DC-Build-Header: nanopolish 0.5.0-1 / 2017-07-06 20:55:52 +0000 DC-Task: type:rebuild-binarch-only source:nanopolish version:0.5.0-1 chroot:unstable esttime:85 logfile:/tmp/nanopolish_0.5.0-1_unstable_clang4.0.log modes:clang40:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang40 nanopolish_0.5.0-1' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-45-233.eu-central-1.compute.internal +==============================================================================+ | nanopolish 0.5.0-1 (amd64) Thu, 06 Jul 2017 20:55:52 +0000 | +==============================================================================+ Package: nanopolish Version: 0.5.0-1 Source Version: 0.5.0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-e7b2e121-139d-4f6d-a0ca-a02e8bd20ee7' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang40 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=4.0 + echo 'Install of clang-4.0' Install of clang-4.0 + apt-get update Hit:1 http://127.0.0.1:9999/debian unstable InRelease Get:2 http://127.0.0.1:9999/debian unstable/main Translation-en [5730 kB] Fetched 5730 kB in 1s (3949 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-4.0 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-4.0-dev libclang1-4.0 libedit2 libjsoncpp1 libllvm4.0 libncurses5 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-4.0-doc libomp-dev Recommended packages: llvm-4.0-dev python libgpm2 The following NEW packages will be installed: clang-4.0 libbsd0 libclang-common-4.0-dev libclang1-4.0 libedit2 libjsoncpp1 libllvm4.0 libncurses5 libobjc-6-dev libobjc4 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 74.4 MB of archives. After this operation, 320 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.5-1 [89.6 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.0+20161126-1 [93.4 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm4.0 amd64 1:4.0.1-1 [12.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-4.0 amd64 1:4.0.1-1 [6355 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 7.1.0-9 [51.0 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.4.0-1 [197 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-4.0-dev amd64 1:4.0.1-1 [2495 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 clang-4.0 amd64 1:4.0.1-1 [52.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.4 MB in 0s (95.7 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 ... 9711 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.5-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.5-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../1-libncurses5_6.0+20161126-1_amd64.deb ... Unpacking libncurses5:amd64 (6.0+20161126-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../2-libedit2_3.1-20170329-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20170329-1) ... Selecting previously unselected package libllvm4.0:amd64. Preparing to unpack .../3-libllvm4.0_1%3a4.0.1-1_amd64.deb ... Unpacking libllvm4.0:amd64 (1:4.0.1-1) ... Selecting previously unselected package libclang1-4.0:amd64. Preparing to unpack .../4-libclang1-4.0_1%3a4.0.1-1_amd64.deb ... Unpacking libclang1-4.0:amd64 (1:4.0.1-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../5-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../6-libobjc4_7.1.0-9_amd64.deb ... Unpacking libobjc4:amd64 (7.1.0-9) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../7-libobjc-6-dev_6.4.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.4.0-1) ... Selecting previously unselected package libclang-common-4.0-dev. Preparing to unpack .../8-libclang-common-4.0-dev_1%3a4.0.1-1_amd64.deb ... Unpacking libclang-common-4.0-dev (1:4.0.1-1) ... Selecting previously unselected package clang-4.0. Preparing to unpack .../9-clang-4.0_1%3a4.0.1-1_amd64.deb ... Unpacking clang-4.0 (1:4.0.1-1) ... Setting up libncurses5:amd64 (6.0+20161126-1) ... Setting up libobjc4:amd64 (7.1.0-9) ... Setting up libbsd0:amd64 (0.8.5-1) ... Processing triggers for libc-bin (2.24-12) ... Setting up libobjc-6-dev:amd64 (6.4.0-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libllvm4.0:amd64 (1:4.0.1-1) ... Setting up libclang1-4.0:amd64 (1:4.0.1-1) ... Setting up libclang-common-4.0-dev (1:4.0.1-1) ... Setting up clang-4.0 (1:4.0.1-1) ... Processing triggers for libc-bin (2.24-12) ... 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' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-4.0 g++-4.6 + ln -s clang-4.0 gcc-4.6 + ln -s clang-4.0 cpp-4.6 + ln -s clang-4.0 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++-4.0 g++-4.7 + ln -s clang-4.0 gcc-4.7 + ln -s clang-4.0 cpp-4.7 + ln -s clang-4.0 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++-4.0 g++-4.8 + ln -s clang-4.0 gcc-4.8 + ln -s clang-4.0 cpp-4.8 + ln -s clang-4.0 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++-4.0 g++-4.9 + ln -s clang-4.0 gcc-4.9 + ln -s clang-4.0 cpp-4.9 + ln -s clang-4.0 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++-4.0 g++-5 + ln -s clang-4.0 gcc-5 + ln -s clang-4.0 cpp-5 + ln -s clang-4.0 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-4.0 g++-6 + ln -s clang-4.0 gcc-6 + ln -s clang-4.0 cpp-6 + ln -s clang-4.0 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-4.0 g++-7 + ln -s clang-4.0 gcc-7 + ln -s clang-4.0 cpp-7 + ln -s clang-4.0 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 + cd - /build/nanopolish-vPmppR + 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/clang40'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'nanopolish' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/nanopolish.git Please use: git clone https://anonscm.debian.org/git/debian-med/nanopolish.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1742 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main nanopolish 0.5.0-1 (dsc) [2011 B] Get:2 http://127.0.0.1:9999/debian unstable/main nanopolish 0.5.0-1 (tar) [1734 kB] Get:3 http://127.0.0.1:9999/debian unstable/main nanopolish 0.5.0-1 (diff) [6332 B] Fetched 1742 kB in 0s (12.