Michael R. Crusoe pushed to branch master at Debian Med / mmseqs2
Commits: 50930473 by Michael R. Crusoe at 2020-05-04T17:29:59+02:00 Accept the patch from Alberto, thanks! - - - - - f409350a by Michael R. Crusoe at 2020-05-04T17:30:25+02:00 routine-update: Add salsa-ci file - - - - - 2c4db8b6 by Michael R. Crusoe at 2020-05-04T17:30:25+02:00 routine-update: Rules-Requires-Root: no - - - - - e038c1d3 by Michael R. Crusoe at 2020-05-04T17:33:24+02:00 release 11-e1a1c+ds-3 to unstable. - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/fix-ftbfs-gcc10.patch - debian/patches/series - + debian/salsa-ci.yml Changes: ===================================== debian/changelog ===================================== @@ -1,6 +1,20 @@ -mmseqs2 (11-e1a1c+ds-2) unstable; urgency=medium +mmseqs2 (11-e1a1c+ds-3) unstable; urgency=medium * Team upload. + + [ Alberto Garcia ] + * debian/patches/fix-ftbfs-gcc10.patch: + - Fix FTBFS with GCC 10 (Closes: #957552). + + [ Michael R. Crusoe ] + * Accept the patch from Alberto, thanks! + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + + -- Michael R. Crusoe <[email protected]> Mon, 04 May 2020 17:30:26 +0200 + +mmseqs2 (11-e1a1c+ds-2) unstable; urgency=medium + * Install binaries only in the mmseqs2 binary package, not also the mmseqs2-examples binary package * Report the Debian package version instead of "GITDIR-NOTFOUND" ===================================== debian/control ===================================== @@ -4,22 +4,23 @@ Uploaders: Shayan Doust <[email protected]> Section: science Priority: optional Build-Depends: debhelper-compat (= 12) -Build-Depends-arch: cmake, +Build-Depends-Arch: cmake, libgzstream-dev, libzstd-dev, zlib1g-dev, libbz2-dev, - libsimde-dev (>= 0.0.0.git.20200424) + libsimde-dev Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/mmseqs2 Vcs-Git: https://salsa.debian.org/med-team/mmseqs2.git Homepage: https://github.com/soedinglab/MMseqs2 +Rules-Requires-Root: no Package: mmseqs2 Architecture: any -Built-Using: ${simde:Built-Using} Depends: ${shlibs:Depends}, ${misc:Depends} +Built-Using: ${simde:Built-Using} Description: ultra fast and sensitive protein search and clustering MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge proteins/nucleotide sequence sets. MMseqs2 is ===================================== debian/patches/fix-ftbfs-gcc10.patch ===================================== @@ -0,0 +1,24 @@ +Author: Milot Mirdita <[email protected]> +Subject: Fix FTBFS with GCC 10 +Bug-Debian: https://bugs.debian.org/957552 +Origin: https://github.com/soedinglab/MMseqs2/commit/f6f001c8cc5820e50b33b355877664f7ca66cdb1 +--- mmseqs2.orig/src/commons/Sequence.cpp ++++ mmseqs2/src/commons/Sequence.cpp +@@ -154,7 +154,7 @@ + for(size_t i = 0; i < kmerSize; i++){ + pattern[i]=1; + } +- return std::make_pair<const char *, unsigned int>((const char *) pattern, static_cast<unsigned int>(kmerSize)); ++ return std::make_pair<const char *, unsigned int>(const_cast<const char*>(pattern), static_cast<unsigned int>(kmerSize)); + + // Debug(Debug::ERROR) << "Did not find spaced pattern for kmerSize: " << kmerSize << ". \n"; + // Debug(Debug::ERROR) << "Please report this bug to the developer\n"; +@@ -165,7 +165,7 @@ + if (pair.second > 0) { + memcpy(pattern, pair.first, pair.second * sizeof(char)); + } +- return std::make_pair<const char *, unsigned int>(pattern, static_cast<unsigned int>(pair.second)); ++ return std::make_pair<const char *, unsigned int>(const_cast<const char*>(pattern), static_cast<unsigned int>(pair.second)); + #undef CASE + } + ===================================== debian/patches/series ===================================== @@ -3,3 +3,4 @@ fix_util_installation.patch use_system_zstd.patch use_system_gzstream.patch simde +fix-ftbfs-gcc10.patch ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/c274189adac033cda0e895146c1f92b6996df313...e038c1d3117000b13e9bea1c775403c1b85fee7c -- View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/c274189adac033cda0e895146c1f92b6996df313...e038c1d3117000b13e9bea1c775403c1b85fee7c You're receiving this email because of your account on salsa.debian.org.
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