Source: abyss Version: 1.9.0-1 Severity: serious Justification: makes the package in question unusable or mostly so Control: block 836917 by -1
Dear Maintainer, The upload of openmpi (2.0.1-3) has triggered an uncoordinated transition (#836917). Unfortunately your package FTBFS: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc db-csv.cc: In function 'bool existFile(const char*)': db-csv.cc:23:9: error: cannot convert 'std::ifstream {aka std::basic_ifstream<char>}' to 'bool' in return return file; ^~~~ The full buildlog is attached. Kind Regards, Bas
I: using cowbuilder as pbuilder dpkg-checkbuilddeps: Unmet build dependencies: libboost-graph-dev libsparsehash-dev libtext-multimarkdown-perl libgtest-dev W: Unmet build-dependency in source dpkg-buildpackage: source package abyss dpkg-buildpackage: source version 1.9.0-2 dpkg-buildpackage: source distribution UNRELEASED dpkg-buildpackage: source changed by Andreas Tille <ti...@debian.org> dpkg-source --before-build abyss-1.9.0 fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean dpkg-source -b abyss-1.9.0 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building abyss using existing ./abyss_1.9.0.orig.tar.gz dpkg-source: info: building abyss in abyss_1.9.0-2.debian.tar.xz dpkg-source: info: building abyss in abyss_1.9.0-2.dsc dpkg-genchanges -S >../abyss_1.9.0-2_source.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build abyss-1.9.0 dpkg-buildpackage: binary and diff upload (original source NOT included) -> Copying COW directory forking: rm -rf /var/cache/pbuilder/build/cow.12652 forking: cp -al /var/cache/pbuilder/base-sid+rebuild.cow /var/cache/pbuilder/build/cow.12652 I: removed stale ilistfile /var/cache/pbuilder/build/cow.12652/.ilist forking: chroot /var/cache/pbuilder/build/cow.12652 cowdancer-ilistcreate /.ilist find . -xdev -path ./home -prune -o \( \( -type l -o -type f \) -a -links +1 -print0 \) | xargs -0 stat --format '%d %i ' -> Invoking pbuilder forking: pbuilder build --debbuildopts --debbuildopts --buildplace /var/cache/pbuilder/build/cow.12652 --buildresult /var/cache/pbuilder/result/ --debbuildopts --no-targz --internal-chrootexec chroot /var/cache/pbuilder/build/cow.12652 cow-shell /home/bas/tmp/debian/abyss_1.9.0-2.dsc I: Running in no-targz mode I: using fakeroot in build. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 7 20:43:54 CEST 2016 I: pbuilder-time-stamp: 1473273834 I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: mounting /run/shm filesystem I: mounting /dev/pts filesystem I: policy-rc.d already exists W: no hooks of type H found -- ignoring I: Obtaining the cached apt archive contents I: Installing the build-deps W: no hooks of type D found -- ignoring -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team <pbuilder-ma...@lists.alioth.debian.org> Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 9), dh-autoreconf, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 13373 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 9); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-autoreconf; however: Package dh-autoreconf is not installed. pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however: Package libboost-graph-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libtext-multimarkdown-perl; however: Package libtext-multimarkdown-perl is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-chrono1.61.0{a} libboost-graph-dev{a} libboost-graph1.61-dev{a} libboost-graph1.61.0{a} libboost-regex1.61.0{a} libboost-serialization1.61-dev{a} libboost-serialization1.61.0{a} libboost-test1.61-dev{a} libboost-test1.61.0{a} libboost-timer1.61.0{a} libboost1.61-dev{a} libbsd0{a} libcroco3{a} libfabric1{a} libffi6{a} libfile-stripnondeterminism-perl{a} libgfortran3{a} libglib2.0-0{a} libgtest-dev{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu57{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libnl-3-200{a} libnl-route-3-200{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi2{a} libpciaccess0{a} libpipeline1{a} libpsm-infinipath1{a} librdmacm1{a} libsi gsegv2{a} libsparsehash-dev{a} libsqlite3-dev{a} libtext-markdown-perl{a} libtext-multimarkdown-perl{a} libtool{a} libunistring0{a} liburi-perl{a} libxml2{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-common{a} po-debconf{a} The following packages are RECOMMENDED but will NOT be installed: curl libglib2.0-data libhttp-message-perl libmail-sendmail-perl lynx-cur openmpi-bin shared-mime-info wget xdg-user-dirs xml-core 0 packages upgraded, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 1438 kB/34.3 MB of archives. After unpacking 213 MB will be used. Writing extended state information... Get: 1 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-chrono1.61.0 amd64 1.61.0+dfsg-2.1 [35.8 kB] Get: 2 http://ftp.nl.debian.org/debian sid/main amd64 