DC-Build-Header: freebayes 1.2.0-2 / 2019-01-09 21:53:19 +0000 DC-Task: type:rebuild-binarch-only source:freebayes version:1.2.0-2 chroot:unstable esttime:163 logfile:/tmp/freebayes_1.2.0-2_unstable_clang7.log modes:clang7:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang7 freebayes_1.2.0-2' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-11-16.eu-central-1.compute.internal +==============================================================================+ | freebayes 1.2.0-2 (amd64) Wed, 09 Jan 2019 21:53:19 +0000 | +==============================================================================+ Package: freebayes Version: 1.2.0-2 Source Version: 1.2.0-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-c40bd878-b368-4928-bb7f-fdc3d2a20b52' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang7 ----------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=7 + echo 'Install of clang-7' Install of clang-7 + apt-get update Get:1 http://127.0.0.1:9999/debian sid InRelease [238 kB] Get:2 http://127.0.0.1:9999/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-1430.36.pdiff [24.1 kB] Get:4 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-1430.36.pdiff [24.1 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-1430.36.pdiff [40.9 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-1430.36.pdiff [40.9 kB] Get:6 http://127.0.0.1:9999/debian sid/main Translation-en [6275 kB] Fetched 6633 kB in 2s (3337 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-7 libomp-7-dev libobjc-8-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-7-dev libclang1-7 libedit2 libgc1c2 libllvm7 libobjc4 libomp5-7 Suggested packages: clang-7-doc libomp-7-doc Recommended packages: llvm-7-dev python The following NEW packages will be installed: clang-7 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-7-dev libclang1-7 libedit2 libgc1c2 libllvm7 libobjc-8-dev libobjc4 libomp-7-dev libomp5-7 0 upgraded, 14 newly installed, 0 to remove and 5 not upgraded. Need to get 34.5 MB of archives. After this operation, 185 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian sid/main amd64 libbsd0 amd64 0.9.1-1 [99.3 kB] Get:2 http://127.0.0.1:9999/debian sid/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libllvm7 amd64 1:7.0.1-4 [13.0 MB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libobjc4 amd64 8.2.0-14 [50.4 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 libobjc-8-dev amd64 8.2.0-14 [225 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 libc6-i386 amd64 2.28-4 [2873 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 lib32gcc1 amd64 1:8.2.0-14 [47.9 kB] Get:9 http://127.0.0.1:9999/debian sid/main amd64 lib32stdc++6 amd64 8.2.0-14 [406 kB] Get:10 http://127.0.0.1:9999/debian sid/main amd64 libclang-common-7-dev amd64 1:7.0.1-4 [3155 kB] Get:11 http://127.0.0.1:9999/debian sid/main amd64 libclang1-7 amd64 1:7.0.1-4 [5991 kB] Get:12 http://127.0.0.1:9999/debian sid/main amd64 clang-7 amd64 1:7.0.1-4 [7887 kB] Get:13 http://127.0.0.1:9999/debian sid/main amd64 libomp5-7 amd64 1:7.0.1-4 [318 kB] Get:14 http://127.0.0.1:9999/debian sid/main amd64 libomp-7-dev amd64 1:7.0.1-4 [57.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.5 MB in 1s (48.3 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11802 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20181209-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20181209-1) ... Selecting previously unselected package libllvm7:amd64. Preparing to unpack .../02-libllvm7_1%3a7.0.1-4_amd64.deb ... Unpacking libllvm7:amd64 (1:7.0.1-4) ... Selecting previously unselected package libgc1c2:amd64. Preparing to unpack .../03-libgc1c2_1%3a7.6.4-0.4_amd64.deb ... Unpacking libgc1c2:amd64 (1:7.6.4-0.4) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../04-libobjc4_8.2.0-14_amd64.deb ... Unpacking libobjc4:amd64 (8.2.0-14) ... Selecting previously unselected package libobjc-8-dev:amd64. Preparing to unpack .../05-libobjc-8-dev_8.2.0-14_amd64.deb ... Unpacking libobjc-8-dev:amd64 (8.2.0-14) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../06-libc6-i386_2.28-4_amd64.deb ... Unpacking libc6-i386 (2.28-4) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../07-lib32gcc1_1%3a8.2.0-14_amd64.deb ... Unpacking lib32gcc1 (1:8.2.0-14) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../08-lib32stdc++6_8.2.0-14_amd64.deb ... Unpacking lib32stdc++6 (8.2.0-14) ... Selecting previously unselected package libclang-common-7-dev. Preparing to unpack .../09-libclang-common-7-dev_1%3a7.0.1-4_amd64.deb ... Unpacking libclang-common-7-dev (1:7.0.1-4) ... Selecting previously unselected package libclang1-7:amd64. Preparing to unpack .../10-libclang1-7_1%3a7.0.1-4_amd64.deb ... Unpacking libclang1-7:amd64 (1:7.0.1-4) ... Selecting previously unselected package clang-7. Preparing to unpack .../11-clang-7_1%3a7.0.1-4_amd64.deb ... Unpacking clang-7 (1:7.0.1-4) ... Selecting previously unselected package libomp5-7:amd64. Preparing to unpack .../12-libomp5-7_1%3a7.0.1-4_amd64.deb ... Unpacking libomp5-7:amd64 (1:7.0.1-4) ... Selecting previously unselected package libomp-7-dev. Preparing to unpack .../13-libomp-7-dev_1%3a7.0.1-4_amd64.deb ... Unpacking libomp-7-dev (1:7.0.1-4) ... Setting up libgc1c2:amd64 (1:7.6.4-0.4) ... Setting up libc6-i386 (2.28-4) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libomp5-7:amd64 (1:7.0.1-4) ... Processing triggers for libc-bin (2.28-4) ... Setting up libomp-7-dev (1:7.0.1-4) ... Setting up lib32gcc1 (1:8.2.0-14) ... Setting up libedit2:amd64 (3.1-20181209-1) ... Setting up libobjc4:amd64 (8.2.0-14) ... Setting up libobjc-8-dev:amd64 (8.2.0-14) ... Setting up libllvm7:amd64 (1:7.0.1-4) ... Setting up libclang1-7:amd64 (1:7.0.1-4) ... Setting up lib32stdc++6 (8.2.0-14) ... Setting up libclang-common-7-dev (1:7.0.1-4) ... Setting up clang-7 (1:7.0.1-4) ... Processing triggers for libc-bin (2.28-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-7 g++-4.6 + ln -s clang-7 gcc-4.6 + ln -s clang-7 cpp-4.6 + ln -s clang-7 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-7 g++-4.7 + ln -s clang-7 gcc-4.7 + ln -s clang-7 cpp-4.7 + ln -s clang-7 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-7 g++-4.8 + ln -s clang-7 gcc-4.8 + ln -s clang-7 cpp-4.8 + ln -s clang-7 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-7 g++-4.9 + ln -s clang-7 gcc-4.9 + ln -s clang-7 cpp-4.9 + ln -s clang-7 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-7 g++-5 + ln -s clang-7 gcc-5 + ln -s clang-7 cpp-5 + ln -s clang-7 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-7 g++-6 + ln -s clang-7 gcc-6 + ln -s clang-7 cpp-6 + ln -s clang-7 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-7 g++-7 + ln -s clang-7 gcc-7 + ln -s clang-7 cpp-7 + ln -s clang-7 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-7 g++-8 + ln -s clang-7 gcc-8 + ln -s clang-7 cpp-8 + ln -s clang-7 gcc + echo 'gcc-8 hold' + dpkg --set-selections + echo 'g++-8 hold' + dpkg --set-selections + cd - /build/freebayes-bUpB4o + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang7'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libmpfr6 libpam-modules libpam-modules-bin libpam-runtime libpam0g 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1519 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian sid/main amd64 libpam0g amd64 1.1.8-4 [124 kB] Get:2 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules-bin amd64 1.1.8-4 [106 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules amd64 1.1.8-4 [305 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 libpam-runtime all 1.1.8-4 [211 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libmpfr6 amd64 4.0.2~rc1-1 [773 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1519 kB in 0s (28.0 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.1.8-4_all.deb ... Unpacking libpam-runtime (1.1.8-4) over (1.1.8-3.8) ... Setting up libpam-runtime (1.1.8-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.0.2~rc1-1_amd64.deb ... Unpacking libmpfr6:amd64 (4.0.2~rc1-1) over (4.0.1-2) ... Setting up libmpfr6:amd64 (4.0.2~rc1-1) ... Processing triggers for libc-bin (2.28-4) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'freebayes' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/freebayes.git Please use: git clone https://salsa.debian.org/med-team/freebayes.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2653 kB of source archives. Get:1 http://127.0.0.1:9999/debian sid/main freebayes 1.2.0-2 (dsc) [2171 B] Get:2 http://127.0.0.1:9999/debian sid/main freebayes 1.2.0-2 (tar) [2640 kB] Get:3 http://127.0.0.1:9999/debian sid/main freebayes 1.2.0-2 (diff) [10.8 kB] Fetched 2653 kB in 1s (4745 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/freebayes-bUpB4o/freebayes-1.2.0' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-bUpB4o' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-QFQTWU/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-QFQTWU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-QFQTWU/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-QFQTWU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-QFQTWU/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-QFQTWU/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (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 NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-QFQTWU/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), cmake, pkg-config, python, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-2~), libtabixpp-dev, libseqlib-dev, bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) Filtered Build-Depends: debhelper (>= 11~), cmake, pkg-config, python, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-2~), libtabixpp-dev, libseqlib-dev, bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) dpkg-deb: building package 'sbuild-build-depends-freebayes-dummy' in '/<>/resolver-QFQTWU/apt_archive/sbuild-build-depends-freebayes-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-freebayes-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-QFQTWU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-QFQTWU/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-QFQTWU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-QFQTWU/apt_archive ./ Sources [589 B] Get:5 copy:/<>/resolver-QFQTWU/apt_archive ./ Packages [667 B] Fetched 2219 B in 0s (0 B/s) Reading package lists... Reading package lists... Install freebayes build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbamtools-dev libbamtools2.5.1 libblas3 libbwa-dev libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts-dev libhts-private-dev libhts2 libice6 libicu63 libjbig0 libjpeg62-turbo libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libprocps7 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib1 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libsqlite3-0 libssh2-1 libssl1.1 libssw-dev libssw0 libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler lsb-base m4 man-db mime-support openssl parallel pkg-config po-debconf procps python python-minimal python2 python2-minimal python2.7 python2.7-minimal r-base-core r-cran-assertthat r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-withr readline-common samtools sensible-utils sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc krb5-doc krb5-user liblzma-doc lm-sensors tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-webshot r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-dichromat r-cran-shiny r-cran-shinyjs r-cran-rstudioapi r-cran-knitr r-cran-rmarkdown r-cran-dplyr r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats libgdal-dev r-cran-getopt r-cran-testthat r-cran-foreach r-cran-doparallel r-cran-iterators r-cran-inline r-cran-htmltools readline-doc isag Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-lubridate r-cran-domc r-cran-abind r-cran-bit64 r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-dbi cwltool cron | cron-daemon 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 bc bsdmainutils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbamtools-dev libbamtools2.5.1 libblas3 libbwa-dev libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts-dev libhts-private-dev libhts2 libice6 