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/nanopolish-vPmppR/nanopolish-0.5.0' with '<>' I: NOTICE: Log filtering will replace 'build/nanopolish-vPmppR' 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-5jcpHp/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-5jcpHp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5jcpHp/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-5jcpHp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5jcpHp/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-5jcpHp/apt_archive ./ Packages [432 B] Fetched 1738 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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-5jcpHp/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10206 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 (>= 9), zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev Filtered Build-Depends: debhelper (>= 9), zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev dpkg-deb: building package 'sbuild-build-depends-nanopolish-dummy' in '/<>/resolver-5jcpHp/apt_archive/sbuild-build-depends-nanopolish-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-nanopolish-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-5jcpHp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5jcpHp/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-5jcpHp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5jcpHp/apt_archive ./ Sources [515 B] Get:5 copy:/<>/resolver-5jcpHp/apt_archive ./ Packages [597 B] Fetched 2075 B in 0s (0 B/s) Reading package lists... Reading package lists... Install nanopolish build dependencies (apt-based resolver) ---------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libcroco3 libcurl3-gnutls libeigen3-dev libfast5-dev libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhts-dev libhts2 libicu57 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libsz2 libtimedate-perl libtool libxml2 m4 man-db pkg-config po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libeigen3-doc libmrpt-dev krb5-doc krb5-user libhdf5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libcroco3 libcurl3-gnutls libeigen3-dev libfast5-dev libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhts-dev libhts2 libicu57 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libsz2 libtimedate-perl libtool libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-nanopolish-dummy zlib1g-dev 0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 28.8 MB of archives. After this operation, 103 MB of additional disk space will be used. Get:1 copy:/<>/resolver-5jcpHp/apt_archive ./ sbuild-build-depends-nanopolish-dummy 0.invalid.0 [808 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.1 amd64 1.1.0f-3 [1342 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.15-1 [61.7 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.15-1 [119 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.15-1 [311 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.15-1 [154 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3 [68.2 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3 [105 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libldap-common all 2.4.44+dfsg-7 [85.2 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-7 [219 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.6.2 [968 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 hdf5-helpers amd64 1.10.0-patch1+docs-3 [35.9 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libaec0 amd64 0.3.2-1 [18.5 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libsz2 amd64 0.3.2-1 [5730 B] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libaec-dev amd64 0.3.2-1 [17.4 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.24.0-1 [81.6 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libpsl5 amd64 0.17.0-4+b1 [43.0 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.8.0-1 [138 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.52.1-5 [289 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 pkg-config amd64 0.29-4+b1 [63.3 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libeigen3-dev all 3.3.4-2 [842 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran3 amd64 6.4.0-1 [265 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-3 [1284 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:1.5.1-2 [210 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg-dev all 1:1.5.1-2 [56.1 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libhdf5-cpp-100 amd64 1.10.0-patch1+docs-3 [130 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libhdf5-dev amd64 1.10.0-patch1+docs-3 [2437 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libfast5-dev all 0.5.8-1 [23.3 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libhts2 amd64 1.4.1-2 [294 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 libhts-dev amd64 1.4.1-2 [398 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.8 MB in 0s (65.6 MB/s) Selecting previously unselected package groff-base. (Reading database ... 10206 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../04-libssl1.1_1.1.0f-3_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0f-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.30-1_amd64.deb ... Unpacking libmagic-mgc (1:5.30-1) ... 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Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up gettext-base (0.19.8.1-2+b1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libxml2:amd64 (2.9.4+dfsg1-3) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up libcroco3:amd64 (0.6.12-1) ... Setting up pkg-config (0.29-4+b1) ... Setting up libssh2-1:amd64 (1.8.0-1) ... Processing triggers for libc-bin (2.24-12) ... Setting up autotools-dev (20161112.1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-7) ... Setting up libssl1.1:amd64 (1.1.0f-3) ... Setting up libjpeg62-turbo-dev:amd64 (1:1.5.1-2) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.12+nmu1) ... 