armhf libicu60 armhf 60.2-6ubuntu1 [7801 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libxml2 armhf 2.9.4+dfsg1-7build1 [568 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main armhf gettext-base armhf 0.19.8.1-6build1 [46.2 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main armhf libkrb5support0 armhf 1.16-2build1 [27.5 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main armhf libk5crypto3 armhf 1.16-2build1 [83.2 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main armhf libkeyutils1 armhf 1.5.9-9.2ubuntu3 [7780 B] Get:49 http://ftpmaster.internal/ubuntu cosmic/main armhf libkrb5-3 armhf 1.16-2build1 [233 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main armhf libgssapi-krb5-2 armhf 1.16-2build1 [101 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main armhf libpsl5 armhf 0.20.2-1 [48.0 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main armhf libxmuu1 armhf 2:1.1.2-2 [9130 B] Get:53 http://ftpmaster.internal/ubuntu cosmic/main armhf xauth armhf 1:1.0.10-1 [21.7 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main armhf m4 armhf 1.4.18-1 [181 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main armhf autoconf all 2.69-11 [322 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main armhf automake all 1:1.15.1-3ubuntu2 [509 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main armhf autopoint all 0.19.8.1-6build1 [412 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main armhf dctrl-tools armhf 2.24-2build1 [52.9 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main armhf libtool all 2.4.6-2.1 [195 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-autoreconf all 19 [16.1 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main armhf libarchive-zip-perl all 1.60-1 [83.9 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main armhf libfile-stripnondeterminism-perl all 0.042-1 [15.2 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-strip-nondeterminism all 0.042-1 [5188 B] Get:67 http://ftpmaster.internal/ubuntu cosmic/main armhf dwz armhf 0.12-2 [72.0 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main armhf libcroco3 armhf 0.6.12-2 [69.4 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main armhf gettext armhf 0.19.8.1-6build1 [834 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main armhf po-debconf all 1.0.20 [232 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main armhf debhelper all 11.3.2ubuntu1 [883 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main armhf mysql-common all 5.8+1.0.4 [7308 B] Get:74 http://ftpmaster.internal/ubuntu cosmic/main armhf libmysqlclient20 armhf 5.7.22-0ubuntu18.04.1 [754 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu2 [168 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main armhf libmysqlclient-dev armhf 5.7.22-0ubuntu18.04.1 [1108 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main armhf default-libmysqlclient-dev armhf 1.0.4 [3736 B] Get:78 http://ftpmaster.internal/ubuntu cosmic/main armhf zip armhf 3.0-11build1 [145 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main armhf unzip armhf 6.0-21ubuntu1 [148 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main armhf libpaper1 armhf 1.1.24+nmu5ubuntu1 [12.9 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main armhf libpaper-utils armhf 1.1.24+nmu5ubuntu1 [8026 B] Get:82 http://ftpmaster.internal/ubuntu cosmic/main armhf xdg-utils all 1.1.3-1ubuntu1 [60.3 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic/main armhf libblas3 armhf 3.8.0-1 [97.7 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic/main armhf libpixman-1-0 armhf 0.34.0-2 [157 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic/main armhf libxcb-render0 armhf 1.13-1 [13.9 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic/main armhf libxcb-shm0 armhf 1.13-1 [5404 B] Get:87 http://ftpmaster.internal/ubuntu cosmic/main armhf libxrender1 armhf 1:0.9.10-1 [15.6 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic/main armhf libcairo2 armhf 1.15.10-3 [507 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main armhf libroken18-heimdal armhf 7.5.0+dfsg-2 [34.3 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic/main armhf libasn1-8-heimdal armhf 7.5.0+dfsg-2 [136 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic/main armhf libheimbase1-heimdal armhf 7.5.0+dfsg-2 [24.1 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main armhf libhcrypto4-heimdal armhf 7.5.0+dfsg-2 [76.5 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main armhf libwind0-heimdal armhf 7.5.0+dfsg-2 [47.2 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic/main armhf libhx509-5-heimdal armhf 7.5.0+dfsg-2 [88.0 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main armhf libkrb5-26-heimdal armhf 7.5.0+dfsg-2 [168 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main armhf libheimntlm0-heimdal armhf 7.5.0+dfsg-2 [13.1 kB] Get:97 http://ftpmaster.internal/ubuntu cosmic/main armhf libgssapi3-heimdal armhf 7.5.0+dfsg-2 [79.0 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [13.0 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [42.0 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic/main armhf libldap-common all 2.4.46+dfsg-5ubuntu1 [16.6 kB] Get:101 http://ftpmaster.internal/ubuntu cosmic/main armhf libldap-2.4-2 armhf 2.4.46+dfsg-5ubuntu1 [131 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/main armhf libnghttp2-14 armhf 1.32.0-1 [67.3 kB] Get:103 http://ftpmaster.internal/ubuntu cosmic/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [49.2 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic/main armhf libcurl4 armhf 7.60.0-2ubuntu1 [185 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main armhf libjpeg8 armhf 8c-2ubuntu8 [2202 B] Get:106 http://ftpmaster.internal/ubuntu cosmic/main armhf libgfortran4 armhf 7.3.0-24ubuntu1 [201 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic/main armhf liblapack3 armhf 3.8.0-1 [1640 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic/main armhf libthai-data all 0.1.27-2 [133 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main armhf libdatrie1 armhf 0.2.12-1 [15.0 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic/main armhf libthai0 armhf 0.1.27-2 [14.7 kB] Get:111 http://ftpmaster.internal/ubuntu cosmic/main armhf libpango-1.0-0 armhf 1.42.1-2 [136 kB] Get:112 http://ftpmaster.internal/ubuntu cosmic/main armhf libgraphite2-3 armhf 1.3.11-2 [67.5 kB] Get:113 http://ftpmaster.internal/ubuntu cosmic/main armhf libharfbuzz0b armhf 1.7.6-1ubuntu1 [231 kB] Get:114 http://ftpmaster.internal/ubuntu cosmic/main armhf libpangoft2-1.0-0 armhf 1.42.1-2 [29.1 kB] Get:115 http://ftpmaster.internal/ubuntu cosmic/main armhf libpangocairo-1.0-0 armhf 1.42.1-2 [19.0 kB] Get:116 http://ftpmaster.internal/ubuntu cosmic/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [777 kB] Get:117 http://ftpmaster.internal/ubuntu cosmic/main armhf libjbig0 armhf 2.1-3.1build1 [23.9 kB] Get:118 http://ftpmaster.internal/ubuntu cosmic/main armhf libtiff5 armhf 4.0.9-6 [134 kB] Get:119 http://ftpmaster.internal/ubuntu cosmic/main armhf libxft2 armhf 2.3.2-2 [31.6 kB] Get:120 http://ftpmaster.internal/ubuntu cosmic/main armhf libtk8.6 armhf 8.6.8-4 [612 kB] Get:121 http://ftpmaster.internal/ubuntu cosmic/main armhf libxt6 armhf 1:1.1.5-1 [129 kB] Get:122 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-base-core armhf 3.5.1-1 [23.5 MB] Get:123 http://ftpmaster.internal/ubuntu cosmic/main armhf libgfortran-7-dev armhf 7.3.0-24ubuntu1 [249 kB] Get:124 http://ftpmaster.internal/ubuntu cosmic/main armhf gfortran-7 armhf 7.3.0-24ubuntu1 [5641 kB] Get:125 http://ftpmaster.internal/ubuntu cosmic/main armhf gfortran armhf 4:7.3.0-3ubuntu3 [1352 B] Get:126 http://ftpmaster.internal/ubuntu cosmic/main armhf libblas-dev armhf 3.8.0-1 [104 kB] Get:127 http://ftpmaster.internal/ubuntu cosmic/main armhf liblapack-dev armhf 3.8.0-1 [1690 kB] Get:128 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses-dev armhf 6.1+20180210-4ubuntu1 [295 kB] Get:129 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses5-dev armhf 6.1+20180210-4ubuntu1 [972 B] Get:130 http://ftpmaster.internal/ubuntu cosmic/main armhf libreadline-dev armhf 7.0-5 [121 kB] Get:131 http://ftpmaster.internal/ubuntu cosmic/main armhf libjpeg-turbo8-dev armhf 1.5.2-0ubuntu6 [199 kB] Get:132 http://ftpmaster.internal/ubuntu cosmic/main armhf libjpeg8-dev armhf 8c-2ubuntu8 [1554 B] Get:133 http://ftpmaster.internal/ubuntu cosmic/main armhf libjpeg-dev armhf 8c-2ubuntu8 [1554 B] Get:134 http://ftpmaster.internal/ubuntu cosmic/main armhf libpcre16-3 armhf 2:8.39-9 [128 kB] Get:135 http://ftpmaster.internal/ubuntu cosmic/main armhf libpcre32-3 armhf 2:8.39-9 [120 kB] Get:136 http://ftpmaster.internal/ubuntu cosmic/main armhf libpcrecpp0v5 armhf 2:8.39-9 [13.2 kB] Get:137 http://ftpmaster.internal/ubuntu cosmic/main armhf libpcre3-dev armhf 2:8.39-9 [473 kB] Get:138 http://ftpmaster.internal/ubuntu cosmic/main armhf libpng-dev armhf 1.6.34-1 [162 kB] Get:139 http://ftpmaster.internal/ubuntu cosmic/main armhf libbz2-dev armhf 1.0.6-8.1 [27.6 kB] Get:140 http://ftpmaster.internal/ubuntu cosmic/main armhf liblzma-dev armhf 5.2.2-1.3 [138 kB] Get:141 http://ftpmaster.internal/ubuntu cosmic/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.6 kB] Get:142 http://ftpmaster.internal/ubuntu cosmic/main armhf libiculx60 armhf 60.2-6ubuntu1 [16.1 kB] Get:143 http://ftpmaster.internal/ubuntu cosmic/main armhf icu-devtools armhf 60.2-6ubuntu1 [164 kB] Get:144 http://ftpmaster.internal/ubuntu cosmic/main armhf libharfbuzz-icu0 armhf 1.7.6-1ubuntu1 [5196 B] Get:145 http://ftpmaster.internal/ubuntu cosmic/main armhf libharfbuzz-gobject0 armhf 1.7.6-1ubuntu1 [12.0 kB] Get:146 http://ftpmaster.internal/ubuntu cosmic/main armhf gir1.2-harfbuzz-0.0 armhf 1.7.6-1ubuntu1 [18.6 kB] Get:147 http://ftpmaster.internal/ubuntu cosmic/main armhf libglib2.0-bin armhf 2.56.1-2ubuntu1 [62.9 kB] Get:148 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-lib2to3 all 3.6.6-1 [76.9 kB] Get:149 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-distutils all 3.6.6-1 [141 kB] Get:150 http://ftpmaster.internal/ubuntu cosmic/main armhf libglib2.0-dev-bin armhf 2.56.1-2ubuntu1 [99.7 kB] Get:151 http://ftpmaster.internal/ubuntu cosmic/main armhf pkg-config armhf 0.29.1-0ubuntu2 [42.0 kB] Get:152 http://ftpmaster.internal/ubuntu cosmic/main armhf libglib2.0-dev armhf 2.56.1-2ubuntu1 [1283 kB] Get:153 http://ftpmaster.internal/ubuntu cosmic/main armhf libgraphite2-dev armhf 1.3.11-2 [14.5 kB] Get:154 http://ftpmaster.internal/ubuntu cosmic/main armhf libharfbuzz-dev armhf 1.7.6-1ubuntu1 [319 kB] Get:155 http://ftpmaster.internal/ubuntu cosmic/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [27.8 kB] Get:156 http://ftpmaster.internal/ubuntu cosmic/main armhf libicu-dev armhf 60.2-6ubuntu1 [8712 kB] Get:157 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-base-dev all 3.5.1-1 [4520 B] Get:158 http://ftpmaster.internal/ubuntu cosmic/main armhf libfile-which-perl all 1.21-1 [11.8 kB] Get:159 http://ftpmaster.internal/ubuntu cosmic/universe armhf dh-r all 20180617 [31.8 kB] Get:160 http://ftpmaster.internal/ubuntu cosmic/universe armhf gdal-data all 2.3.1+dfsg-1ubuntu1 [511 kB] Get:161 http://ftpmaster.internal/ubuntu cosmic/universe armhf hdf5-helpers armhf 1.10.0-patch1+docs-4build1 [12.3 kB] Get:162 http://ftpmaster.internal/ubuntu cosmic/universe armhf libaec0 armhf 1.0.2-1 [19.1 kB] Get:163 http://ftpmaster.internal/ubuntu cosmic/universe armhf libarpack2 armhf 3.5.0+real-2build1 [75.1 kB] Get:164 http://ftpmaster.internal/ubuntu cosmic/universe armhf libsuperlu5 armhf 5.2.1+dfsg1-3 [131 kB] Get:165 http://ftpmaster.internal/ubuntu cosmic/universe armhf libarmadillo8 armhf 1:8.400.0+dfsg-3 [80.7 kB] Get:166 http://ftpmaster.internal/ubuntu cosmic/universe armhf libarpack2-dev armhf 3.5.0+real-2build1 [84.7 kB] Get:167 http://ftpmaster.internal/ubuntu cosmic/universe armhf libsz2 armhf 1.0.2-1 [5072 B] Get:168 http://ftpmaster.internal/ubuntu cosmic/universe armhf libhdf5-100 armhf 1.10.0-patch1+docs-4build1 [1215 kB] Get:169 http://ftpmaster.internal/ubuntu cosmic/universe armhf libaec-dev armhf 1.0.2-1 [16.3 kB] Get:170 http://ftpmaster.internal/ubuntu cosmic/universe armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-4build1 [93.5 kB] Get:171 http://ftpmaster.internal/ubuntu cosmic/universe armhf libhdf5-dev armhf 1.10.0-patch1+docs-4build1 [2411 kB] Get:172 http://ftpmaster.internal/ubuntu cosmic/universe armhf libsuperlu-dev armhf 5.2.1+dfsg1-3 [16.3 kB] Get:173 http://ftpmaster.internal/ubuntu cosmic/universe armhf libarmadillo-dev armhf 1:8.400.0+dfsg-3 [340 kB] Get:174 http://ftpmaster.internal/ubuntu cosmic/main armhf libboost1.65-dev armhf 1.65.1+dfsg-0ubuntu9 [7218 kB] Get:175 http://ftpmaster.internal/ubuntu cosmic/main armhf libboost-dev armhf 1.65.1.0ubuntu1 [3128 B] Get:176 http://ftpmaster.internal/ubuntu cosmic/universe armhf libcharls1 armhf 1.1.0+dfsg-2 [48.2 kB] Get:177 http://ftpmaster.internal/ubuntu cosmic/universe armhf libcharls-dev armhf 1.1.0+dfsg-2 [20.4 kB] Get:178 http://ftpmaster.internal/ubuntu cosmic/main armhf libcurl3-gnutls armhf 7.60.0-2ubuntu1 [183 kB] Get:179 http://ftpmaster.internal/ubuntu cosmic/main armhf libcurl4-gnutls-dev armhf 7.60.0-2ubuntu1 [272 kB] Get:180 http://ftpmaster.internal/ubuntu cosmic/universe armhf libdap25 armhf 3.19.1-2build1 [374 kB] Get:181 http://ftpmaster.internal/ubuntu cosmic/universe armhf libdapserver7v5 armhf 3.19.1-2build1 [19.3 kB] Get:182 http://ftpmaster.internal/ubuntu cosmic/universe armhf libdapclient6v5 armhf 3.19.1-2build1 [79.2 kB] Get:183 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libxml2-dev armhf 2.9.4+dfsg1-7build1 [691 kB] Get:184 http://ftpmaster.internal/ubuntu cosmic/main armhf uuid-dev armhf 2.32-0.1ubuntu1 [32.7 kB] Get:185 http://ftpmaster.internal/ubuntu cosmic/universe armhf libdap-dev armhf 3.19.1-2build1 [703 kB] Get:186 http://ftpmaster.internal/ubuntu cosmic/universe armhf libepsilon1 armhf 0.9.2+dfsg-2 [35.9 kB] Get:187 http://ftpmaster.internal/ubuntu cosmic/main armhf libexpat1-dev armhf 2.2.5-3 [106 kB] Get:188 http://ftpmaster.internal/ubuntu cosmic/universe armhf libfyba0 armhf 4.1.1-3build1 [98.4 kB] Get:189 http://ftpmaster.internal/ubuntu cosmic/universe armhf libfyba-dev armhf 4.1.1-3build1 [433 kB] Get:190 http://ftpmaster.internal/ubuntu cosmic/universe armhf libfreexl1 armhf 1.0.5-1 [31.7 