libicu63 libjbig0 libjpeg62-turbo libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libprocps7 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib1 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libsqlite3-0 libssh2-1 libssl1.1 libssw-dev libssw0 libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler lsb-base m4 man-db mime-support openssl parallel pkg-config po-debconf procps python python-minimal python2 python2-minimal python2.7 python2.7-minimal r-base-core r-cran-assertthat r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-withr readline-common samtools sbuild-build-depends-freebayes-dummy sensible-utils sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 193 newly installed, 0 to remove and 0 not upgraded. Need to get 115 MB of archives. After this operation, 303 MB of additional disk space will be used. Get:1 copy:/<>/resolver-QFQTWU/apt_archive ./ sbuild-build-depends-freebayes-dummy 0.invalid.0 [960 B] Get:2 http://127.0.0.1:9999/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 groff-base amd64 1.22.4-2 [917 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libpipeline1 amd64 1.5.0-2 [29.5 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 man-db amd64 2.8.5-1 [1274 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 libpython2.7-minimal amd64 2.7.15-5 [394 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 python2.7-minimal amd64 2.7.15-5 [1365 kB] Get:9 http://127.0.0.1:9999/debian sid/main amd64 python2-minimal amd64 2.7.15-3 [41.3 kB] Get:10 http://127.0.0.1:9999/debian sid/main amd64 python-minimal amd64 2.7.15-3 [20.9 kB] Get:11 http://127.0.0.1:9999/debian sid/main amd64 mime-support all 3.61 [37.1 kB] Get:12 http://127.0.0.1:9999/debian sid/main amd64 libexpat1 amd64 2.2.6-1 [105 kB] Get:13 http://127.0.0.1:9999/debian sid/main amd64 readline-common all 7.0-5 [70.6 kB] Get:14 http://127.0.0.1:9999/debian sid/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:15 http://127.0.0.1:9999/debian sid/main amd64 libsqlite3-0 amd64 3.26.0+fossilbc891ac6b-1 [634 kB] Get:16 http://127.0.0.1:9999/debian sid/main amd64 libssl1.1 amd64 1.1.1a-1 [1527 kB] Get:17 http://127.0.0.1:9999/debian sid/main amd64 libpython2.7-stdlib amd64 2.7.15-5 [1909 kB] Get:18 http://127.0.0.1:9999/debian sid/main amd64 python2.7 amd64 2.7.15-5 [299 kB] Get:19 http://127.0.0.1:9999/debian sid/main amd64 libpython2-stdlib amd64 2.7.15-3 [20.7 kB] Get:20 http://127.0.0.1:9999/debian sid/main amd64 libpython-stdlib amd64 2.7.15-3 [20.7 kB] Get:21 http://127.0.0.1:9999/debian sid/main amd64 python2 amd64 2.7.15-3 [41.5 kB] Get:22 http://127.0.0.1:9999/debian sid/main amd64 python amd64 2.7.15-3 [22.7 kB] Get:23 http://127.0.0.1:9999/debian sid/main amd64 libncurses6 amd64 6.1+20181013-1 [102 kB] Get:24 http://127.0.0.1:9999/debian sid/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get:25 http://127.0.0.1:9999/debian sid/main amd64 lsb-base all 10.2018112800 [28.3 kB] Get:26 http://127.0.0.1:9999/debian sid/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get:27 http://127.0.0.1:9999/debian sid/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:28 http://127.0.0.1:9999/debian sid/main amd64 libmagic-mgc amd64 1:5.34-2 [239 kB] Get:29 http://127.0.0.1:9999/debian sid/main amd64 libmagic1 amd64 1:5.34-2 [116 kB] Get:30 http://127.0.0.1:9999/debian sid/main amd64 file amd64 1:5.34-2 [65.8 kB] Get:31 http://127.0.0.1:9999/debian sid/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:32 http://127.0.0.1:9999/debian sid/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:33 http://127.0.0.1:9999/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:34 http://127.0.0.1:9999/debian sid/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:35 http://127.0.0.1:9999/debian sid/main amd64 autoconf all 2.69-11 [341 kB] Get:36 http://127.0.0.1:9999/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:37 http://127.0.0.1:9999/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB] Get:38 http://127.0.0.1:9999/debian sid/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:39 http://127.0.0.1:9999/debian sid/main amd64 bc amd64 1.07.1-2+b1 [109 kB] Get:40 http://127.0.0.1:9999/debian sid/main amd64 openssl amd64 1.1.1a-1 [836 kB] Get:41 http://127.0.0.1:9999/debian sid/main amd64 ca-certificates all 20180409 [161 kB] Get:42 http://127.0.0.1:9999/debian sid/main amd64 cmake-data all 3.13.2-1 [1476 kB] Get:43 http://127.0.0.1:9999/debian sid/main amd64 libicu63 amd64 63.1-5 [8293 kB] Get:44 http://127.0.0.1:9999/debian sid/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:45 http://127.0.0.1:9999/debian sid/main amd64 libarchive13 amd64 3.3.3-3 [313 kB] Get:46 http://127.0.0.1:9999/debian sid/main amd64 libkeyutils1 amd64 1.5.9-9.3 [13.0 kB] Get:47 http://127.0.0.1:9999/debian sid/main amd64 libkrb5support0 amd64 1.16.2-1 [63.3 kB] Get:48 http://127.0.0.1:9999/debian sid/main amd64 libk5crypto3 amd64 1.16.2-1 [121 kB] Get:49 http://127.0.0.1:9999/debian sid/main amd64 libkrb5-3 amd64 1.16.2-1 [320 kB] Get:50 http://127.0.0.1:9999/debian sid/main amd64 libgssapi-krb5-2 amd64 1.16.2-1 [158 kB] Get:51 http://127.0.0.1:9999/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27~rc8-1 [68.4 kB] Get:52 http://127.0.0.1:9999/debian sid/main amd64 libsasl2-2 amd64 2.1.27~rc8-1 [105 kB] Get:53 http://127.0.0.1:9999/debian sid/main amd64 libldap-common all 2.4.47+dfsg-1 [88.8 kB] Get:54 http://127.0.0.1:9999/debian sid/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-1 [224 kB] Get:55 http://127.0.0.1:9999/debian sid/main amd64 libnghttp2-14 amd64 1.35.1-1+b1 [82.4 kB] Get:56 http://127.0.0.1:9999/debian sid/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:57 http://127.0.0.1:9999/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:58 http://127.0.0.1:9999/debian sid/main amd64 libssh2-1 amd64 1.8.0-2 [138 kB] Get:59 http://127.0.0.1:9999/debian sid/main amd64 libcurl4 amd64 7.62.0-1 [324 kB] Get:60 http://127.0.0.1:9999/debian sid/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:61 http://127.0.0.1:9999/debian sid/main amd64 librhash0 amd64 1.3.7-1 [104 kB] Get:62 