Your message dated Sun, 18 Sep 2016 13:03:35 +0000
with message-id <e1blbkt-0007ov...@franck.debian.org>
and subject line Bug#837059: fixed in abyss 1.9.0-1.1
has caused the Debian Bug report #837059,
regarding abyss: FTBFS (error: cannot convert 'std::ifstream {aka
std::basic_ifstream<char>}' to 'bool' in return)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
837059: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=837059
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
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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]
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Reading package lists...
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The following additional packages will be installed:
libfakeroot
The following NEW packages will be installed:
fakeroot libfakeroot
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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
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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
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./configure: line 5327: : command not found
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checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
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checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
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checking fcntl.h usability... yes
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checking float.h usability... yes
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checking stddef.h usability... yes
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checking sys/param.h usability... yes
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checking vfork.h usability... no
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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
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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
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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
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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
--- End Message ---
--- Begin Message ---
Source: abyss
Source-Version: 1.9.0-1.1
We believe that the bug you reported is fixed in the latest version of
abyss, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 837...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Alastair McKinstry <mckins...@debian.org> (supplier of updated abyss package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 13 Sep 2016 09:03:05 +0100
Source: abyss
Binary: abyss
Architecture: source amd64
Version: 1.9.0-1.1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Alastair McKinstry <mckins...@debian.org>
Description:
abyss - de novo, parallel, sequence assembler for short reads
Closes: 837059
Changes:
abyss (1.9.0-1.1) unstable; urgency=medium
.
* Non-maintainer upload.
* Fix for FTBFS in g++6 : tuple now in std::tuple. Closes: #837059
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abyss-dbgsym_1.9.0-1.1_amd64.deb
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Files:
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abyss_1.9.0-1.1.dsc
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abyss-dbgsym_1.9.0-1.1_amd64.deb
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--- End Message ---