kB] Get:191 http://ftpmaster.internal/ubuntu cosmic/universe armhf libgeos-3.6.2 armhf 3.6.2-1build2 [399 kB] Get:192 http://ftpmaster.internal/ubuntu cosmic/universe armhf libgeos-c1v5 armhf 3.6.2-1build2 [48.7 kB] Get:193 http://ftpmaster.internal/ubuntu cosmic/universe armhf proj-data all 5.1.0-1 [6955 kB] Get:194 http://ftpmaster.internal/ubuntu cosmic/universe armhf libproj13 armhf 5.1.0-1 [156 kB] Get:195 http://ftpmaster.internal/ubuntu cosmic/universe armhf libgeotiff2 armhf 1.4.2-2build2 [49.9 kB] Get:196 http://ftpmaster.internal/ubuntu cosmic/main armhf libgif7 armhf 5.1.4-3 [28.3 kB] Get:197 http://ftpmaster.internal/ubuntu cosmic/universe armhf libhdf4-0-alt armhf 4.2.13-2 [231 kB] Get:198 http://ftpmaster.internal/ubuntu cosmic/universe armhf libminizip1 armhf 1.1-8build1 [18.5 kB] Get:199 http://ftpmaster.internal/ubuntu cosmic/universe armhf liburiparser1 armhf 0.8.5-1.1 [29.6 kB] Get:200 http://ftpmaster.internal/ubuntu cosmic/universe armhf libkmlbase1 armhf 1.3.0-5 [38.9 kB] Get:201 http://ftpmaster.internal/ubuntu cosmic/universe armhf libkmldom1 armhf 1.3.0-5 [143 kB] Get:202 http://ftpmaster.internal/ubuntu cosmic/universe armhf libkmlengine1 armhf 1.3.0-5 [64.0 kB] Get:203 http://ftpmaster.internal/ubuntu cosmic/universe armhf libnetcdf13 armhf 1:4.6.1-1 [304 kB] Get:204 http://ftpmaster.internal/ubuntu cosmic/main armhf libltdl7 armhf 2.4.6-2.1 [35.8 kB] Get:205 http://ftpmaster.internal/ubuntu cosmic/main armhf libodbc1 armhf 2.3.4-1.1ubuntu3 [154 kB] Get:206 http://ftpmaster.internal/ubuntu cosmic/universe armhf libogdi3.2 armhf 3.2.1+ds-2 [184 kB] Get:207 http://ftpmaster.internal/ubuntu cosmic/universe armhf libopenjp2-7 armhf 2.3.0-1 [130 kB] Get:208 http://ftpmaster.internal/ubuntu cosmic/main armhf liblcms2-2 armhf 2.9-2 [114 kB] Get:209 http://ftpmaster.internal/ubuntu cosmic/main armhf libnspr4 armhf 2:4.18-1ubuntu1 [89.8 kB] Get:210 http://ftpmaster.internal/ubuntu cosmic/main armhf libnss3 armhf 2:3.36.1-1ubuntu1 [951 kB] Get:211 http://ftpmaster.internal/ubuntu cosmic/main armhf libpoppler73 armhf 0.62.0-2ubuntu3 [674 kB] Get:212 http://ftpmaster.internal/ubuntu cosmic/main armhf libpq5 armhf 10.4-2 [90.0 kB] Get:213 http://ftpmaster.internal/ubuntu cosmic/universe armhf libqhull7 armhf 2015.2-4 [134 kB] Get:214 http://ftpmaster.internal/ubuntu cosmic/universe armhf libspatialite7 armhf 4.3.0a-5build2 [1298 kB] Get:215 http://ftpmaster.internal/ubuntu cosmic/main armhf libwebp6 armhf 0.6.1-2 [152 kB] Get:216 http://ftpmaster.internal/ubuntu cosmic/universe armhf libxerces-c3.2 armhf 3.2.1+debian-2 [724 kB] Get:217 http://ftpmaster.internal/ubuntu cosmic/main armhf odbcinst armhf 2.3.4-1.1ubuntu3 [11.8 kB] Get:218 http://ftpmaster.internal/ubuntu cosmic/main armhf odbcinst1debian2 armhf 2.3.4-1.1ubuntu3 [33.6 kB] Get:219 http://ftpmaster.internal/ubuntu cosmic/universe armhf libgdal20 armhf 2.3.1+dfsg-1ubuntu1 [4775 kB] Get:220 http://ftpmaster.internal/ubuntu cosmic/universe armhf libgeos-dev armhf 3.6.2-1build2 [72.0 kB] Get:221 http://ftpmaster.internal/ubuntu cosmic/main armhf libgif-dev armhf 5.1.4-3 [18.1 kB] Get:222 http://ftpmaster.internal/ubuntu cosmic/universe armhf libkmlconvenience1 armhf 1.3.0-5 [39.4 kB] Get:223 http://ftpmaster.internal/ubuntu cosmic/universe armhf libkmlregionator1 armhf 1.3.0-5 [16.6 kB] Get:224 http://ftpmaster.internal/ubuntu cosmic/universe armhf libkmlxsd1 armhf 1.3.0-5 [23.3 kB] Get:225 http://ftpmaster.internal/ubuntu cosmic/main armhf libltdl-dev armhf 2.4.6-2.1 [159 kB] Get:226 http://ftpmaster.internal/ubuntu cosmic/universe armhf libminizip-dev armhf 1.1-8build1 [25.7 kB] Get:227 http://ftpmaster.internal/ubuntu cosmic/universe armhf libnetcdf-dev armhf 1:4.6.1-1 [37.7 kB] Get:228 http://ftpmaster.internal/ubuntu cosmic/main armhf libpoppler-dev armhf 0.62.0-2ubuntu3 [4616 B] Get:229 http://ftpmaster.internal/ubuntu cosmic/main armhf libpoppler-private-dev armhf 0.62.0-2ubuntu3 [169 kB] Get:230 http://ftpmaster.internal/ubuntu cosmic/main armhf libpq-dev armhf 10.4-2 [143 kB] Get:231 http://ftpmaster.internal/ubuntu cosmic/universe armhf libqhull-r7 armhf 2015.2-4 [132 kB] Get:232 http://ftpmaster.internal/ubuntu cosmic/universe armhf libqhull-dev armhf 2015.2-4 [332 kB] Get:233 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libsqlite3-dev armhf 3.24.0-1 [584 kB] Get:234 http://ftpmaster.internal/ubuntu cosmic/main armhf libjbig-dev armhf 2.1-3.1build1 [22.9 kB] Get:235 http://ftpmaster.internal/ubuntu cosmic/main armhf libtiffxx5 armhf 4.0.9-6 [5788 B] Get:236 http://ftpmaster.internal/ubuntu cosmic/main armhf libtiff5-dev armhf 4.0.9-6 [258 kB] Get:237 http://ftpmaster.internal/ubuntu cosmic/main armhf libtiff-dev armhf 4.0.9-6 [2252 B] Get:238 http://ftpmaster.internal/ubuntu cosmic/universe armhf liburiparser-dev armhf 0.8.5-1.1 [10.2 kB] Get:239 http://ftpmaster.internal/ubuntu cosmic/main armhf libwebpdemux2 armhf 0.6.1-2 [8760 B] Get:240 http://ftpmaster.internal/ubuntu cosmic/main armhf libwebpmux3 armhf 0.6.1-2 [16.0 kB] Get:241 http://ftpmaster.internal/ubuntu cosmic/universe armhf libxerces-c-dev armhf 3.2.1+debian-2 [1545 kB] Get:242 http://ftpmaster.internal/ubuntu cosmic/main armhf libzstd-dev armhf 1.3.3+dfsg-2ubuntu1 [211 kB] Get:243 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-biocgenerics all 0.26.0-3build1 [641 kB] Get:244 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-cran-formatr all 1.5-3 [144 kB] Get:245 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-cran-lambda.r all 1.2.3-2 [117 kB] Get:246 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-cran-futile.options all 1.0.1-2 [19.8 kB] Get:247 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-cran-futile.logger all 1.4.3-3 [102 kB] Get:248 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-cran-snow all 1:0.4.2-2 [107 kB] Get:249 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-biocparallel armhf 1.14.1-1build1 [1051 kB] Get:250 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-s4vectors armhf 0.18.3-1 [1802 kB] Get:251 http://ftpmaster.internal/ubuntu cosmic/universe armhf libepsilon-dev armhf 0.9.2+dfsg-2 [44.9 kB] Get:252 http://ftpmaster.internal/ubuntu cosmic/universe armhf libfreexl-dev armhf 1.0.5-1 [29.3 kB] Get:253 http://ftpmaster.internal/ubuntu cosmic/universe armhf libgeotiff-dev armhf 1.4.2-2build2 [77.0 kB] Get:254 http://ftpmaster.internal/ubuntu cosmic/universe armhf libhdf4-alt-dev armhf 4.2.13-2 [333 kB] Get:255 http://ftpmaster.internal/ubuntu cosmic/main armhf libjson-c-dev armhf 0.12.1-1.3 [29.1 kB] Get:256 http://ftpmaster.internal/ubuntu cosmic/universe armhf libkml-dev armhf 1.3.0-5 [933 kB] Get:257 http://ftpmaster.internal/ubuntu cosmic/universe armhf libproj-dev armhf 5.1.0-1 [195 kB] Get:258 http://ftpmaster.internal/ubuntu cosmic/universe armhf libogdi3.2-dev armhf 3.2.1+ds-2 [23.8 kB] Get:259 http://ftpmaster.internal/ubuntu cosmic/universe armhf libopenjp2-7-dev armhf 2.3.0-1 [26.6 kB] Get:260 http://ftpmaster.internal/ubuntu cosmic/universe armhf libspatialite-dev armhf 4.3.0a-5build2 [1524 kB] Get:261 http://ftpmaster.internal/ubuntu cosmic/main armhf libwebp-dev armhf 0.6.1-2 [228 kB] Get:262 http://ftpmaster.internal/ubuntu cosmic/main armhf unixodbc-dev armhf 2.3.4-1.1ubuntu3 [199 kB] Get:263 http://ftpmaster.internal/ubuntu cosmic/universe armhf libgdal-dev armhf 2.3.1+dfsg-1ubuntu1 [6645 kB] Get:264 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-iranges armhf 2.14.10-1build1 [2128 kB] Get:265 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-xvector armhf 0.20.0-2build1 [592 kB] Get:266 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-biostrings armhf 2.48.0-2build1 [14.1 MB] Get:267 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-cran-bitops armhf 1.0-6-4 [23.3 kB] Get:268 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-cran-rcurl armhf 1.95-4.10-2 [712 kB] Get:269 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-genomeinfodbdata all 1.1.0-3build1 [8213 kB] Get:270 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-genomeinfodb all 1.16.0-3 [3686 kB] Get:271 http://ftpmaster.internal/ubuntu cosmic/universe armhf r-bioc-genomicranges armhf 1.32.3-1build1 [1937 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 159 MB in 7s (23.8 MB/s) Selecting previously unselected package libpython3.6-minimal:armhf. (Reading database ... 12440 files and directories currently installed.) Preparing to unpack .../libpython3.6-minimal_3.6.6-1_armhf.deb ... Unpacking libpython3.6-minimal:armhf (3.6.6-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.2.5-3_armhf.deb ... Unpacking libexpat1:armhf (2.2.5-3) ... Selecting previously unselected package python3.6-minimal. Preparing to unpack .../python3.6-minimal_3.6.6-1_armhf.deb ... Unpacking python3.6-minimal (3.6.6-1) ... Setting up libpython3.6-minimal:armhf (3.6.6-1) ... Setting up libexpat1:armhf (2.2.5-3) ... Setting up python3.6-minimal (3.6.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12687 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.6.6-1_armhf.deb ... Unpacking python3-minimal (3.6.6-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.60ubuntu1_all.deb ... 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Setting up libpsl5:armhf (0.20.2-1) ... Setting up libcharls1:armhf (1.1.0+dfsg-2) ... Setting up libelf1:armhf (0.170-0.5) ... Setting up libgeos-3.6.2:armhf (3.6.2-1build2) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:armhf (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up mysql-common (5.8+1.0.4) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up unzip (6.0-21ubuntu1) ... Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up uuid-dev:armhf (2.32-0.1ubuntu1) ... Setting up dctrl-tools (2.24-2build1) ... Setting up libopenjp2-7-dev (2.3.0-1) ... Setting up libdatrie1:armhf (0.2.12-1) ... Setting up gettext-base (0.19.8.1-6build1) ... Setting up libgif7:armhf (5.1.4-3) ... Setting up libjpeg-turbo8:armhf (1.5.2-0ubuntu6) ... Setting up libpipeline1:armhf (1.5.0-1) ... Setting up libroken18-heimdal:armhf (7.5.0+dfsg-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up libepsilon1:armhf (0.9.2+dfsg-2) ... Setting up m4 (1.4.18-1) ... Setting up libminizip-dev:armhf (1.1-8build1) ... Setting up libbsd0:armhf (0.9.1-1) ... Setting up libkrb5support0:armhf (1.16-2build1) ... Setting up libnspr4:armhf (2:4.18-1ubuntu1) ... Setting up ucf (3.0038) ... Setting up libgirepository-1.0-1:armhf (1.56.1-1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7build1) ... Setting up zip (3.0-11build1) ... Setting up libfreexl1:armhf (1.0.5-1) ... Setting up libfreetype6:armhf (2.8.1-2ubuntu2) ... Setting up libmagic-mgc (1:5.33-3) ... Setting up libfyba0:armhf (4.1.1-3build1) ... Setting up libmagic1:armhf (1:5.33-3) ... Setting up libgraphite2-3:armhf (1.3.11-2) ... Setting up libjbig-dev:armhf (2.1-3.1build1) ... Setting up libcroco3:armhf (0.6.12-2) ... Setting up gdal-data (2.3.1+dfsg-1ubuntu1) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Setting up libgeos-c1v5:armhf (3.6.2-1build2) ... Setting up libpixman-1-0:armhf (0.34.0-2) ... Setting up libblas3:armhf (3.8.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up gir1.2-glib-2.0:armhf (1.56.1-1) ... Setting up libjpeg-turbo8-dev:armhf (1.5.2-0ubuntu6) ... Setting up libglib2.0-data (2.56.1-2ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:armhf (7.5.0+dfsg-2) ... Setting up libcharls-dev:armhf (1.1.0+dfsg-2) ... Setting up libzstd-dev:armhf (1.3.3+dfsg-2ubuntu1) ... Processing triggers for systemd (238-5ubuntu2) ... Setting up libltdl7:armhf (2.4.6-2.1) ... Setting up libgfortran-7-dev:armhf (7.3.0-24ubuntu1) ... Setting up libjson-c-dev:armhf (0.12.1-1.3) ... Setting up libfribidi0:armhf (0.19.7-3) ... 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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 x11-common (1:7.7+19ubuntu8) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.3-1ubuntu1) ... Setting up libncurses-dev:armhf (6.1+20180210-4ubuntu1) ... Setting up libglib2.0-bin (2.56.1-2ubuntu1) ... Setting up libfyba-dev:armhf (4.1.1-3build1) ... Setting up libboost1.65-dev:armhf (1.65.1+dfsg-0ubuntu9) ... Setting up libgraphite2-dev:armhf (1.3.11-2) ... Setting up hdf5-helpers (1.10.0-patch1+docs-4build1) ... Setting up libqhull-r7:armhf (2015.2-4) ... Setting up libx11-data (2:1.6.5-1) ... Setting up libxau6:armhf (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-6build1) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up liburiparser1:armhf (0.8.5-1.1) ... Setting up libsz2:armhf (1.0.2-1) ... Setting up proj-data (5.1.0-1) ... Setting up libwebp6:armhf (0.6.1-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.042-1) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libfreexl-dev:armhf (1.0.5-1) ... Setting up libpaper1:armhf (1.1.24+nmu5ubuntu1) ... Creating config file /etc/papersize with new version Setting up gfortran (4:7.3.0-3ubuntu3) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libpython3.6-stdlib:armhf (3.6.6-1) ... Setting up libk5crypto3:armhf (1.16-2build1) ... Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ... Setting up libpcre3-dev:armhf (2:8.39-9) ... Setting up libdap25:armhf (3.19.1-2build1) ... Setting up fontconfig-config (2.12.6-0ubuntu2) ... Setting up python3.6 (3.6.6-1) ... Setting up libodbc1:armhf (2.3.4-1.1ubuntu3) ... Setting up libhdf5-100:armhf (1.10.0-patch1+docs-4build1) ... Setting up libmysqlclient-dev (5.7.22-0ubuntu18.04.1) ... Setting up libltdl-dev:armhf (2.4.6-2.1) ... Setting up libwind0-heimdal:armhf (7.5.0+dfsg-2) ... Setting up gettext (0.19.8.1-6build1) ... Setting up libblas-dev:armhf (3.8.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up libgif-dev (5.1.4-3) ... Setting up libepsilon-dev:armhf (0.9.2+dfsg-2) ... Setting up libasn1-8-heimdal:armhf (7.5.0+dfsg-2) ... Setting up liblapack3:armhf (3.8.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libhcrypto4-heimdal:armhf (7.5.0+dfsg-2) ... Setting up libaec-dev:armhf (1.0.2-1) ... Setting up libnss3:armhf (2:3.36.1-1ubuntu1) ... Setting up libproj13:armhf (5.1.0-1) ... Setting up libgeos-dev (3.6.2-1build2) ... Setting up libharfbuzz0b:armhf (1.7.6-1ubuntu1) ... Setting up libtiff5:armhf (4.0.9-6) ... Setting up autoconf (2.69-11) ... Setting up libthai0:armhf (0.1.27-2) ... Setting up file (1:5.33-3) ... Setting up libsuperlu5:armhf (5.2.1+dfsg1-3) ... Setting up libkmlbase1:armhf (1.3.0-5) ... Setting up libhx509-5-heimdal:armhf (7.5.0+dfsg-2) ... Setting up libqhull-dev:armhf (2015.2-4) ... Setting up libncurses5-dev:armhf (6.1+20180210-4ubuntu1) ... Setting up libogdi3.2 (3.2.1+ds-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libkmlxsd1:armhf (1.3.0-5) ... Setting up libjpeg8-dev:armhf (8c-2ubuntu8) ... Setting up libsuperlu-dev:armhf (5.2.1+dfsg1-3) ... Setting up gir1.2-harfbuzz-0.0:armhf (1.7.6-1ubuntu1) ... Setting up libjpeg-dev:armhf (8c-2ubuntu8) ... Setting up libdapserver7v5:armhf (3.19.1-2build1) ... Setting up libwebpmux3:armhf (0.6.1-2) ... Setting up libgeotiff2:armhf (1.4.2-2build2) ... 