http://127.0.0.1:9999/debian sid/main amd64 libuv1 amd64 1.24.0-1 [109 kB] Get:63 http://127.0.0.1:9999/debian sid/main amd64 cmake amd64 3.13.2-1 [3485 kB] Get:64 http://127.0.0.1:9999/debian sid/main amd64 libtool all 2.4.6-6 [547 kB] Get:65 http://127.0.0.1:9999/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:66 http://127.0.0.1:9999/debian sid/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:67 http://127.0.0.1:9999/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB] Get:68 http://127.0.0.1:9999/debian sid/main amd64 dh-strip-nondeterminism all 1.0.0-1 [12.5 kB] Get:69 http://127.0.0.1:9999/debian sid/main amd64 libelf1 amd64 0.175-2 [160 kB] Get:70 http://127.0.0.1:9999/debian sid/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:71 http://127.0.0.1:9999/debian sid/main amd64 libglib2.0-0 amd64 2.58.2-3 [1257 kB] Get:72 http://127.0.0.1:9999/debian sid/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:73 http://127.0.0.1:9999/debian sid/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:74 http://127.0.0.1:9999/debian sid/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:75 http://127.0.0.1:9999/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:76 http://127.0.0.1:9999/debian sid/main amd64 debhelper all 12 [1002 kB] Get:77 http://127.0.0.1:9999/debian sid/main amd64 libpng16-16 amd64 1.6.36-2 [292 kB] Get:78 http://127.0.0.1:9999/debian sid/main amd64 libfreetype6 amd64 2.9.1-3 [379 kB] Get:79 http://127.0.0.1:9999/debian sid/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:80 http://127.0.0.1:9999/debian sid/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:81 http://127.0.0.1:9999/debian sid/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:82 http://127.0.0.1:9999/debian sid/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get:83 http://127.0.0.1:9999/debian sid/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [154 kB] Get:84 http://127.0.0.1:9999/debian sid/main amd64 libbamtools-dev amd64 2.5.1+dfsg-3 [21.8 kB] Get:85 http://127.0.0.1:9999/debian sid/main amd64 libgfortran5 amd64 8.2.0-14 [581 kB] Get:86 http://127.0.0.1:9999/debian sid/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:87 http://127.0.0.1:9999/debian sid/main amd64 libbwa-dev amd64 0.7.17-2 [130 kB] Get:88 http://127.0.0.1:9999/debian sid/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:89 http://127.0.0.1:9999/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:90 http://127.0.0.1:9999/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:91 http://127.0.0.1:9999/debian sid/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:92 http://127.0.0.1:9999/debian sid/main amd64 libx11-data all 2:1.6.7-1 [298 kB] Get:93 http://127.0.0.1:9999/debian sid/main amd64 libx11-6 amd64 2:1.6.7-1 [754 kB] Get:94 http://127.0.0.1:9999/debian sid/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:95 http://127.0.0.1:9999/debian sid/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:96 http://127.0.0.1:9999/debian sid/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:97 http://127.0.0.1:9999/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:98 http://127.0.0.1:9999/debian sid/main amd64 libcairo2 amd64 1.16.0-2 [690 kB] Get:99 http://127.0.0.1:9999/debian sid/main amd64 libcurl3-gnutls amd64 7.62.0-1 [321 kB] Get:100 http://127.0.0.1:9999/debian sid/main amd64 libdatrie1 amd64 0.2.12-1 [39.1 kB] Get:101 http://127.0.0.1:9999/debian sid/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-1 [4264 B] Get:102 http://127.0.0.1:9999/debian sid/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-1 [4212 B] Get:103 http://127.0.0.1:9999/debian sid/main amd64 libfastahack0 amd64 0.0+git20160702.bbc645f+dfsg-6 [24.3 kB] Get:104 http://127.0.0.1:9999/debian sid/main amd64 libfastahack-dev amd64 0.0+git20160702.bbc645f+dfsg-6 [24.3 kB] Get:105 http://127.0.0.1:9999/debian sid/main amd64 libfml0 amd64 0.1-5 [69.3 kB] Get:106 http://127.0.0.1:9999/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get:107 http://127.0.0.1:9999/debian sid/main amd64 libfml-dev amd64 0.1-5 [81.4 kB] Get:108 http://127.0.0.1:9999/debian sid/main amd64 libfribidi0 amd64 1.0.5-3 [63.3 kB] Get:109 http://127.0.0.1:9999/debian sid/main amd64 libgraphite2-3 amd64 1.3.12-1 [80.2 kB] Get:110 http://127.0.0.1:9999/debian sid/main amd64 libharfbuzz0b amd64 2.3.0-1 [1176 kB] Get:111 http://127.0.0.1:9999/debian sid/main amd64 libhts2 amd64 1.9-8 [306 kB] Get:112 http://127.0.0.1:9999/debian sid/main amd64 liblzma-dev amd64 5.2.2-1.3 [292 kB] Get:113 http://127.0.0.1:9999/debian sid/main amd64 libhts-dev amd64 1.9-8 [4345 kB] Get:114 http://127.0.0.1:9999/debian sid/main amd64 libhts-private-dev all 1.9-8 [41.8 kB] Get:115 http://127.0.0.1:9999/debian sid/main amd64 x11-common all 1:7.7+19 [251 kB] Get:116 http://127.0.0.1:9999/debian sid/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:117 http://127.0.0.1:9999/debian sid/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:118 http://127.0.0.1:9999/debian sid/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:119 http://127.0.0.1:9999/debian sid/main amd64 libjsoncpp-dev amd64 1.7.4-3 [86.2 kB] Get:120 http://127.0.0.1:9999/debian sid/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:121 http://127.0.0.1:9999/debian sid/main amd64 libthai-data all 0.1.28-1 [170 kB] Get:122 http://127.0.0.1:9999/debian sid/main amd64 libthai0 amd64 0.1.28-1 [53.9 kB] Get:123 http://127.0.0.1:9999/debian sid/main amd64 libpango-1.0-0 amd64 1.42.4-6 [185 kB] Get:124 http://127.0.0.1:9999/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.42.4-6 [67.9 kB] Get:125 http://127.0.0.1:9999/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.42.4-6 [55.5 kB] Get:126 http://127.0.0.1:9999/debian sid/main amd64 libpaper1 amd64 1.1.26 [20.8 kB] Get:127 http://127.0.0.1:9999/debian sid/main amd64 libpaper-utils amd64 1.1.26 [17.9 kB] Get:128 http://127.0.0.1:9999/debian sid/main amd64 libsensors-config all 1:3.5.0-3 [31.6 kB] Get:129 http://127.0.0.1:9999/debian sid/main amd64 libsensors5 amd64 1:3.5.0-3 [52.6 kB] Get:130 http://127.0.0.1:9999/debian