Your message dated Mon, 03 Jan 2022 20:43:10 +0000 with message-id <e1n4uag-000gqf...@fasolo.debian.org> and subject line Bug#1002142: fixed in shasta 0.8.0-2 has caused the Debian Bug report #1002142, regarding shasta: FTBFS: PythonModule.cpp:40:29: error: expected primary-expression before ‘(’ token 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.) -- 1002142: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1002142 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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.
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--- Begin Message ---Source: shasta Source-Version: 0.8.0-2 Done: Nilesh Patra <nil...@debian.org> We believe that the bug you reported is fixed in the latest version of shasta, 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 1002...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Nilesh Patra <nil...@debian.org> (supplier of updated shasta 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: SHA512 Format: 1.8 Date: Tue, 04 Jan 2022 01:10:16 +0530 Source: shasta Architecture: source Version: 0.8.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Nilesh Patra <nil...@debian.org> Closes: 1002142 Changes: shasta (0.8.0-2) unstable; urgency=medium . * Team Upload. * Cherry-pick upstream patch to fix FTBFS (Closes: #1002142) Checksums-Sha1: 87e6c25c634284e7a2bc29f1e341812aeff1a959 2369 shasta_0.8.0-2.dsc 5e8d24d743709a04acd66c86a00c84ca4cc7b60f 11688 shasta_0.8.0-2.debian.tar.xz c7a7541f7983f75da03f426fe67e32b37c0b05be 15291 shasta_0.8.0-2_amd64.buildinfo Checksums-Sha256: 525fdfc4fec915068e3bbe5a51808230db1833bbd2d82ff6afd5b6be6be6a674 2369 shasta_0.8.0-2.dsc 1f0793a5973666fa9d1f92d91468ed519287f451e70e166b8af5990e9045f519 11688 shasta_0.8.0-2.debian.tar.xz 86985b2890ce2dc41dfdf57147f1738178d97a7bc8a33d587c90210fb853c255 15291 shasta_0.8.0-2_amd64.buildinfo Files: f6371bce9981e703465ddc9cf11d5b72 2369 science optional shasta_0.8.0-2.dsc 3e7beba5a56daf5f8de4695def7caad6 11688 science optional shasta_0.8.0-2.debian.tar.xz 8650fca22e27911481fcbaebdc45458f 15291 science optional shasta_0.8.0-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmHTU+4SHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxKx8QAJqZqnJaUGyOHTVLo1EU3qwzo/j8qgDs MG4WvIQAte6e7F74mc4gi4N+QM4uIitzYsHvXENC7msORlKgCD2doauni6xU0roC N+YYGCR1R1AVtPNQFbWjpMjOz8ZZIY3AkvDI7ONO1khim7CHtmiP/HzX2XF9A1MY W9+ydF4GxjHJQtFgdCfcbf7GWmPJZ/zFuWT803T5rxmovuav2JB4UsUEZmt5hbIF ceGAF53Jc5KzKqgBdox9rxvTT5qviRVfNz1GEsBrauUqfL4ugh/PAOZ9MbwxCGUz DXfYr27GOgnwv98d4agf5leWEkmQNmQSPaa4JXPkIiUppGD4pemmA7IpTVkzmpBK MSJSZGxcwOEiHrdgyu6DcGnF2aQXQkCf11PPFJiL9dB6fS6GxiIeABtRRyeprEZK mMwnpTwiTCnx0BxXdcjpJlLHEmbPtdjOvWnnzYwhU4zAOo0lg88ATN84iYAYO0D7 XlMI8e2BWQ/SynEWTHe6YaDhA+GcCDuxYhRwSx64n/OuQA4N93/aSklGZNIPwUn7 kAs2QNzJWuKGJJxObmnr/udD/PxhhMSC+81326QE4vFO8cAswGFJIVzV0+lGu/rP 3vojATsTSw4LzgAw3FhRgHQae6mNEUjlPy2JOmqtADXLRVE6jmAiwKoSD/PUF9Aj c9jkxspynSlj =H1WZ -----END PGP SIGNATURE-----
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