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 libreadline-dev:armhf (7.0-5) ... Setting up libice6:armhf (2:1.0.9-2) ... Setting up libtiffxx5:armhf (4.0.9-6) ... Setting up libwebpdemux2:armhf (0.6.1-2) ... Setting up libspatialite7:armhf (4.3.0a-5build2) ... Setting up libarpack2:armhf (3.5.0+real-2build1) ... Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up liburiparser-dev (0.8.5-1.1) ... Setting up libkrb5-3:armhf (1.16-2build1) ... Setting up libkmldom1:armhf (1.3.0-5) ... Setting up default-libmysqlclient-dev:armhf (1.0.4) ... Setting up libkrb5-26-heimdal:armhf (7.5.0+dfsg-2) ... Setting up libboost-dev:armhf (1.65.1.0ubuntu1) ... Setting up libpng-dev:armhf (1.6.34-1) ... Setting up libhdf4-0-alt (4.2.13-2) ... Setting up libspatialite-dev:armhf (4.3.0a-5build2) ... Setting up libxcb1:armhf (1.13-1) ... Setting up libharfbuzz-gobject0:armhf (1.7.6-1ubuntu1) ... Setting up libheimntlm0-heimdal:armhf (7.5.0+dfsg-2) ... Setting up liblapack-dev:armhf (3.8.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libtool (2.4.6-2.1) ... Setting up libpython3-stdlib:armhf (3.6.6-1) ... Setting up libfontconfig1:armhf (2.12.6-0ubuntu2) ... Setting up libsm6:armhf (2:1.2.2-1) ... Setting up libproj-dev:armhf (5.1.0-1) ... Setting up libhdf5-cpp-100:armhf (1.10.0-patch1+docs-4build1) ... Setting up libxcb-render0:armhf (1.13-1) ... Setting up libharfbuzz-icu0:armhf (1.7.6-1ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up python3 (3.6.6-1) ... Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ... Setting up libtiff5-dev:armhf (4.0.9-6) ... Setting up libx11-6:armhf (2:1.6.5-1) ... Setting up libhdf5-dev (1.10.0-patch1+docs-4build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libxmuu1:armhf (2:1.1.2-2) ... Setting up libogdi3.2-dev (3.2.1+ds-2) ... Setting up libwebp-dev:armhf (0.6.1-2) ... Setting up libgssapi-krb5-2:armhf (1.16-2build1) ... Setting up libarmadillo8 (1:8.400.0+dfsg-3) ... Setting up libpoppler73:armhf (0.62.0-2ubuntu3) ... Setting up libkmlengine1:armhf (1.3.0-5) ... Setting up libiculx60:armhf (60.2-6ubuntu1) ... Setting up libarpack2-dev:armhf (3.5.0+real-2build1) ... Setting up libxcb-shm0:armhf (1.13-1) ... Setting up libxt6:armhf (1:1.1.5-1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libxft2:armhf (2.3.2-2) ... Setting up libgssapi3-heimdal:armhf (7.5.0+dfsg-2) ... Setting up python3-lib2to3 (3.6.6-1) ... Setting up python3-distutils (3.6.6-1) ... Setting up fontconfig (2.12.6-0ubuntu2) ... Regenerating fonts cache... done. Setting up libarmadillo-dev (1:8.400.0+dfsg-3) ... Setting up libtiff-dev (4.0.9-6) ... Setting up libgeotiff-dev:armhf (1.4.2-2build2) ... Setting up libpoppler-dev:armhf (0.62.0-2ubuntu3) ... Setting up libxext6:armhf (2:1.3.3-1) ... Setting up libglib2.0-dev-bin (2.56.1-2ubuntu1) ... Setting up libxss1:armhf (1:1.2.2-1) ... Setting up libkmlconvenience1:armhf (1.3.0-5) ... Setting up libglib2.0-dev:armhf (2.56.1-2ubuntu1) ... Setting up xauth (1:1.0.10-1) ... Setting up libldap-2.4-2:armhf (2.4.46+dfsg-5ubuntu1) ... Setting up libkmlregionator1:armhf (1.3.0-5) ... Setting up libpango-1.0-0:armhf (1.42.1-2) ... Setting up libcairo2:armhf (1.15.10-3) ... Setting up libpoppler-private-dev:armhf (0.62.0-2ubuntu3) ... Setting up libcurl3-gnutls:armhf (7.60.0-2ubuntu1) ... Setting up libtk8.6:armhf (8.6.8-4) ... Setting up libcurl4:armhf (7.60.0-2ubuntu1) ... Setting up libkml-dev:armhf (1.3.0-5) ... Setting up libpangoft2-1.0-0:armhf (1.42.1-2) ... Setting up libdapclient6v5:armhf (3.19.1-2build1) ... Setting up libpq5:armhf (10.4-2) ... Setting up libnetcdf13:armhf (1:4.6.1-1) ... Setting up libcurl4-gnutls-dev:armhf (7.60.0-2ubuntu1) ... Setting up libnetcdf-dev (1:4.6.1-1) ... Setting up libxerces-c3.2:armhf (3.2.1+debian-2) ... Setting up libpq-dev (10.4-2) ... Setting up libpangocairo-1.0-0:armhf (1.42.1-2) ... Setting up libhdf4-alt-dev (4.2.13-2) ... Setting up r-base-core (3.5.1-1) ... Creating config file /etc/R/Renviron with new version Setting up r-bioc-biocgenerics (0.26.0-3build1) ... Setting up r-cran-bitops (1.0-6-4) ... Setting up r-cran-formatr (1.5-3) ... Setting up r-cran-futile.options (1.0.1-2) ... Setting up r-cran-rcurl (1.95-4.10-2) ... Setting up r-cran-lambda.r (1.2.3-2) ... Setting up r-cran-snow (1:0.4.2-2) ... Setting up r-bioc-s4vectors (0.18.3-1) ... Setting up r-bioc-genomeinfodbdata (1.1.0-3build1) ... Setting up r-cran-futile.logger (1.4.3-3) ... Setting up r-bioc-biocparallel (1.14.1-1build1) ... Setting up odbcinst1debian2:armhf (2.3.4-1.1ubuntu3) ... Setting up libharfbuzz-dev:armhf (1.7.6-1ubuntu1) ... Setting up unixodbc-dev:armhf (2.3.4-1.1ubuntu3) ... Setting up dh-autoreconf (19) ... Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ... Setting up odbcinst (2.3.4-1.1ubuntu3) ... Setting up libgdal20 (2.3.1+dfsg-1ubuntu1) ... Setting up libicu-dev (60.2-6ubuntu1) ... Setting up r-base-dev (3.5.1-1) ... Setting up libxml2-dev:armhf (2.9.4+dfsg1-7build1) ... Setting up debhelper (11.3.2ubuntu1) ... Setting up dh-r (20180617) ... Setting up libxerces-c-dev (3.2.1+debian-2) ... Setting up libdap-dev:armhf (3.19.1-2build1) ... Setting up dh-strip-nondeterminism (0.042-1) ... Setting up libgdal-dev (2.3.1+dfsg-1ubuntu1) ... Setting up r-bioc-iranges (2.14.10-1build1) ... Setting up r-bioc-genomeinfodb (1.16.0-3) ... Setting up r-bioc-xvector (0.20.0-2build1) ... Setting up r-bioc-biostrings (2.48.0-2build1) ... Setting up r-bioc-genomicranges (1.32.3-1build1) ... Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Processing triggers for systemd (238-5ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-130-generic arm64 (armv7l) Toolchain package versions: binutils_2.30-22ubuntu1 dpkg-dev_1.19.0.5ubuntu3 g++-7_7.3.0-24ubuntu1 gcc-7_7.3.0-24ubuntu1 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-24ubuntu1 libstdc++6_8.1.0-9ubuntu1 linux-libc-dev_4.17.0-4.5 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0~alpha1 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_2.30-22ubuntu1 binutils-arm-linux-gnueabihf_2.30-22ubuntu1 binutils-common_2.30-22ubuntu1 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_7.3.0-24ubuntu1 dash_0.5.8-2.10 dctrl-tools_2.24-2build1 debconf_1.5.67 debhelper_11.3.2ubuntu1 debianutils_4.8.6 default-libmysqlclient-dev_1.0.4 dh-autoreconf_19 dh-r_20180617 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu3 dpkg-dev_1.19.0.5ubuntu3 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu1 file_1:5.33-3 findutils_4.6.0+git+20170828-2 fontconfig_2.12.6-0ubuntu2 fontconfig-config_2.12.6-0ubuntu2 fonts-dejavu-core_2.37-1 g++_4:7.3.0-3ubuntu3 g++-7_7.3.0-24ubuntu1 gcc_4:7.3.0-3ubuntu3 gcc-7_7.3.0-24ubuntu1 gcc-7-base_7.3.0-24ubuntu1 gcc-8-base_8.1.0-9ubuntu1 gdal-data_2.3.1+dfsg-1ubuntu1 gettext_0.19.8.1-6build1 gettext-base_0.19.8.1-6build1 gfortran_4:7.3.0-3ubuntu3 gfortran-7_7.3.0-24ubuntu1 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.7.6-1ubuntu1 gpg_2.2.8-1ubuntu1 gpg-agent_2.2.8-1ubuntu1 gpgconf_2.2.8-1ubuntu1 gpgv_2.2.8-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hdf5-helpers_1.10.0-patch1+docs-4build1 hostname_3.20 icu-devtools_60.2-6ubuntu1 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 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.12-4ubuntu6 libapt-pkg5.0_1.7.0~alpha1 libarchive-zip-perl_1.60-1 libargon2-0_0~20171227-0.1 libargon2-1_0~20171227-0.1 libarmadillo-dev_1:8.400.0+dfsg-3 libarmadillo8_1:8.400.0+dfsg-3 libarpack2_3.5.0+real-2build1 libarpack2-dev_3.5.0+real-2build1 libasan4_7.3.0-24ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2 libassuan0_2.5.1-2 libatomic1_8.1.