sid/main amd64 libseqlib1 amd64 1.1.2+dfsg-2 [117 kB] Get:131 http://127.0.0.1:9999/debian sid/main amd64 libseqlib-dev amd64 1.1.2+dfsg-2 [165 kB] Get:132 http://127.0.0.1:9999/debian sid/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:133 http://127.0.0.1:9999/debian sid/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-7 [36.0 kB] Get:134 http://127.0.0.1:9999/debian sid/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-7 [38.9 kB] Get:135 http://127.0.0.1:9999/debian sid/main amd64 libssw0 amd64 1.1-2 [16.5 kB] Get:136 http://127.0.0.1:9999/debian sid/main amd64 libssw-dev amd64 1.1-2 [19.3 kB] Get:137 http://127.0.0.1:9999/debian sid/main amd64 libtabixpp0 amd64 1.0.0-4 [7828 B] Get:138 http://127.0.0.1:9999/debian sid/main amd64 libtabixpp-dev amd64 1.0.0-4 [7160 B] Get:139 http://127.0.0.1:9999/debian sid/main amd64 libtcl8.6 amd64 8.6.9+dfsg-1 [1004 kB] Get:140 http://127.0.0.1:9999/debian sid/main amd64 libwebp6 amd64 0.6.1-2 [263 kB] Get:141 http://127.0.0.1:9999/debian sid/main amd64 libtiff5 amd64 4.0.10-3 [257 kB] Get:142 http://127.0.0.1:9999/debian sid/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:143 http://127.0.0.1:9999/debian sid/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:144 http://127.0.0.1:9999/debian sid/main amd64 libtk8.6 amd64 8.6.9-1 [768 kB] Get:145 http://127.0.0.1:9999/debian sid/main amd64 libvcflib1 amd64 1.0.0~rc2+dfsg-2 [138 kB] Get:146 http://127.0.0.1:9999/debian sid/main amd64 libvcflib-dev amd64 1.0.0~rc2+dfsg-2 [25.7 kB] Get:147 http://127.0.0.1:9999/debian sid/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:148 http://127.0.0.1:9999/debian sid/main amd64 unzip amd64 6.0-21 [170 kB] Get:149 http://127.0.0.1:9999/debian sid/main amd64 xdg-utils all 1.1.3-1 [73.3 kB] Get:150 http://127.0.0.1:9999/debian sid/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:151 http://127.0.0.1:9999/debian sid/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get:152 http://127.0.0.1:9999/debian sid/main amd64 r-cran-littler amd64 0.3.5-1+b1 [305 kB] Get:153 http://127.0.0.1:9999/debian sid/main amd64 littler all 0.3.5-1 [13.4 kB] Get:154 http://127.0.0.1:9999/debian sid/main amd64 r-cran-pkgkitten all 0.1.4-2 [22.4 kB] Get:155 http://127.0.0.1:9999/debian sid/main amd64 r-cran-rcpp amd64 1.0.0-1 [3381 kB] Get:156 http://127.0.0.1:9999/debian sid/main amd64 r-cran-plyr amd64 1.8.4-2 [813 kB] Get:157 http://127.0.0.1:9999/debian sid/main amd64 r-cran-digest amd64 0.6.18-1 [136 kB] Get:158 http://127.0.0.1:9999/debian sid/main amd64 r-cran-gtable all 0.2.0-3 [93.6 kB] Get:159 http://127.0.0.1:9999/debian sid/main amd64 r-cran-lazyeval amd64 0.2.1-3 [138 kB] Get:160 http://127.0.0.1:9999/debian sid/main amd64 r-cran-mass amd64 7.3-51.1-1 [1100 kB] Get:161 http://127.0.0.1:9999/debian sid/main amd64 r-cran-lattice amd64 0.20-38-1 [1121 kB] Get:162 http://127.0.0.1:9999/debian sid/main amd64 r-cran-nlme amd64 3.1.137-1+b3 [2223 kB] Get:163 http://127.0.0.1:9999/debian sid/main amd64 r-cran-matrix amd64 1.2-15-1 [3421 kB] Get:164 http://127.0.0.1:9999/debian sid/main amd64 r-cran-mgcv amd64 1.8-26-1 [2590 kB] Get:165 http://127.0.0.1:9999/debian sid/main amd64 r-cran-glue amd64 1.3.0-1 [92.0 kB] Get:166 http://127.0.0.1:9999/debian sid/main amd64 r-cran-magrittr all 1.5-5 [152 kB] Get:167 http://127.0.0.1:9999/debian sid/main amd64 r-cran-stringi amd64 1.2.4-2 [8702 kB] Get:168 http://127.0.0.1:9999/debian sid/main amd64 r-cran-stringr all 1.3.1-2 [179 kB] Get:169 http://127.0.0.1:9999/debian sid/main amd64 r-cran-reshape2 amd64 1.4.3-2 [114 kB] Get:170 http://127.0.0.1:9999/debian sid/main amd64 r-cran-rlang amd64 0.3.0.1-2 [1035 kB] Get:171 http://127.0.0.1:9999/debian sid/main amd64 r-cran-labeling all 0.3-3 [61.4 kB] Get:172 http://127.0.0.1:9999/debian sid/main amd64 r-cran-colorspace amd64 1.3-2-3 [474 kB] Get:173 http://127.0.0.1:9999/debian sid/main amd64 r-cran-munsell all 0.5.0-1 [235 kB] Get:174 http://127.0.0.1:9999/debian sid/main amd64 r-cran-r6 all 2.3.0-1 [73.5 kB] Get:175 http://127.0.0.1:9999/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB] Get:176 http://127.0.0.1:9999/debian sid/main amd64 r-cran-viridislite all 0.3.0-3 [59.2 kB] Get:177 http://127.0.0.1:9999/debian sid/main amd64 r-cran-scales amd64 1.0.0-2 [546 kB] Get:178 http://127.0.0.1:9999/debian sid/main amd64 r-cran-assertthat all 0.2.0-2 [54.4 kB] Get:179 http://127.0.0.1:9999/debian sid/main amd64 r-cran-crayon all 1.3.4-4 [750 kB] Get:180 http://127.0.0.1:9999/debian sid/main amd64 r-cran-cli all 1.0.1-1 [519 kB] Get:181 http://127.0.0.1:9999/debian sid/main amd64 r-cran-fansi amd64 0.4.0-1 [339 kB] Get:182 http://127.0.0.1:9999/debian sid/main amd64 r-cran-utf8 amd64 1.1.4-1+b1 [131 kB] Get:183 http://127.0.0.1:9999/debian sid/main amd64 r-cran-pillar all 1.3.1-1 [203 kB] Get:184 http://127.0.0.1:9999/debian sid/main amd64 r-cran-pkgconfig all 2.0.2-1 [19.4 kB] Get:185 http://127.0.0.1:9999/debian sid/main amd64 r-cran-tibble amd64 2.0.0-1 [322 kB] Get:186 http://127.0.0.1:9999/debian sid/main amd64 r-cran-withr all 2.1.2-3 [152 kB] Get:187 http://127.0.0.1:9999/debian sid/main amd64 r-cran-ggplot2 all 3.1.0-1 [3740 kB] Get:188 http://127.0.0.1:9999/debian sid/main amd64 r-cran-gridbase all 0.4-7-4 [170 kB] Get:189 http://127.0.0.1:9999/debian sid/main amd64 libvcflib-tools amd64 1.0.0~rc2+dfsg-2 [629 kB] Get:190 http://127.0.0.1:9999/debian sid/main amd64 sysstat amd64 12.0.1-1+b1 [561 kB] Get:191 http://127.0.0.1:9999/debian sid/main amd64 parallel all 20161222-1.1 [306 kB] Get:192 http://127.0.0.1:9999/debian sid/main amd64 pkg-config amd64 0.29-4+b1 [63.3 kB] Get:193 http://127.0.0.1:9999/debian sid/main amd64 samtools amd64 1.9-2 [424 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 115 MB in 12s (9747 kB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../00-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-2_amd64.deb ... Unpacking groff-base (1.22.4-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.0-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.0-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.5-1_amd64.deb ... Unpacking man-db (2.8.5-1) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../05-libpython2.7-minimal_2.7.15-5_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.15-5) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../06-python2.7-minimal_2.7.15-5_amd64.deb ... Unpacking python2.7-minimal (2.7.15-5) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../07-python2-minimal_2.7.15-3_amd64.deb ... Unpacking python2-minimal (2.7.15-3) ... Selecting previously unselected package python-minimal. Preparing to unpack .../08-python-minimal_2.7.15-3_amd64.deb ... Unpacking python-minimal (2.7.15-3) ... Selecting previously unselected package mime-support. Preparing to unpack .../09-mime-support_3.61_all.deb ... Unpacking mime-support (3.61) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../10-libexpat1_2.2.6-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../11-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../12-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../13-libsqlite3-0_3.26.0+fossilbc891ac6b-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.26.0+fossilbc891ac6b-1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../14-libssl1.1_1.1.1a-1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1a-1) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.15-5_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.15-5) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.15-5_amd64.deb ... Unpacking python2.7 (2.7.15-5) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../17-libpython2-stdlib_2.7.15-3_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.15-3) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../18-libpython-stdlib_2.7.15-3_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.15-3) ... Setting up libpython2.7-minimal:amd64 (2.7.15-5) ... Setting up python2.7-minimal (2.7.15-5) ... Setting up python2-minimal (2.7.15-3) ... Selecting previously unselected package python2. (Reading database ... 14057 files and directories currently installed.) Preparing to unpack .../python2_2.7.15-3_amd64.deb ... Unpacking python2 (2.7.15-3) ... Setting up python-minimal (2.7.15-3) ... Selecting previously unselected package python. (Reading database ... 14090 files and directories currently installed.) Preparing to unpack .../000-python_2.7.15-3_amd64.deb ... Unpacking python (2.7.15-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../001-libncurses6_6.1+20181013-1_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-1) ... Selecting previously unselected package libprocps7:amd64. Preparing to unpack .../002-libprocps7_2%3a3.3.15-2_amd64.deb ... Unpacking libprocps7:amd64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../003-lsb-base_10.2018112800_all.deb ... Unpacking lsb-base (10.2018112800) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a3.3.15-2_amd64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.34-2_amd64.deb ... Unpacking libmagic-mgc (1:5.34-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../007-libmagic1_1%3a5.34-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.34-2) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.34-2_amd64.deb ... Unpacking file (1:5.34-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../010-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../011-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package bc. Preparing to unpack .../017-bc_1.07.1-2+b1_amd64.deb ... Unpacking bc (1.07.1-2+b1) ... Selecting previously unselected package openssl. Preparing to unpack .../018-openssl_1.1.1a-1_amd64.deb ... Unpacking openssl (1.1.1a-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../019-ca-certificates_20180409_all.deb ... Unpacking ca-certificates (20180409) ... Selecting previously unselected package cmake-data. Preparing to unpack .../020-cmake-data_3.13.2-1_all.deb ... Unpacking cmake-data (3.13.2-1) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../021-libicu63_63.1-5_amd64.deb ... Unpacking libicu63:amd64 (63.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../022-libxml2_2.9.4+dfsg1-7+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../023-libarchive13_3.3.3-3_amd64.deb ... Unpacking libarchive13:amd64 (3.3.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../024-libkeyutils1_1.5.9-9.3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-9.3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../025-libkrb5support0_1.16.2-1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.16.2-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../026-libk5crypto3_1.16.2-1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.16.2-1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../027-libkrb5-3_1.16.2-1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.16.2-1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../028-libgssapi-krb5-2_1.16.2-1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.16.2-1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../029-libsasl2-modules-db_2.1.27~rc8-1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27~rc8-1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../030-libsasl2-2_2.1.27~rc8-1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27~rc8-1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../031-libldap-common_2.4.47+dfsg-1_all.deb ... Unpacking libldap-common (2.4.47+dfsg-1) ... Selecting previously unselected package libldap-2.4-2:amd64. 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Setting up libpixman-1-0:amd64 (0.36.0-1) ... Setting up libssh2-1:amd64 (1.8.0-2) ... Processing triggers for libc-bin (2.28-4) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up libssl1.1:amd64 (1.1.1a-1) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Setting up libfml0 (0.1-5) ... Setting up openssl (1.1.1a-1) ... Setting up libsqlite3-0:amd64 (3.26.0+fossilbc891ac6b-1) ... Setting up libseqlib1 (1.1.2+dfsg-2) ... Setting up libfribidi0:amd64 (1.0.5-3) ... Setting up libbwa-dev (0.7.17-2) ... Setting up libtcl8.6:amd64 (8.6.9+dfsg-1) ... Setting up libthai-data (0.1.28-1) ... Setting up liblzma-dev:amd64 (5.2.2-1.3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2+b1) ... 