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 hdf5-helpers (1.10.0-patch1+docs-3) ... Setting up autopoint (0.19.8.1-2) ... Setting up libsz2:amd64 (0.3.2-1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3) ... Setting up gettext (0.19.8.1-2+b1) ... Setting up libeigen3-dev (3.3.4-2) ... Setting up libaec-dev:amd64 (0.3.2-1) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libkrb5support0:amd64 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libjpeg-dev (1:1.5.1-2) ... Setting up automake (1:1.15.1-2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up libk5crypto3:amd64 (1.15-1) ... Setting up libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3) ... Setting up po-debconf (1.0.20) ... Setting up libhdf5-dev (1.10.0-patch1+docs-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libkrb5-3:amd64 (1.15-1) ... Setting up libfast5-dev (0.5.8-1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5) ... Setting up libhts2:amd64 (1.4.1-2) ... Setting up libhts-dev:amd64 (1.4.1-2) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.6.2) ... Setting up sbuild-build-depends-nanopolish-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-12) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-2-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1 gcc-6_6.4.0-1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 linux-libc-dev_4.11.6-1 Package versions: adduser_3.115 apt_1.5~beta1 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 clang-4.0_1:4.0.1-1 coreutils_8.26-3 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1 dash_0.5.8-2.4 debconf_1.5.62 debfoster_2.7-2.1+b1 debhelper_10.6.2 debian-archive-keyring_2017.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 eatmydata_105-5 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-2 g++_4:6.3.0-4d1 g++-6_6.4.0-1 gcc_4:6.3.0-4d1 gcc-6_6.4.0-1 gcc-6-base_6.4.0-1 gcc-7-base_7.1.0-9 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gpgv_2.1.18-8 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5+b1 hdf5-helpers_1.10.0-patch1+docs-3 hostname_3.18+b1 init-system-helpers_1.48 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1 libatomic1_7.1.0-9 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libblkid1_2.29.2-1 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3+b1 libcc1-0_7.1.0-9 libcilkrts5_7.1.0-9 libclang-common-4.0-dev_1:4.0.1-1 libclang1-4.0_1:4.0.1-1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcurl3-gnutls_7.52.1-5 libdb5.3_5.3.28-12+b1 libdebconfclient0_0.229 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libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-3 linux-libc-dev_4.11.6-1 login_1:4.4-4.1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mount_2.29.2-1 multiarch-support_2.24-12 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.24.1-6 perl-base_5.24.1-6 perl-modules-5.24_5.24.1-6 pkg-config_0.29-4+b1 po-debconf_1.0.20 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-nanopolish-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 util-linux_2.29.2-1 xz-utils_5.2.2-1.2+b1 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Aug 12 07:07:36 2016 UTC gpgv: using RSA key 59B2306F3AF9DDC1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./nanopolish_0.5.0-1.dsc dpkg-source: info: extracting nanopolish in /<> dpkg-source: info: unpacking nanopolish_0.5.0.orig.tar.gz dpkg-source: info: unpacking nanopolish_0.5.0-1.debian.tar.xz dpkg-source: info: applying adjust-include-path.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying external-libs.patch dpkg-source: info: applying add-shebang-to-script.patch dpkg-source: info: applying fix-ftbfs-with-gcc6.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying fast5-0.5.6.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-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-e7b2e121-139d-4f6d-a0ca-a02e8bd20ee7 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package nanopolish dpkg-buildpackage: info: source version 0.5.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Afif Elghraoui dpkg-source --before-build nanopolish-0.5.0 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' /usr/bin/make clean make[2]: Entering directory '/<>' Makefile:94: .depend: No such file or directory rm -f ./.depend g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_common.cpp src/common/nanopolish_fast5_map.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_model_names.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_pore_model_set.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_transition_parameters.cpp src/nanopolish_call_variants.cpp src/nanopolish_consensus.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_methyltest.cpp src/nanopolish_methyltrain.cpp src/nanopolish_poremodel.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/training_core.cpp src/thirdparty/stdaln.c > ./.depend; clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] src/alignment/nanopolish_eventalign.cpp:20:10: fatal error: 'omp.h' file not found #include ^~~~~~~ 1 error generated. Makefile:91: recipe for target '.depend' failed make[2]: *** [.depend] Error 1 make[2]: Leaving directory '/<>' debian/rules:14: recipe for target 'override_dh_auto_clean' failed make[1]: *** [override_dh_auto_clean] Error 2 make[1]: Leaving directory '/<>' debian/rules:11: recipe for target 'clean' failed make: *** [clean] Error 2 dpkg-buildpackage: error: fakeroot debian/rules clean gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-07-06T20:56:17Z 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: 3536 Build-Time: 1 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 7 Job: nanopolish_0.5.0-1 Machine Architecture: amd64 Package: nanopolish Package-Time: 25 Source-Version: 0.5.0-1 Space: 3536 Status: attempted Version: 0.5.0-1 -------------------------------------------------------------------------------- Finished at 2017-07-06T20:56:17Z Build needed 00:00:25, 3536k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 25.387816728s DC-Time-Estimation: 25.387816728 versus expected 85 (r/m: 2.348062612499256 ; m: 25.387816728)