Your message dated Thu, 30 Dec 2021 00:48:27 +0000 with message-id <e1n2jcj-0004sr...@fasolo.debian.org> and subject line Bug#996541: fixed in libedlib 1.2.7-3 has caused the Debian Bug report #996541, regarding racon: FTBFS when rebuilt against libedlib1 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.) -- 996541: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=996541 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: racon Version: 1.4.21-1 Severity: serious X-Debbugs-Cc: ni...@thykier.net Hi, A new version of libedlib (with a new ABI) has been uploaded to unstable and that causes racon to fail to build from source. Relevant parts of the amd64 log: ``` > /usr/bin/cmake -E cmake_link_script CMakeFiles/racon_test.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 -Wall -Wextra -pedantic -Wl,-z,relro -Wl,-z,now -rdynamic > CMakeFiles/racon_test.dir/test/racon_test.cpp.o > CMakeFiles/racon_test.dir/src/logger.cpp.o > CMakeFiles/racon_test.dir/src/polisher.cpp.o > CMakeFiles/racon_test.dir/src/overlap.cpp.o > CMakeFiles/racon_test.dir/src/sequence.cpp.o > CMakeFiles/racon_test.dir/src/window.cpp.o -o bin/racon_test -lspoa -ledlib > -lz /usr/lib/x86_64-linux-gnu/libgtest_main.a > /usr/lib/x86_64-linux-gnu/libgtest.a -pthread > /usr/bin/ld: CMakeFiles/racon_test.dir/test/racon_test.cpp.o: in function > `calculateEditDistance(std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&, > std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > const&)': > ./obj-x86_64-linux-gnu/./test/racon_test.cpp:18: undefined reference to > `edlibDefaultAlignConfig' > /usr/bin/ld: ./obj-x86_64-linux-gnu/./test/racon_test.cpp:18: undefined > reference to `edlibAlign' > /usr/bin/ld: ./obj-x86_64-linux-gnu/./test/racon_test.cpp:22: undefined > reference to `edlibFreeAlignResult' > /usr/bin/ld: CMakeFiles/racon_test.dir/src/overlap.cpp.o: in function > `racon::Overlap::align_overlaps(char const*, unsigned int, char const*, > unsigned int)': > ./obj-x86_64-linux-gnu/./src/overlap.cpp:208: undefined reference to > `edlibNewAlignConfig' > /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:208: undefined > reference to `edlibAlign' > /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:213: undefined > reference to `edlibAlignmentToCigar' > /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:223: undefined > reference to `edlibFreeAlignResult' > collect2: error: ld returned 1 exit status > make[3]: *** [CMakeFiles/racon_test.dir/build.make:182: bin/racon_test] Error > 1 > make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[2]: *** [CMakeFiles/Makefile2:88: CMakeFiles/racon_test.dir/all] Error 2 > make[2]: *** Waiting for unfinished jobs.... > [100%] Linking CXX executable bin/racon > /usr/bin/cmake -E cmake_link_script CMakeFiles/racon.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 -Wall -Wextra -pedantic -Wl,-z,relro -Wl,-z,now -rdynamic > -pthread CMakeFiles/racon.dir/src/main.cpp.o > CMakeFiles/racon.dir/src/logger.cpp.o CMakeFiles/racon.dir/src/polisher.cpp.o > CMakeFiles/racon.dir/src/overlap.cpp.o > CMakeFiles/racon.dir/src/sequence.cpp.o CMakeFiles/racon.dir/src/window.cpp.o > -o bin/racon -lspoa -ledlib -lz > /usr/bin/ld: CMakeFiles/racon.dir/src/overlap.cpp.o: in function > `racon::Overlap::align_overlaps(char const*, unsigned