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu2 libaudit1_1:2.8.3-1ubuntu2 libbinutils_2.30-22ubuntu1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.32-0.1ubuntu1 libboost-dev_1.65.1.0ubuntu1 libboost1.65-dev_1.65.1+dfsg-0ubuntu9 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_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 libcairo2_1.15.10-3 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-9ubuntu1 libcharls-dev_1.1.0+dfsg-2 libcharls1_1.1.0+dfsg-2 libcilkrts5_7.3.0-24ubuntu1 libcom-err2_1.44.2-1 libcomerr2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu2 libcurl3-gnutls_7.60.0-2ubuntu1 libcurl4_7.60.0-2ubuntu1 libcurl4-gnutls-dev_7.60.0-2ubuntu1 libdap-dev_3.19.1-2build1 libdap25_3.19.1-2build1 libdapclient6v5_3.19.1-2build1 libdapserver7v5_3.19.1-2build1 libdatrie1_0.2.12-1 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 libelf1_0.170-0.5 libepsilon-dev_0.9.2+dfsg-2 libepsilon1_0.9.2+dfsg-2 libexpat1_2.2.5-3 libexpat1-dev_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_0.042-1 libfile-which-perl_1.21-1 libfontconfig1_2.12.6-0ubuntu2 libfreetype6_2.8.1-2ubuntu2 libfreexl-dev_1.0.5-1 libfreexl1_1.0.5-1 libfribidi0_0.19.7-3 libfyba-dev_4.1.1-3build1 libfyba0_4.1.1-3build1 libgcc-7-dev_7.3.0-24ubuntu1 libgcc1_1:8.1.0-9ubuntu1 libgcrypt20_1.8.2-2ubuntu1 libgdal-dev_2.3.1+dfsg-1ubuntu1 libgdal20_2.3.1+dfsg-1ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libgeos-3.6.2_3.6.2-1build2 libgeos-c1v5_3.6.2-1build2 libgeos-dev_3.6.2-1build2 libgeotiff-dev_1.4.2-2build2 libgeotiff2_1.4.2-2build2 libgfortran-7-dev_7.3.0-24ubuntu1 libgfortran4_7.3.0-24ubuntu1 libgif-dev_5.1.4-3 libgif7_5.1.4-3 libgirepository-1.0-1_1.56.1-1 libglib2.0-0_2.56.1-2ubuntu1 libglib2.0-bin_2.56.1-2ubuntu1 libglib2.0-data_2.56.1-2ubuntu1 libglib2.0-dev_2.56.1-2ubuntu1 libglib2.0-dev-bin_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.1.0-9ubuntu1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libgraphite2-dev_1.3.11-2 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-2 libharfbuzz-dev_1.7.6-1ubuntu1 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r-bioc-iranges_2.14.10-1build1 r-bioc-s4vectors_0.18.3-1 r-bioc-xvector_0.20.0-2build1 r-cran-bitops_1.0-6-4 r-cran-formatr_1.5-3 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-lambda.r_1.2.3-2 r-cran-rcurl_1.95-4.10-2 r-cran-snow_1:0.4.2-2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-5ubuntu2 systemd-sysv_238-5ubuntu2 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 ucf_3.0038 unixodbc-dev_2.3.4-1.1ubuntu3 unzip_6.0-21ubuntu1 util-linux_2.32-0.1ubuntu1 uuid-dev_2.32-0.1ubuntu1 x11-common_1:7.7+19ubuntu8 xauth_1:1.0.10-1 xdg-utils_1.1.3-1ubuntu1 xz-utils_5.2.2-1.3 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Jul 5 06:44:29 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-bioc-rsamtools_1.32.2-1.dsc dpkg-source: info: extracting r-bioc-rsamtools in r-bioc-rsamtools-1.32.2 dpkg-source: info: unpacking r-bioc-rsamtools_1.32.2.orig.tar.gz dpkg-source: info: unpacking r-bioc-rsamtools_1.32.2-1.debian.tar.xz dpkg-source: info: applying use_debian_packaged_zlib.patch dpkg-source: info: applying skip_test_requiring_network.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-15094779 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15094779 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15094779 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package r-bioc-rsamtools dpkg-buildpackage: info: source version 1.32.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build r-bioc-rsamtools-1.32.2 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --buildsystem R dh_testdir -O--buildsystem=R dh_auto_clean -O--buildsystem=R dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules build-arch dh build-arch --buildsystem R dh_testdir -a -O--buildsystem=R dh_update_autotools_config -a -O--buildsystem=R dh_autoreconf -a -O--buildsystem=R dh_auto_configure -a -O--buildsystem=R dh_auto_build -a -O--buildsystem=R dh_auto_test -a -O--buildsystem=R create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --buildsystem R dh_testroot -a -O--buildsystem=R dh_prep -a -O--buildsystem=R dh_installdirs -a -O--buildsystem=R dh_auto_install -a -O--buildsystem=R I: R packages needed for DEP8: runit, shortread I: R Package: Rsamtools Version: 1.32.2 I: Building using R version 3.5.1-1 I: R API version: r-api-3.5 I: Using built-time from d/changelog: Thu, 05 Jul 2018 08:25:42 +0200 mkdir -p /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library R CMD INSTALL -l /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 05 Jul 2018 08:25:42 +0200'" * installing *source* package ‘Rsamtools’ ... ** libs make[1]: Entering directory '/<>/src' gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PileupBuffer.cpp -o PileupBuffer.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PosCacheColl.cpp -o PosCacheColl.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_Rsamtools.c -o R_init_Rsamtools.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ResultManager.cpp -o ResultManager.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c as_bam.c -o as_bam.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bam_data.c -o bam_data.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bam_mate_iter.cpp -o bam_mate_iter.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bambuffer.c -o bambuffer.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bamfile.c -o bamfile.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bcffile.c -o bcffile.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c encode.c -o encode.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fafile.c -o fafile.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c idxstats.c -o idxstats.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_sam.c -o io_sam.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o g++ -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pileup.cpp -o pileup.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pileupbam.c -o pileupbam.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools_patch.c -o samtools_patch.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scan_bam_data.c -o scan_bam_data.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabixfile.c -o tabixfile.