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+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.3-1) ... Setting up ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 133 added, 0 removed; done. Setting up libgfortran5:amd64 (8.2.0-14) ... Setting up libncurses6:amd64 (6.1+20181013-1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.15-5) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libsmithwaterman0 (0.0+git20160702.2610e25-7) ... 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Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:amd64 (2:1.0.9-2) ... Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2-stdlib:amd64 (2.7.15-3) ... Setting up bc (1.07.1-2+b1) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libtool (2.4.6-6) ... Setting up libpaper1:amd64 (1.1.26) ... Creating config file /etc/papersize with new version Setting up libsm6:amd64 (2:1.2.2-1+b3) ... Setting up libk5crypto3:amd64 (1.16.2-1) ... Setting up libpaper-utils (1.1.26) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up sysstat (12.0.1-1+b1) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up po-debconf (1.0.21) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up python2 (2.7.15-3) ... Setting up libpython-stdlib:amd64 (2.7.15-3) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libkrb5-3:amd64 (1.16.2-1) ... Setting up python (2.7.15-3) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up parallel (20161222-1.1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libgssapi-krb5-2:amd64 (1.16.2-1) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libcairo2:amd64 (1.16.0-2) ... Setting up libtk8.6:amd64 (8.6.9-1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~rc8-1) ... Setting up libsasl2-2:amd64 (2.1.27~rc8-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-1) ... Setting up libpango-1.0-0:amd64 (1.42.4-6) ... Setting up libcurl3-gnutls:amd64 (7.62.0-1) ... Setting up libcurl4:amd64 (7.62.0-1) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-6) ... Setting up cmake (3.13.2-1) ... Setting up libhts2:amd64 (1.9-8) ... Setting up libtabixpp0:amd64 (1.0.0-4) ... Setting up libhts-dev:amd64 (1.9-8) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-6) ... Setting up libhts-private-dev (1.9-8) ... Setting up samtools (1.9-2) ... Setting up libseqlib-dev (1.1.2+dfsg-2) ... Setting up libtabixpp-dev:amd64 (1.0.0-4) ... Setting up r-base-core (3.5.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-withr (2.1.2-3) ... Setting up r-cran-littler (0.3.5-1+b1) ... Setting up littler (0.3.5-1) ... Setting up r-cran-fansi (0.4.0-1) ... Setting up r-cran-crayon (1.3.4-4) ... Setting up libvcflib-dev (1.0.0~rc2+dfsg-2) ... Setting up r-cran-gtable (0.2.0-3) ... Setting up r-cran-assertthat (0.2.0-2) ... Setting up r-cran-rcolorbrewer (1.1-2-2) ... Setting up r-cran-gridbase (0.4-7-4) ... Setting up r-cran-stringi (1.2.4-2) ... Setting up r-cran-pkgkitten (0.1.4-2) ... Setting up r-cran-rcpp (1.0.0-1) ... Setting up r-cran-labeling (0.3-3) ... Setting up r-cran-r6 (2.3.0-1) ... Setting up r-cran-colorspace (1.3-2-3) ... Setting up r-cran-utf8 (1.1.4-1+b1) ... Setting up r-cran-mass (7.3-51.1-1) ... Setting up r-cran-plyr (1.8.4-2) ... Setting up r-cran-rlang (0.3.0.1-2) ... Setting up r-cran-digest (0.6.18-1) ... Setting up r-cran-cli (1.0.1-1) ... Setting up r-cran-magrittr (1.5-5) ... Setting up r-cran-pkgconfig (2.0.2-1) ... Setting up r-cran-glue (1.3.0-1) ... Setting up r-cran-viridislite (0.3.0-3) ... 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Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11 dpkg-dev_1.19.2 g++-8_8.2.0-14 gcc-8_8.2.0-14 libc6-dev_2.28-4 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 linux-libc-dev_4.19.13-1 Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-3.1 bc_1.07.1-2+b1 binutils_2.31.1-11 binutils-common_2.31.1-11 binutils-x86-64-linux-gnu_2.31.1-11 bsdmainutils_11.1.2+b1 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20180409 clang-7_1:7.0.1-4 cmake_3.13.2-1 cmake-data_3.13.2-1 coreutils_8.30-1 cpp_4:8.2.0-2 cpp-8_8.2.0-14 dash_0.5.10.2-4 debconf_1.5.69 debhelper_12 debian-archive-keyring_2018.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.2.0-2 g++-8_8.2.0-14 gcc_4:8.2.0-2 gcc-8_8.2.0-14 gcc-8-base_8.2.0-14 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.12-1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.4 lib32gcc1_1:8.2.0-14 lib32stdc++6_8.2.0-14 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-3 libasan5_8.2.0-14 libatomic1_8.2.0-14 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.31.1-11 libblas3_3.8.0-2 libblkid1_2.33-0.2 libbsd0_0.9.1-1 libbwa-dev_0.7.17-2 libbz2-1.0_1.0.6-9 libc-bin_2.28-4 libc-dev-bin_2.28-4 libc6_2.28-4 libc6-dev_2.28-4 libc6-i386_2.28-4 libcairo2_1.16.0-2 libcap-ng0_0.7.9-1+b1 libcc1-0_8.2.0-14 libclang-common-7-dev_1:7.0.1-4 libclang1-7_1:7.0.1-4 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcurl3-gnutls_7.62.0-1 libcurl4_7.62.0-1 libdatrie1_0.2.12-1 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.246 libdisorder-dev_0.0.2+git20130809.8062ee1-1 libdisorder0_0.0.2+git20130809.8062ee1-1 libdpkg-perl_1.19.2 libedit2_3.1-20181209-1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfastahack-dev_0.0+git20160702.bbc645f+dfsg-6 libfastahack0_0.0+git20160702.bbc645f+dfsg-6 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libfml-dev_0.1-5 libfml0_0.1-5 libfontconfig1_2.13.1-2 libfreetype6_2.9.1-3 libfribidi0_1.0.5-3 libgc1c2_1:7.6.4-0.4 libgcc-8-dev_8.2.0-14 libgcc1_1:8.2.0-14 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm6_1.18.1-2 libgfortran5_8.2.0-14 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2 libgomp1_8.2.0-14 libgpg-error0_1.33-3 libgraphite2-3_1.3.12-1 libgssapi-krb5-2_1.16.2-1 libharfbuzz0b_2.3.0-1 libhogweed4_3.4.1~rc1-1 libhts-dev_1.9-8 libhts-private-dev_1.9-8 libhts2_1.9-8 libice6_2:1.0.9-2 libicu63_63.1-5 libidn2-0_2.0.5-1 libisl19_0.20-2 libitm1_8.2.0-14 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:1.5.2-2+b1 libjsoncpp-dev_1.7.4-3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.2-1 