Source: shasta
Version: 0.8.0-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20211220 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0
> -DNDEBUG -DSHASTA_HTTP_SERVER -I/<<PKGBUILDDIR>>/staticLibrary/../src -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall
> -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT
> staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o -MF
> CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o.d -o
> CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o -c
> /<<PKGBUILDDIR>>/src/ReadLoader.cpp
> /<<PKGBUILDDIR>>/src/PythonModule.cpp: In function ‘void
> pybind11_init_shasta(pybind11::module_& (*)(pybind11::module))’:
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:40:29: error: expected
> primary-expression before ‘(’ token
> 40 | class_<OrientedReadPair>(module, "OrientedReadPair")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:40:36: error: expected
> primary-expression before ‘,’ token
> 40 | class_<OrientedReadPair>(module, "OrientedReadPair")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:46:18: error: expected
> primary-expression before ‘(’ token
> 46 | class_<Reads>(module, "Reads")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:46:25: error: expected
> primary-expression before ‘,’ token
> 46 | class_<Reads>(module, "Reads")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:83:25: error: expected
> primary-expression before ‘(’ token
> 83 | class_<AlignOptions>(module, "AlignOptions")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:83:32: error: expected
> primary-expression before ‘,’ token
> 83 | class_<AlignOptions>(module, "AlignOptions")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:110:22: error: expected
> primary-expression before ‘(’ token
> 110 | class_<Assembler>(module, "Assembler")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:110:29: error: expected
> primary-expression before ‘,’ token
> 110 | class_<Assembler>(module, "Assembler")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:664:29: error: expected
> primary-expression before ‘(’ token
> 664 | class_<AssembledSegment>(module, "AssembledSegment")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:664:36: error: expected
> primary-expression before ‘,’ token
> 664 | class_<AssembledSegment>(module, "AssembledSegment")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:674:35: error: expected
> primary-expression before ‘(’ token
> 674 | class_<CompressedCoverageData>(module, "CompressedCoverageData")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:674:42: error: expected
> primary-expression before ‘,’ token
> 674 | class_<CompressedCoverageData>(module, "CompressedCoverageData")
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:684:11: error: expected unqualified-id
> before ‘.’ token
> 684 | module.attr("invalidGlobalMarkerGraphVertexId") =
> MarkerGraph::invalidVertexId;
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:685:11: error: expected unqualified-id
> before ‘.’ token
> 685 | module.attr("invalidCompressedGlobalMarkerGraphVertexId") =
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:691:11: error: expected unqualified-id
> before ‘.’ token
> 691 | module.def("testMultithreadedObject",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:694:11: error: expected unqualified-id
> before ‘.’ token
> 694 | module.def("testMemoryMappedVector",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:697:11: error: expected unqualified-id
> before ‘.’ token
> 697 | module.def("testBase",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:700:11: error: expected unqualified-id
> before ‘.’ token
> 700 | module.def("testShortBaseSequence",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:703:11: error: expected unqualified-id
> before ‘.’ token
> 703 | module.def("testLongBaseSequence",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:706:11: error: expected unqualified-id
> before ‘.’ token
> 706 | module.def("testSplitRange",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:709:11: error: expected unqualified-id
> before ‘.’ token
> 709 | module.def("testCompactUndirectedGraph1",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:712:11: error: expected unqualified-id
> before ‘.’ token
> 712 | module.def("testCompactUndirectedGraph2",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:715:11: error: expected unqualified-id
> before ‘.’ token
> 715 | module.def("testSpoa",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:718:11: error: expected unqualified-id
> before ‘.’ token
> 718 | module.def("testSimpleBayesianConsensusCaller",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:721:11: error: expected unqualified-id
> before ‘.’ token
> 721 | module.def("testMedianConsensusCaller",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:724:11: error: expected unqualified-id
> before ‘.’ token
> 724 | module.def("testDeduplicateAndCount",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:727:11: error: expected unqualified-id
> before ‘.’ token
> 727 | module.def("dset64Test",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:735:11: error: expected unqualified-id
> before ‘.’ token
> 735 | module.def("mappedCopy",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:738:11: error: expected unqualified-id
> before ‘.’ token
> 738 | module.def("testAlignmentCompression",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:741:11: error: expected unqualified-id
> before ‘.’ token
> 741 | module.def("testMap",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:744:11: error: expected unqualified-id
> before ‘.’ token
> 744 | module.def("testMemoryMappedAllocator",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:747:11: error: expected unqualified-id
> before ‘.’ token
> 747 | module.def("testLapack",
> | ^
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:750:11: error: expected unqualified-id
> before ‘.’ token
> 750 | module.def("testShortestPathBoundedDistance",
> | ^
> [ 78%] Building CXX object
> dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0
> -DNDEBUG -DSHASTA_HTTP_SERVER -DSHASTA_PYTHON_API
> -I/<<PKGBUILDDIR>>/dynamicLibrary/../src -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++17
> -Wall -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -I/usr/include/python3.9
> -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT
> dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o
> -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o.d -o
> CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o -c
> /<<PKGBUILDDIR>>/src/ReadLoader.cpp
> In file included from
> /usr/lib/python3/dist-packages/pybind11/include/pybind11/pytypes.h:12,
> from
> /usr/lib/python3/dist-packages/pybind11/include/pybind11/cast.h:13,
> from
> /usr/lib/python3/dist-packages/pybind11/include/pybind11/attr.h:13,
> from
> /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:13,
> from /<<PKGBUILDDIR>>/src/PythonModule.cpp:29:
> /<<PKGBUILDDIR>>/src/PythonModule.cpp: At global scope:
> /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/common.h:413:33:
> warning: ‘void pybind11_init_shasta(pybind11::module_&)’ declared ‘static’
> but never defined [-Wunused-function]
> 413 | static void PYBIND11_CONCAT(pybind11_init_,
> name)(::pybind11::module_ &); \
> | ^~~~~~~~~~~~~~
> /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/common.h:317:40:
> note: in definition of macro ‘PYBIND11_CONCAT’
> 317 | #define PYBIND11_CONCAT(first, second) first##second
> | ^~~~~
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:36:1: note: in expansion of macro
> ‘PYBIND11_MODULE’
> 36 | PYBIND11_MODULE(shasta, module)
> | ^~~~~~~~~~~~~~~
> [ 79%] Building CXX object
> staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.8.0
> -DNDEBUG -DSHASTA_HTTP_SERVER -I/<<PKGBUILDDIR>>/staticLibrary/../src -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wall
> -Wconversion -Wno-unused-result -g0 -O3 -mcx16 -MD -MT
> staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -MF
> CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o.d -o
> CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -c
> /<<PKGBUILDDIR>>/src/Reads.cpp
> /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/common.h:413:33:
> warning: ‘void pybind11_init_shasta(pybind11::module_&)’ used but never
> defined
> 413 | static void PYBIND11_CONCAT(pybind11_init_,
> name)(::pybind11::module_ &); \
> | ^~~~~~~~~~~~~~
> /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/common.h:317:40:
> note: in definition of macro ‘PYBIND11_CONCAT’
> 317 | #define PYBIND11_CONCAT(first, second) first##second
> | ^~~~~
> /<<PKGBUILDDIR>>/src/PythonModule.cpp:36:1: note: in expansion of macro
> ‘PYBIND11_MODULE’
> 36 | PYBIND11_MODULE(shasta, module)
> | ^~~~~~~~~~~~~~~
> make[4]: ***
> [dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make:1129:
> dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o]
> Error 1
The full build log is available from:
http://qa-logs.debian.net/2021/12/20/shasta_0.8.0-1_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