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tagfilter.c -o tagfilter.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zip_compression.c -o zip_compression.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bgzf.c -o samtools/bgzf.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/kstring.c -o samtools/kstring.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_aux.c -o samtools/bam_aux.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam.c -o samtools/bam.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_import.c -o samtools/bam_import.o In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0, from /usr/include/limits.h:26, from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:194, from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/syslimits.h:7, from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:34, from /usr/include/zconf.h:418, from /usr/include/zlib.h:34, from samtools/bam_import.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/sam.c -o samtools/sam.o In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0, from /usr/include/string.h:26, from samtools/sam.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_index.c -o samtools/bam_index.o samtools/bam_index.c: In function ‘bam_index_load_core’: samtools/bam_index.c:335:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(magic, 1, 4, fp); ^~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:342:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&idx->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:355:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&size, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:358:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&key, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:362:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&p->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:366:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p->list, 16, p->n, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:376:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&index2->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam_index.c:380:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(index2->offset, index2->n, 8, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_pileup.c -o samtools/bam_pileup.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_md.c -o samtools/bam_md.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/razf.c -o samtools/razf.o samtools/razf.c: In function ‘razf_flush’: samtools/razf.c:221:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:234:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c: In function ‘_razf_write’: samtools/razf.c:201:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c: In function ‘razf_close’: samtools/razf.c:810:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->in, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:811:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->out, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:814:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:816:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c: In function ‘razf_end_flush’: samtools/razf.c:258:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c: In function ‘save_zindex’: samtools/razf.c:96:12: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:99:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:106:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/razf.c:107:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/faidx.c -o samtools/faidx.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/knetfile.c -o samtools/knetfile.o In file included from /usr/include/time.h:25:0, from samtools/knetfile.c:33: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from samtools/knetfile.c:49:0: samtools/knetfile.c: In function ‘kftp_send_cmd’: samtools/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ samtools/knetfile.c:239:2: note: in expansion of macro ‘netwrite’ netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^~~~~~~~ samtools/knetfile.c: In function ‘khttp_connect_file’: samtools/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ samtools/knetfile.c:418:2: note: in expansion of macro ‘netwrite’ netwrite(fp->fd, buf, l); ^~~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_sort.c -o samtools/bam_sort.o In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0, from /usr/include/stdlib.h:25, from samtools/bam_sort.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/sam_header.c -o samtools/sam_header.o In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0, from /usr/include/stdio.h:27, from samtools/sam_header.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_reheader.c -o samtools/bam_reheader.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/kprobaln.c -o samtools/kprobaln.o ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0, from /usr/include/limits.h:26, from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:194, from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/syslimits.h:7, from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:34, from /usr/include/zconf.h:418, from /usr/include/zlib.h:34, from samtools/bcftools/vcf.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o In file included from /usr/include/alloca.h:21:0, from samtools/bcftools/bcfutils.c:3: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/index.c -o samtools/bcftools/index.o In file included from /usr/include/assert.h:35:0, from samtools/bcftools/index.c:2: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabix/index.c -o tabix/index.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-HaWyuj/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabix/bedidx.c -o tabix/bedidx.o ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools" mkdir -p "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix" cp samtools/*.h "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/" cp samtools/bcftools/*h "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/" cp tabix/*h "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/" cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \ "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/" mkdir -p "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib" cp libbam.a libbcf.a libtabix.a "/<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib" g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbam.a /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -L/usr/lib/R/lib -lR make[1]: Leaving directory '/<>/src' make[1]: Entering directory '/<>/src' make[1]: Leaving directory '/<>/src' installing to /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rsamtools) rm -f /<>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.1.3) I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.8) I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6) I: Using r-cran-runit for Recommends:runit I: Using r-bioc-shortread for Recommends:shortread I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures W: Cannot find a debian package for Suggests:TxDb.Dmelanogaster.UCSC.dm3.ensGene W: Cannot find a debian package for Suggests:KEGG.db W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg18.knownGene