Your message dated Wed, 20 Oct 2021 17:03:47 +0000 with message-id <e1mdf0f-000apw...@fasolo.debian.org> and subject line Bug#984139: fixed in libvcflib 1.0.2+dfsg-3 has caused the Debian Bug report #984139, regarding libvcflib: ftbfs with GCC-11 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.) -- 984139: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984139 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:libvcflib Version: 1.0.2+dfsg-2 Severity: normal Tags: sid bookworm User: debian-...@lists.debian.org Usertags: ftbfs-gcc-11 [This bug is not targeted to the upcoming bullseye release] Please keep this issue open in the bug tracker for the package it was filed for. If a fix in another package is required, please file a bug for the other package (or clone), and add a block in this package. Please keep the issue open until the package can be built in a follow-up test rebuild. The package fails to build in a test rebuild on at least amd64 with gcc-11/g++-11, but succeeds to build with gcc-10/g++-10. The severity of this report will be raised before the bookworm release, so nothing has to be done for the bullseye release. The full build log can be found at: http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libvcflib_1.0.2+dfsg-2_unstable_gcc11.log The last lines of the build log are at the end of this report. To build with GCC 11, either set CC=gcc-11 CXX=g++-11 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. apt-get -t=experimental install g++ Common build failures are new warnings resulting in build failures with -Werror turned on, or new/dropped symbols in Debian symbols files. For other C/C++ related build failures see the porting guide at http://gcc.gnu.org/gcc-11/porting_to.html GCC 11 defaults to the GNU++17 standard. If your package installs header files in /usr/include, please don't work around C++17 issues by choosing a lower C++ standard for the package build, but fix these issues to build with the C++17 standard. [...] /usr/include/c++/11/bits/stl_algo.h:3449:5: note: template argument deduction/substitution failed: In file included from /<<PKGBUILDDIR>>/src/BedReader.h:21, from /<<PKGBUILDDIR>>/src/vcf2dag.cpp:11: /<<PKGBUILDDIR>>/intervaltree/IntervalTree.h:271:103: note: candidate expects 1 argument, 0 provided 271 | std::numeric_limits<Scalar>::min() }}; | ^ In file included from /usr/include/c++/11/algorithm:62, from /usr/include/smithwaterman/SmithWatermanGotoh.h:4, from /<<PKGBUILDDIR>>/src/Variant.h:30, from /<<PKGBUILDDIR>>/src/vcf2dag.cpp:10: /usr/include/c++/11/bits/stl_algo.h:3455:5: note: candidate: ‘template<class _Tp, class _Compare> _Tp std::min(std::initializer_list<_Tp>, _Compare)’ 3455 | min(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/11/bits/stl_algo.h:3455:5: note: template argument deduction/substitution failed: In file included from /<<PKGBUILDDIR>>/src/BedReader.h:21, from /<<PKGBUILDDIR>>/src/vcf2dag.cpp:11: /<<PKGBUILDDIR>>/intervaltree/IntervalTree.h:271:103: note: candidate expects 2 arguments, 0 provided 271 | std::numeric_limits<Scalar>::min() }}; | ^ [ 12%] Linking CXX executable vcfsample2info /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /<<PKGBUILDDIR>>/intervaltree/IntervalTree.h: In instantiation of ‘std::pair<bool, std::pair<_FIter, _FIter> > IntervalTree<Scalar, Value>::is_valid() const [with Scalar = long unsigned int; Value = BedTarget*]’: /<<PKGBUILDDIR>>/intervaltree/IntervalTree.h:115:13: required from ‘IntervalTree<Scalar, Value>::IntervalTree(IntervalTree<Scalar, Value>::interval_vector&&, std::size_t, std::size_t, std::size_t, Scalar, Scalar) [with Scalar = long unsigned int; Value = BedTarget*; IntervalTree<Scalar, Value>::interval_vector = std::vector<Interval<long unsigned int, BedTarget*> >; std::size_t = long unsigned int]’ /<<PKGBUILDDIR>>/src/BedReader.h:163:118: required from here /<<PKGBUILDDIR>>/intervaltree/IntervalTree.h:270:52: error: could not convert ‘{true, {<expression error>, <expression error>}}’ from ‘<brace-enclosed initializer list>’ to ‘std::pair<bool, std::pair<long unsigned int, long unsigned int> >’ 270 | std::pair<bool, std::pair<Scalar, Scalar>> result = {true, { std::numeric_limits<Scalar>::max(), | ^~~~~~ | | | <brace-enclosed initializer list> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 12%] Built target vcfsample2info make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= Dependee "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake" is newer than depender "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/depend.internal". Dependee "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/depend.internal". Scanning dependencies of target vcfgenosamplenames make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 13%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/intervaltree -I/<<PKGBUILDDIR>>/multichoose -I/<<PKGBUILDDIR>>/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /<<PKGBUILDDIR>>/src/vcfgenosamplenames.cpp make[4]: *** [CMakeFiles/vcf2dag.dir/build.make:85: CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o] Error 1 make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:372: CMakeFiles/vcf2dag.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 13%] Linking CXX executable vcfgeno2alleles /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 13%] Built target vcfgeno2alleles [ 13%] Linking CXX executable vcfgenosamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 13%] Built target vcfgenosamplenames [ 13%] Linking CXX executable vcfcombine /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 13%] Built target vcfcombine make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[2]: *** [Makefile:163: all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:26: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:12: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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--- Begin Message ---Source: libvcflib Source-Version: 1.0.2+dfsg-3 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of libvcflib, 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 984...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated libvcflib 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: Wed, 20 Oct 2021 18:33:54 +0200 Source: libvcflib Architecture: source Version: 1.0.2+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Closes: 984139 Changes: libvcflib (1.0.2+dfsg-3) unstable; urgency=medium . * Fix build with gcc-11 Closes: #984139 * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: 64e48141a6f95b0cbd0945223df9d5eacfb2e5d3 2290 libvcflib_1.0.2+dfsg-3.dsc 34686f8d9643e3d99adc8b7a61016d339ccba6ab 9316 libvcflib_1.0.2+dfsg-3.debian.tar.xz 43f94ab9110bd92ab0921763e4c7839611d1e73d 8604 libvcflib_1.0.2+dfsg-3_amd64.buildinfo Checksums-Sha256: 01b2fac52fc71e3260fd697c943a8c346ad4d01f43960f882ecba0b9d6307a35 2290 libvcflib_1.0.2+dfsg-3.dsc 6f3bfe0247387891c1f5deb88bf5aa3be61028257c30270b2ae25601bbb89c20 9316 libvcflib_1.0.2+dfsg-3.debian.tar.xz 7584fdbdddd7618324671f85ae2877a35bfb10534698c7db0bfbfcb711ff2b97 8604 libvcflib_1.0.2+dfsg-3_amd64.buildinfo Files: 99fc49903cbd85b83c9017e8a981e59d 2290 science optional libvcflib_1.0.2+dfsg-3.dsc 06ba404513712d859c4193235f335c40 9316 science optional libvcflib_1.0.2+dfsg-3.debian.tar.xz 9d6e3abacd0c6d40b3528b7cef665de1 8604 science optional libvcflib_1.0.2+dfsg-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFwRdARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHT4w/+MIgEYzb0aglv4Q9SnNOCTYWBlN1fAmvn 3bVt8zz0WrpaXAckEAuEhWpXle6xANKy7khhsWlrzDmuoHUVgucWL4Y1Ih86cjoy xtJwJhvXOE2jDXggJpEAlyes5P+CruxDosv+mbfCYpz7Q6eD5KJJBKqxmPPjRYXT 5X2Ld15NeBzntRDMRj+4RxFiGDardHW4zj7zDQEfYjXfHEBSpjS9pOyNo5gOlDFi u4ULt8jecUG1XvvVrsPWNz/1mpI/ERsIsgyEUxmrLEtIUqzrhShblIjM027K2G8m vViXS97U7J3lFmk6aGr2ZboCbvjsWvflrtyjF+UbxOqUbBHDsWOxUE5mQ9AOAJWv Qped4SViT47omuaBCPSAWpCbnc6hFB0PdpGPVSt98X17O2qp4nNLNuWiFnaaI6sd GcmR2Q9ZkpS+VGLRt+OtFyuleyjp7s2uunAjiNgrUDBifYWACno2DjdA6duWoMmb GIVTkhnfzzOQ/wx3Xn3caa/C5x9I4q1DtRBpyXFRzO281iqWsNiwD/vsL+TSYtc4 K0C3s/RCXVKjmf/+w2iPpT32xG0C9t1CYup4VUkEbvQz6itse+t5kuCKb3vvGLPl JkthrAfrSC1sJ15mURi93qSj4noqoGu1U+aHB9hxThX8PK7uEYRF6d26yxkPMLdF ytdKmnGJQ+s= =52S5 -----END PGP SIGNATURE-----
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