libtext-markdown-perl all 1.000031-2 [34.4 kB] Get: 3 http://ftp.nl.debian.org/debian sid/main amd64 libtext-multimarkdown-perl all 1.000035-1 [29.4 kB] Get: 4 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-regex1.61.0 amd64 1.61.0+dfsg-2.1 [288 kB] Get: 5 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-graph1.61.0 amd64 1.61.0+dfsg-2.1 [118 kB] Get: 6 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-serialization1.61.0 amd64 1.61.0+dfsg-2.1 [125 kB] Get: 7 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-serialization1.61-dev amd64 1.61.0+dfsg-2.1 [160 kB] Get: 8 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-timer1.61.0 amd64 1.61.0+dfsg-2.1 [34.2 kB] Get: 9 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-test1.61.0 amd64 1.61.0+dfsg-2.1 [226 kB] Get: 10 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-test1.61-dev amd64 1.61.0+dfsg-2.1 [262 kB] Get: 11 http://debian.linuxminded.nl sid-rebuild/main amd64 libboost-graph1.61-dev amd64 1.61.0+dfsg-2.1 [124 kB] Fetched 1438 kB in 0s (5984 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package groff-base. (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 ... 13373 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-8_amd64.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.8.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.10_amd64.deb ... 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Setting up bsdmainutils (9.0.10) ... 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 libnl-3-200:amd64 (3.2.27-1) ... Setting up libboost-serialization1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up autopoint (0.19.8.1-1) ... Setting up libfile-stripnondeterminism-perl (0.025-1) ... Setting up libltdl-dev:amd64 (2.4.6-2) ... Setting up libboost-regex1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up libboost-serialization1.61-dev:amd64 (1.61.0+dfsg-2.1) ... Setting up libglib2.0-0:amd64 (2.49.6-1) ... No schema files found: doing nothing. Setting up libboost-timer1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up libnl-route-3-200:amd64 (3.2.27-1) ... Setting up autoconf (2.69-10) ... Setting up libboost-graph1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up file (1:5.28-4) ... Setting up libhwloc5:amd64 (1.11.4-1) ... Setting up libtext-multimarkdown-perl (1.000035-1) ... Setting up libcroco3:amd64 (0.6.11-1) ... Setting up libhwloc-plugins (1.11.4-1) ... Setting up automake (1:1.15-4) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.5-1) ... Building database of manual pages ... Setting up libboost-test1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up libtool (2.4.6-2) ... Setting up libibverbs1 (1.2.1-1) ... Setting up libhwloc-dev:amd64 (1.11.4-1) ... Setting up gettext (0.19.8.1-1) ... Setting up libboost-test1.61-dev:amd64 (1.61.0+dfsg-2.1) ... Setting up librdmacm1 (1.1.0-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libboost-graph1.61-dev:amd64 (1.61.0+dfsg-2.1) ... Setting up libibverbs-dev (1.2.1-1) ... Setting up po-debconf (1.0.19) ... Setting up libfabric1 (1.3.0-3) ... Setting up libboost-graph-dev:amd64 (1.61.0.2) ... Setting up libopenmpi2 (2.0.1-3) ... Setting up libopenmpi-dev (2.0.1-3) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up dh-strip-nondeterminism (0.025-1) ... Setting up debhelper (9.20160814) ... Setting up dh-autoreconf (12) ... Processing triggers for libc-bin (2.24-2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfakeroot The following NEW packages will be installed: fakeroot libfakeroot debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/131 kB of archives. After this operation, 370 kB of additional disk space will be used. Selecting previously unselected package libfakeroot: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 ... 30103 files and directories currently installed.) Preparing to unpack .../0-libfakeroot_1.21-2_amd64.deb ... Unpacking libfakeroot:amd64 (1.21-2) ... Selecting previously unselected package fakeroot. Preparing to unpack .../1-fakeroot_1.21-2_amd64.deb ... Unpacking fakeroot (1.21-2) ... Processing triggers for libc-bin (2.24-2) ... Setting up libfakeroot:amd64 (1.21-2) ... Processing triggers for man-db (2.7.5-1) ... Setting up fakeroot (1.21-2) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.24-2) ... I: Copying back the cached apt archive contents I: new cache content 'libtext-multimarkdown-perl_1.000035-1_all.deb' added I: new cache content 'libtext-markdown-perl_1.000031-2_all.deb' added I: Copying source file I: copying [/home/bas/tmp/debian/abyss_1.9.0-2.dsc] I: copying [/home/bas/tmp/debian/abyss_1.9.0.orig.tar.gz] I: copying [/home/bas/tmp/debian/abyss_1.9.0-2.debian.tar.xz] I: Extracting source dpkg-source: warning: extracting unsigned source package (abyss_1.9.0-2.dsc) dpkg-source: info: extracting abyss in abyss-1.9.0 dpkg-source: info: unpacking abyss_1.9.0.orig.tar.gz dpkg-source: info: unpacking abyss_1.9.0-2.debian.tar.xz dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying privacy-breach.patch dpkg-source: info: applying abyss-32-bit.patch dpkg-source: info: applying fix_bash_script.patch I: Building the package W: no hooks of type A found -- ignoring I: Running cd /build/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc -rfakeroot dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 1.9.0-2 dpkg-buildpackage: info: source distribution UNRELEASED dpkg-buildpackage: info: source changed by Andreas Tille <ti...