Package: src:sniffles
Version: 1.0.8+ds-1
Severity: serious
Tags: ftbfs
Dear maintainer:
I tried to build this package in buster but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/sniffles-1.0.8+ds'
dh_auto_configure -- \
-DCMAKE_INCLUDE_PATH="/usr/include/bamtools"
cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None
-DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var
-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles"
-DCMAKE_INCLUDE_PATH=/usr/include/bamtools ..
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
[... snipped ...]
/<<BUILDDIR>>/sniffles-1.0.8+ds/src/cluster/Cluster_SVs.cpp: In member function
'void Cluster_SVS::update_SVs(std::vector<combine_str>&)':
/<<BUILDDIR>>/sniffles-1.0.8+ds/src/cluster/Cluster_SVs.cpp:84:8: warning:
ignoring return value of 'int system(const char*)', declared with attribute
warn_unused_result [-Wunused-result]
system(move.c_str());
~~~~~~^~~~~~~~~~~~~~
/<<BUILDDIR>>/sniffles-1.0.8+ds/src/cluster/Cluster_SVs.cpp: In member function
'void Cluster_SVS::update_SVs()':
/<<BUILDDIR>>/sniffles-1.0.8+ds/src/cluster/Cluster_SVs.cpp:154:8: warning:
ignoring return value of 'int system(const char*)', declared with attribute
warn_unused_result [-Wunused-result]
system(del.c_str());
~~~~~~^~~~~~~~~~~~~
[ 91%] Building CXX object
src/CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o
cd /<<BUILDDIR>>/sniffles-1.0.8+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/usr/include/bamtools
-I/<<BUILDDIR>>/sniffles-1.0.8+ds/src/../lib/bamtools-2.3.0/src
-I/<<BUILDDIR>>/sniffles-1.0.8+ds/src/../lib/tclap-1.2.1/include -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/sniffles-1.0.8+ds=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o
CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o -c
/<<BUILDDIR>>/sniffles-1.0.8+ds/src/force_calling/Force_calling.cpp
[ 95%] Building CXX object
src/CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o
cd /<<BUILDDIR>>/sniffles-1.0.8+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/usr/include/bamtools
-I/<<BUILDDIR>>/sniffles-1.0.8+ds/src/../lib/bamtools-2.3.0/src
-I/<<BUILDDIR>>/sniffles-1.0.8+ds/src/../lib/tclap-1.2.1/include -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/sniffles-1.0.8+ds=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o
CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o -c
/<<BUILDDIR>>/sniffles-1.0.8+ds/src/force_calling/VCF_parser.cpp
[100%] Linking CXX executable ../../bin/sniffles-core-1.0.8/sniffles
cd /<<BUILDDIR>>/sniffles-1.0.8+ds/obj-x86_64-linux-gnu/src && /usr/bin/cmake
-E cmake_link_script CMakeFiles/sniffles.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/sniffles-1.0.8+ds=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic
CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o
CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o
CMakeFiles/sniffles.dir/Alignment.cpp.o CMakeFiles/sniffles.dir/BamParser.cpp.o
CMakeFiles/sniffles.dir/Sniffles.cpp.o
CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o
CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o
CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o
CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o
CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o
CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o
CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o
CMakeFiles/sniffles.dir/realign/Realign.cpp.o
CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o
CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o
CMakeFiles/sniffles.dir/print/IPrinter.cpp.o
CMakeFiles/sniffles.dir/tree/BinTree.cpp.o CMake
Files/sniffles.dir/print/NGMPrinter.cpp.o
CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o
CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o
CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o
CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o -o
../../bin/sniffles-core-1.0.8/sniffles -lbamtools -lz
make[3]: Leaving directory
'/<<BUILDDIR>>/sniffles-1.0.8+ds/obj-x86_64-linux-gnu'
[100%] Built target sniffles
make[2]: Leaving directory
'/<<BUILDDIR>>/sniffles-1.0.8+ds/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start
/<<BUILDDIR>>/sniffles-1.0.8+ds/obj-x86_64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory
'/<<BUILDDIR>>/sniffles-1.0.8+ds/obj-x86_64-linux-gnu'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/sniffles-1.0.8+ds'
bin/sniffles-*/sniffles -m test_set/reads_region.bam -v test.vcf
Estimating parameter...
Max dist between aln events: 4
Max diff in window: 50
Min score ratio: 2
Avg DEL ratio: 0.0432235
Avg INS ratio: 0.0740733
Start parsing... 21
Switch Chr 21
Finalizing ..
make[1]: Leaving directory '/<<BUILDDIR>>/sniffles-1.0.8+ds'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_installman: Cannot find (any matches for) "debian/sniffles.1" (tried in .)
dh_installman: Aborting due to earlier error
debian/rules:13: recipe for target 'binary-arch' failed
make: *** [binary-arch] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned
exit status 2
--------------------------------------------------------------------------------
The build was made with "dpkg-buildpackage -B" in my autobuilder.
(This one does not seem to fail with plain "dpkg-buildpackage")
[ Note: There has been a recent change in debhelper behaviour, the current
behaviour is the intended one. See Bug #903133 for details ].
Thanks.