int, char const*, > unsigned int)': > ./obj-x86_64-linux-gnu/./src/overlap.cpp:208: undefined reference to > `edlibNewAlignConfig' > /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:208: undefined > reference to `edlibAlign' > /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:213: undefined > reference to `edlibAlignmentToCigar' > /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:223: undefined > reference to `edlibFreeAlignResult' > collect2: error: ld returned 1 exit status ``` Thanks, ~Niels
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--- Begin Message ---Source: libedlib Source-Version: 1.2.7-3 Done: tony mancill <tmanc...@debian.org> We believe that the bug you reported is fixed in the latest version of libedlib, 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 996...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. tony mancill <tmanc...@debian.org> (supplier of updated libedlib 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, 29 Dec 2021 16:18:05 -0800 Source: libedlib Architecture: source Version: 1.2.7-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: tony mancill <tmanc...@debian.org> Closes: 996541 Changes: libedlib (1.2.7-3) unstable; urgency=medium . [ Nilesh Patra ] * Team Upload. * Fix version of package in CMakeLists.txt . [ tony mancill ] * Enable building shared libs; upstream defaults this to OFF (Closes: #996541) * Update symbols file for libedlib1 * Adjust enabled_shared_and_static.patch * Freshen years in debian/copyright * Add Build-Depends-Package metadata to libedlib1.symbols (lintian) Checksums-Sha1: 92cf20e8fd000cde2507e2f4c07c8b6ede524fd1 2225 libedlib_1.2.7-3.dsc 915dcda86296490f68d3e778da799ff43d14e657 7268 libedlib_1.2.7-3.debian.tar.xz 9a83e8e7f0c591cd7fc319d08a30b172330ad587 9787 libedlib_1.2.7-3_amd64.buildinfo Checksums-Sha256: 00db00aeb09fbd0539fde0066a280a48b3c50f4069da99a8ecc86550caf572f7 2225 libedlib_1.2.7-3.dsc 30db26411bd77218a27804118ab7582f8d04512d39a4301c3a94d8d838592ad4 7268 libedlib_1.2.7-3.debian.tar.xz 7e3f9ed38ba0616fda91b2745ac7d9c8c0e1862a0aede64808905733125f79d3 9787 libedlib_1.2.7-3_amd64.buildinfo Files: 55786a118c8b3402803995ec324351a4 2225 science optional libedlib_1.2.7-3.dsc 0cc73885ce27cbbbbd4491626af96fd8 7268 science optional libedlib_1.2.7-3.debian.tar.xz edb0f5b79398e8ea5537eb77dcc56842 9787 science optional libedlib_1.2.7-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEE5Qr9Va3SequXFjqLIdIFiZdLPpYFAmHM/KMUHHRtYW5jaWxs QGRlYmlhbi5vcmcACgkQIdIFiZdLPpZ5Rg/9FjVtv/h2szDzVD+RRFQDYEwFFGK2 9cbIE6rdJDLpw0w8tpo3iwr+mSuE27FMZNB84ezhrf9iBVMyOpPCbu3BApZRCXZe bEygZvt2ctrKXbhycvkbcMMDI/58j0PZKVboxOK0FbJJrt/1eCdhVRCxEdBsf6rI NzjTAdUnUqqNnW8KKvggqCrp3wCYddREQiw0qUEWheppKWD+HeErN8LehorWq09v bxpCJhCNNLnUW9GMLlrqeGQEJZm/dGCFWaavkWwzDQQp4nRib4bPQzBnTMCHSOHj anlvXfXl2UaaOFp84iYo4PrENQt0d1n0yuccWMW4icG0oZ9wekN9ot+tTWCKqdkM 78l3hRwFtasJyrwW/vXNS9N2lNIIv/1xfPQzVBFSE5ZbVyjRnIjcTFcuffBNwite QKKcx5+vdvWmw+6e4D6heVPETIzDvN3hYlB5fXMxrORcOvS23sZKEeq5f9jEkcuB Ysy+wRh2B9TgBvGiInaVSIg7CSrCm2adHVTgw0PS9+c165SCxyVbR0IUXRA9LXSv jCZ/Xouk2KyW0mshkCas2mtoBtnbqkkvRJey67IvHRxzkrnoEgI75fCx5AYQUrHH LxxGRei1vei/0a67ZC5DnFJBU0OkvPywYwsv35ENOWTQj//eUZsdeuPhuqs5ohl0 gfQ+tUS+ad2udDQ= =16Pb -----END PGP SIGNATURE-----
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