W: Cannot find a debian package for Suggests:RNAseqData.HNRNPC.bam.chr14 W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19 W: Cannot find a debian package for Suggests:BiocStyle I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.25.1) I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.25) I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.12) I: Using r-bioc-xvector for Imports:XVector (>= 0.19.7) I: Using r-cran-bitops for Imports:bitops I: Using r-bioc-biocparallel for Imports:BiocParallel dh_install -a -O--buildsystem=R dh_installdocs -a -O--buildsystem=R dh_installchangelogs -a -O--buildsystem=R dh_installexamples -a -O--buildsystem=R dh_installman -a -O--buildsystem=R dh_installcatalogs -a -O--buildsystem=R dh_installcron -a -O--buildsystem=R dh_installdebconf -a -O--buildsystem=R dh_installemacsen -a -O--buildsystem=R dh_installifupdown -a -O--buildsystem=R dh_installinfo -a -O--buildsystem=R dh_installinit -a -O--buildsystem=R dh_installsystemd -a -O--buildsystem=R dh_installmenu -a -O--buildsystem=R dh_installmime -a -O--buildsystem=R dh_installmodules -a -O--buildsystem=R dh_installlogcheck -a -O--buildsystem=R dh_installlogrotate -a -O--buildsystem=R dh_installpam -a -O--buildsystem=R dh_installppp -a -O--buildsystem=R dh_installudev -a -O--buildsystem=R dh_installgsettings -a -O--buildsystem=R dh_bugfiles -a -O--buildsystem=R dh_ucf -a -O--buildsystem=R dh_lintian -a -O--buildsystem=R dh_gconf -a -O--buildsystem=R dh_icons -a -O--buildsystem=R dh_perl -a -O--buildsystem=R dh_usrlocal -a -O--buildsystem=R dh_link -a -O--buildsystem=R dh_installwm -a -O--buildsystem=R dh_installxfonts -a -O--buildsystem=R dh_strip_nondeterminism -a -O--buildsystem=R dh_compress -a -O--buildsystem=R dh_fixperms -a -O--buildsystem=R dh_missing -a -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -a -O--buildsystem=R dh_installdeb -a -O--buildsystem=R dh_gencontrol -a -O--buildsystem=R dh_md5sums -a -O--buildsystem=R dh_builddeb -a -O--buildsystem=R INFO: pkgstriptranslations version 139 INFO: pkgstriptranslations version 139 pkgstriptranslations: processing r-bioc-rsamtools (in debian/r-bioc-rsamtools); do_strip: , oemstrip: pkgstriptranslations: processing r-bioc-rsamtools-dbgsym (in debian/.debhelper/r-bioc-rsamtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-bioc-rsamtools/DEBIAN/control, package r-bioc-rsamtools, directory debian/r-bioc-rsamtools pkgstripfiles: processing control file: debian/.debhelper/r-bioc-rsamtools/dbgsym-root/DEBIAN/control, package r-bioc-rsamtools-dbgsym, directory debian/.debhelper/r-bioc-rsamtools/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-bioc-rsamtools-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-bioc-rsamtools-dbgsym' in 'debian/.debhelper/scratch-space/build-r-bioc-rsamtools/r-bioc-rsamtools-dbgsym_1.32.2-1_armhf.deb'. pkgstripfiles: Truncating usr/share/doc/r-bioc-rsamtools/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-bioc-rsamtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-bioc-rsamtools' in '../r-bioc-rsamtools_1.32.2-1_armhf.deb'. Renaming r-bioc-rsamtools-dbgsym_1.32.2-1_armhf.deb to r-bioc-rsamtools-dbgsym_1.32.2-1_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../r-bioc-rsamtools_1.32.2-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build r-bioc-rsamtools-1.32.2 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180707-0758 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ r-bioc-rsamtools_1.32.2-1_armhf.changes: ---------------------------------------- Format: 1.8 Date: Thu, 05 Jul 2018 08:25:42 +0200 Source: r-bioc-rsamtools Binary: r-bioc-rsamtools Architecture: armhf Version: 1.32.2-1 Distribution: cosmic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i Changes: r-bioc-rsamtools (1.32.2-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 7a4b7908d9a14765af1ea50d306220183ea6a940 829068 r-bioc-rsamtools-dbgsym_1.32.2-1_armhf.ddeb c2e1cf203424ca46dabbf6ad8ba68080733e7457 13172 r-bioc-rsamtools_1.32.2-1_armhf.buildinfo b482af15a4816fe2354a653ef09ae568a8bbc7a8 3491352 r-bioc-rsamtools_1.32.2-1_armhf.deb Checksums-Sha256: f5e4bbd1f5d77258a0ebf758e916b92804e8dce51c3bfa7f8596725a1d3f7880 829068 r-bioc-rsamtools-dbgsym_1.32.2-1_armhf.ddeb 01295cf43fea347154db3e802f9b13ead6c0869c781cde9c81560c591bc4d3cc 13172 r-bioc-rsamtools_1.32.2-1_armhf.buildinfo 82f133851f576ecc12d6f4d04d6b5ca88fa51e5dd21b17640b463b63716066b0 3491352 r-bioc-rsamtools_1.32.2-1_armhf.deb Files: f1a2272a4a329e208a4c08e171a893a4 829068 debug optional r-bioc-rsamtools-dbgsym_1.32.2-1_armhf.ddeb 6e5e906f4c510cc79dbd9e2053aa6691 13172 gnu-r optional r-bioc-rsamtools_1.32.2-1_armhf.buildinfo f9f790e371e5e7885e4404d9f5360869 3491352 gnu-r optional r-bioc-rsamtools_1.32.2-1_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ r-bioc-rsamtools_1.32.2-1_armhf.deb ----------------------------------- new debian package, version 2.0. size 3491352 bytes: control archive=4348 bytes. 1117 bytes, 17 lines control 11990 bytes, 131 lines md5sums Package: r-bioc-rsamtools Version: 1.32.2-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian R Packages Maintainers Installed-Size: 5318 Depends: r-base-core (>= 3.5.1-1), r-api-3.5, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3) Recommends: r-cran-runit, r-bioc-shortread Suggests: r-bioc-genomicalignments, r-bioc-genomicfeatures Section: gnu-r Priority: optional Homepage: https://bioconductor.org/packages/Rsamtools/ Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), binary variant call (BCF) and compressed indexed tab-delimited (tabix) files. drwxr-xr-x root/root 0 2018-07-05 06:25 ./ drwxr-xr-x root/root 0 2018-07-05 06:25 ./usr/ drwxr-xr-x root/root 0 2018-07-05 06:25 ./usr/lib/ drwxr-xr-x root/root 0 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2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf -rw-r--r-- root/root 77 2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.bci -rw-r--r-- root/root 559422 2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam -rw-r--r-- root/root 3778 2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz -rw-r--r-- root/root 259 2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi -rw-r--r-- root/root 348 2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam -rw-r--r-- root/root 96 2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai -rw-r--r-- root/root 368 2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam -rw-r--r-- root/root 203 2018-07-05 06:25 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam -rw-r--r-- root/root 176 2018-07-05 06:25 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+------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 18632 Build-Time: 129 Distribution: cosmic-proposed Host Architecture: armhf Install-Time: 91 Job: r-bioc-rsamtools_1.32.2-1.dsc Machine Architecture: arm64 Package: r-bioc-rsamtools Package-Time: 221 Source-Version: 1.32.2-1 Space: 18632 Status: successful Version: 1.32.2-1 -------------------------------------------------------------------------------- Finished at 20180707-0758 Build needed 00:03:41, 18632k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15094779 Scanning for processes to kill in build PACKAGEBUILD-15094779