Your message dated Sun, 08 Jul 2018 10:09:18 +0000 with message-id <e1fc6d4-0001cd...@fasolo.debian.org> and subject line Bug#903192: fixed in sniffles 1.0.8+ds-2 has caused the Debian Bug report #903192, regarding sniffles: FTBFS in buster/sid (dh_installman: Cannot find "debian/sniffles.1") 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.) -- 903192: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=903192 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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.
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--- Begin Message ---Source: sniffles Source-Version: 1.0.8+ds-2 We believe that the bug you reported is fixed in the latest version of sniffles, 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 903...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Afif Elghraoui <a...@debian.org> (supplier of updated sniffles 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: Sun, 08 Jul 2018 00:49:22 -0400 Source: sniffles Binary: sniffles Architecture: source Version: 1.0.8+ds-2 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Afif Elghraoui <a...@debian.org> Description: sniffles - structural variation caller using third-generation sequencing Closes: 903192 Changes: sniffles (1.0.8+ds-2) unstable; urgency=low . * Use dh_installman rather than debian/manpages (Closes: #903192) Checksums-Sha1: 9696782ef0ac5be07e1bc00ae732cd67f6ec69bf 2068 sniffles_1.0.8+ds-2.dsc f6f276c90fe5d741ed29c9f778ebf6f20828de2b 4612 sniffles_1.0.8+ds-2.debian.tar.xz 1b703a9341abfe9032c113e48cd030f372e528bc 5770 sniffles_1.0.8+ds-2_source.buildinfo Checksums-Sha256: 30b3e53f249730ffc16b5a0642c2fd0c88ab30b5046d7b9a395fafefc9543b65 2068 sniffles_1.0.8+ds-2.dsc 2289ba2818714f62e4709b4515875ad53b840873557d0902d14c607514a5ce7c 4612 sniffles_1.0.8+ds-2.debian.tar.xz d2053049d2990ec907aec3a20f3c7869d50b046eca342889416c51d75d38cbc4 5770 sniffles_1.0.8+ds-2_source.buildinfo Files: ffbc6e1ed451b6c9277c66054e58ea3a 2068 science optional sniffles_1.0.8+ds-2.dsc 3a8eef1f1c7d204d302572e95217491a 4612 science optional sniffles_1.0.8+ds-2.debian.tar.xz 44f68cfb3650fdccb9a2b166c5a353a0 5770 science optional sniffles_1.0.8+ds-2_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJEBAEBCAAuFiEE6rcjomb2J+aAVWFfWbIwbzr53cEFAltBl/kQHGFmaWZAZGVi aWFuLm9yZwAKCRBZsjBvOvndweleEACIZaDvXCLBZNpRkl8iihAa0XGlRHnmiQhM uXBCWF2yP4L+ptiUojTpOVTTMzFUSTwPu+cydYP8upxlMudIdJQeIn5ukfx5oEjo 7E6pdPtNJ2Q/tcUqU5a51/V82pmYwcECGk7GNIpdOY7wOA3TxvV+ABtgAV6u8IoL jYJhauxME4SNWs6nrNEhwcLaD1g4LniA3QCtPaLB+TuYU2+7sWerF00hBTVjdBgF flCm9xVY7dA/0QGqioXLKhF4C48jA2XgIA0dQyzRoPx+fJN0CLRc1Kgmp4460bto lp74OaT4PFVxad7ciJINUlwFNdw/+ejQvB8Drskc3jPS59QnbRIVaRxXckDcEHza 9gmPSZJjqum3QIj3g9gQAklTjlHda578fpZJagAoB1e2nkGu2IwJARyQBTbcUuHO NYrGGqL5QFq/FVB6ZCFETZnnvGH9Mmr65U8suZbVDNr+0/Mcadw2dZxxAw/hKV4E C78wAAPY4Jujk9B9UA9mTK2qlb8R4+4o+mYZ5JV+LVYO6H611fLavd8+11vAiZYY j3eDyXWEYysRkkgXUl3tP0U1Mg0uDolwZiNPFewFWXMeoDwZJaQ9mfwzMc08EdZE XUnBeWTDqZk1sp/nosJ10M8xMbsjeKlOA9+FjdpZvGopJg9+94q4yaq5eWJnxwVQ K9AlMoLZEQ== =19p6 -----END PGP SIGNATURE-----
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