@debian.org> dpkg-source --before-build abyss-1.9.0 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean dpkg-source -b abyss-1.9.0 dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building abyss using existing ./abyss_1.9.0.orig.tar.gz dpkg-source: info: building abyss in abyss_1.9.0-2.debian.tar.xz dpkg-source: info: building abyss in abyss_1.9.0-2.dsc debian/rules build dh build --with autoreconf dh_testdir dh_update_autotools_config dh_autoreconf configure.ac:11: installing './compile' configure.ac:141: installing './config.guess' configure.ac:141: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/abyss-1.9.0' dh_auto_configure -- --with-mpi=/usr/lib/openmpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/openmpi configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking for ghc... no checking for ghc-pkg... no ./configure: line 5327: : command not found checking for pandoc... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash<int>... yes checking for std::tr1::hash<int>... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... g++ -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for g++ option to support OpenMP... -fopenmp ./configure: line 8392: test: too many arguments checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Misc/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating lib/gtest-1.7.0/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating DataBase/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/abyss-1.9.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-1.9.0' dh_auto_build --parallel make -j3 make[2]: Entering directory '/build/abyss-1.9.0' make all-recursive make[3]: Entering directory '/build/abyss-1.9.0' Making all in bin make[4]: Entering directory '/build/abyss-1.9.0/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-1.9.0/bin' Making all in doc make[4]: Entering directory '/build/abyss-1.9.0/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-1.9.0/doc' Making all in Common make[4]: Entering directory '/build/abyss-1.9.0/Common' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcommon.a make[4]: Leaving directory '/build/abyss-1.9.0/Common' Making all in Graph make[4]: Entering directory '/build/abyss-1.9.0/Graph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-z,relro -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -L. -L/usr/lib/openmpi/lib -Wl,-z,relro -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-1.9.0/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-1.9.0/DataLayer' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-z,relro -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-z,relro -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-1.9.0/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-1.9.0/DataBase' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-1.9.0 -isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-1.9.0/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/abyss-1.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc db-csv.cc: In function 'bool existFile(const char*)': db-csv.cc:23:9: error: cannot convert 'std::ifstream {aka std::basic_ifstream<char>}' to 'bool' in return return file; ^~~~ Makefile:527: recipe for target 'abyss_db_csv-db-csv.o' failed make[4]: *** [abyss_db_csv-db-csv.o] Error 1 make[4]: *** Waiting for unfinished jobs.... make[4]: Leaving directory '/build/abyss-1.9.0/DataBase' Makefile:484: recipe for target 'all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory '/build/abyss-1.9.0' Makefile:404: recipe for target 'all' failed make[2]: *** [all] Error 2 make[2]: Leaving directory '/build/abyss-1.9.0' dh_auto_build: make -j3 returned exit code 2 debian/rules:12: recipe for target 'override_dh_auto_build' failed make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory '/build/abyss-1.9.0' debian/rules:6: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 I: copying local configuration E: Failed autobuilding of package W: no hooks of type C found -- ignoring I: unmounting dev/pts filesystem I: unmounting run/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem -> Cleaning COW directory forking: rm -rf /var/cache/pbuilder/build/cow.12652