libkeyutils1_1.5.9-9.3 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 liblapack3_3.8.0-2 libldap-2.4-2_2.4.47+dfsg-1 libldap-common_2.4.47+dfsg-1 libllvm7_1:7.0.1-4 liblsan0_8.2.0-14 liblz4-1_1.8.3-1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.2~rc1-1 libmpx2_8.2.0-14 libncurses6_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1+b1 libobjc-8-dev_8.2.0-14 libobjc4_8.2.0-14 libomp-7-dev_1:7.0.1-4 libomp5-7_1:7.0.1-4 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam0g_1.1.8-4 libpango-1.0-0_1.42.4-6 libpangocairo-1.0-0_1.42.4-6 libpangoft2-1.0-0_1.42.4-6 libpaper-utils_1.1.26 libpaper1_1.1.26 libpcre3_2:8.39-11 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpixman-1-0_0.36.0-1 libpng16-16_1.6.36-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-5 libpython2.7-stdlib_2.7.15-5 libquadmath0_8.2.0-14 libreadline7_7.0-5 librhash0_1.3.7-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsensors-config_1:3.5.0-3 libsensors5_1:3.5.0-3 libsepol1_2.8-1 libseqlib-dev_1.1.2+dfsg-2 libseqlib1_1.1.2+dfsg-2 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.33-0.2 libsmithwaterman-dev_0.0+git20160702.2610e25-7 libsmithwaterman0_0.0+git20160702.2610e25-7 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libssw-dev_1.1-2 libssw0_1.1-2 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 libsystemd0_240-2 libtabixpp-dev_1.0.0-4 libtabixpp0_1.0.0-4 libtasn1-6_4.13-3 libtcl8.6_8.6.9+dfsg-1 libthai-data_0.1.28-1 libthai0_0.1.28-1 libtiff5_4.0.10-3 libtinfo6_6.1+20181013-1 libtk8.6_8.6.9-1 libtool_2.4.6-6 libtsan0_8.2.0-14 libubsan1_8.2.0-14 libuchardet0_0.0.6-3 libudev1_240-2 libunistring2_0.9.10-1 libuuid1_2.33-0.2 libuv1_1.24.0-1 libvcflib-dev_1.0.0~rc2+dfsg-2 libvcflib-tools_1.0.0~rc2+dfsg-2 libvcflib1_1.0.0~rc2+dfsg-2 libwebp6_0.6.1-2 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-7+b3 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.13-1 littler_0.3.5-1 login_1:4.5-1.1 lsb-base_10.2018112800 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17+b3 mime-support_3.61 mount_2.33-0.2 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 openssl_1.1.1a-1 parallel_20161222-1.1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pkg-config_0.29-4+b1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-minimal_2.7.15-5 r-base-core_3.5.2-1 r-cran-assertthat_0.2.0-2 r-cran-cli_1.0.1-1 r-cran-colorspace_1.3-2-3 r-cran-crayon_1.3.4-4 r-cran-digest_0.6.18-1 r-cran-fansi_0.4.0-1 r-cran-ggplot2_3.1.0-1 r-cran-glue_1.3.0-1 r-cran-gridbase_0.4-7-4 r-cran-gtable_0.2.0-3 r-cran-labeling_0.3-3 r-cran-lattice_0.20-38-1 r-cran-lazyeval_0.2.1-3 r-cran-littler_0.3.5-1+b1 r-cran-magrittr_1.5-5 r-cran-mass_7.3-51.1-1 r-cran-matrix_1.2-15-1 r-cran-mgcv_1.8-26-1 r-cran-munsell_0.5.0-1 r-cran-nlme_3.1.137-1+b3 r-cran-pillar_1.3.1-1 r-cran-pkgconfig_2.0.2-1 r-cran-pkgkitten_0.1.4-2 r-cran-plyr_1.8.4-2 r-cran-r6_2.3.0-1 r-cran-rcolorbrewer_1.1-2-2 r-cran-rcpp_1.0.0-1 r-cran-reshape2_1.4.3-2 r-cran-rlang_0.3.0.1-2 r-cran-scales_1.0.0-2 r-cran-stringi_1.2.4-2 r-cran-stringr_1.3.1-2 r-cran-tibble_2.0.0-1 r-cran-utf8_1.1.4-1+b1 r-cran-viridislite_0.3.0-3 r-cran-withr_2.1.2-3 readline-common_7.0-5 samtools_1.9-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-freebayes-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysstat_12.0.1-1+b1 sysvinit-utils_2.93-3 tar_1.30+dfsg-4 tzdata_2018i-1 ucf_3.0038+nmu1 unzip_6.0-21 util-linux_2.33-0.2 x11-common_1:7.7+19 xdg-utils_1.1.3-1 xz-utils_5.2.2-1.3 zip_3.0-11+b1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Oct 9 06:06:09 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 ./freebayes_1.2.0-2.dsc dpkg-source: info: extracting freebayes in /<> dpkg-source: info: unpacking freebayes_1.2.0.orig.tar.gz dpkg-source: info: unpacking freebayes_1.2.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_libs.patch dpkg-source: info: applying fix_all_target.patch dpkg-source: info: applying fix_test.patch dpkg-source: info: applying vcffirstheader.patch dpkg-source: info: applying use_cpp11.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-c40bd878-b368-4928-bb7f-fdc3d2a20b52 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.2.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/<>' cd src && make clean make[2]: Entering directory '/<>/src' rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp make[2]: Leaving directory '/<>/src' rm -fr bin/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules build-arch dh build-arch --no-parallel dh_update_autotools_config -a -O--no-parallel dh_autoreconf -a -O--no-parallel dh_auto_configure -a -O--no-parallel dh_auto_build -a -O--no-parallel make -j1 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' cd src && make make[2]: Entering directory '/<>/src' DETECTED_VERSION = v1.0.0 CURRENT_VERSION = Updating version file. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c freebayes.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c BedReader.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c CNV.cpp gcc -O3 -D_FILE_OFFSET_BITS=64 -g -std=gnu++11 -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c fastlz.c error: invalid argument '-std=gnu++11' not allowed with 'C' make[2]: *** [Makefile:102: fastlz.o] Error 1 make[2]: Leaving directory '/<>/src' make[1]: *** [Makefile:2: all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: make -j1 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:6: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2019-01-09T21:54:21Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 11520 Build-Time: 6 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 42 Job: freebayes_1.2.0-2 Machine Architecture: amd64 Package: freebayes Package-Time: 62 Source-Version: 1.2.0-2 Space: 11520 Status: attempted Version: 1.2.0-2 -------------------------------------------------------------------------------- Finished at 2019-01-09T21:54:21Z Build needed 00:01:02, 11520k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 63.373937147s DC-Time-Estimation: 63.373937147 versus expected 163 (r/m: 1.572035245686422 ; m: 63.373937147)