Michael R. Crusoe pushed to branch master at Debian Med / bedtools
Commits: ec128e29 by Michael R. Crusoe at 2020-10-28T12:28:13+01:00 Include patch from Bernhard Übelacker to fix 32-bit builds (Closes: #955403) - - - - - 0723ef8b by Michael R. Crusoe at 2020-10-28T12:28:43+01:00 routine-update: debhelper-compat 13 - - - - - 15c67124 by Michael R. Crusoe at 2020-10-28T12:28:45+01:00 routine-update: Add salsa-ci file - - - - - 5892a8e3 by Michael R. Crusoe at 2020-10-28T12:28:45+01:00 routine-update: Rules-Requires-Root: no - - - - - cd290726 by Michael R. Crusoe at 2020-10-28T12:28:45+01:00 Set upstream metadata fields: Bug-Database, Bug-Submit. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-bug-tracking See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html - - - - - 9889a387 by Michael R. Crusoe at 2020-10-28T12:28:46+01:00 adjust bin source location - - - - - 7 changed files: - debian/bedtools.install - debian/changelog - debian/control - + debian/patches/32-bit-fixes.patch - debian/patches/series - + debian/salsa-ci.yml - debian/upstream/metadata Changes: ===================================== debian/bedtools.install ===================================== @@ -1,3 +1,3 @@ -bin/* usr/bin +usr/local/bin/* usr/bin genomes usr/share/bedtools debian/bash_completion/* /usr/share/bash-completion/completions ===================================== debian/changelog ===================================== @@ -2,6 +2,12 @@ bedtools (2.29.2+dfsg-4) UNRELEASED; urgency=medium * Team upload. * Remove the need for samtools via patch from upstream. + * Include patch from Bernhard Übelacker to fix 32-bit builds. TODO: the + autopkgtests do not yet pass on i386 (and likely neither on other 32-bit + archs). + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) -- Michael R. Crusoe <[email protected]> Fri, 14 Feb 2020 16:50:58 +0100 ===================================== debian/control ===================================== @@ -4,7 +4,7 @@ Uploaders: Charles Plessy <[email protected]>, Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), python3, zlib1g-dev, libbz2-dev, @@ -13,6 +13,7 @@ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/bedtools Vcs-Git: https://salsa.debian.org/med-team/bedtools.git Homepage: https://github.com/arq5x/bedtools2 +Rules-Requires-Root: no Package: bedtools Architecture: any ===================================== debian/patches/32-bit-fixes.patch ===================================== @@ -0,0 +1,40 @@ +Description: Use a variable type that is 8 bytes in size on 32 bit systems too. + +Author: Bernhard Übelacker <[email protected]> +Bug-Debian: https://bugs.debian.org/955403 +Forwarded: no +Last-Update: 2020-10-27 + +--- bedtools.orig/src/randomBed/randomBed.cpp ++++ bedtools/src/randomBed/randomBed.cpp +@@ -58,7 +58,7 @@ + // we need to combine two consective calls to rand() + // because RAND_MAX is 2^31 (2147483648), whereas + // mammalian genomes are obviously much larger. +- CHRPOS randStart = ((((long) rand()) << 31) | rand()) % genomeSize; ++ CHRPOS randStart = ((((CHRPOS) rand()) << 31) | ((CHRPOS) rand())) % genomeSize; + // use the above randomStart (e.g., for human 0..3.1billion) + // to identify the chrom and start on that chrom. + pair<string, CHRPOS> location = _genome->projectOnGenome(randStart); +--- bedtools.orig/src/slopBed/slopBed.cpp ++++ bedtools/src/slopBed/slopBed.cpp +@@ -67,7 +67,7 @@ + } + _bed->Close(); + } +-static inline long _normalize_coord(long size, long pos) { ++static inline CHRPOS _normalize_coord(CHRPOS size, CHRPOS pos) { + if(pos < 0) return 0; + if(size >= 0 && pos > size) return size; + return pos; +@@ -84,8 +84,8 @@ + } + + bool should_swap = _forceStrand && bed.strand == "-"; +- long left_slop = should_swap ? (long)_rightSlop : (long)_leftSlop; +- long right_slop = should_swap ? (long)_leftSlop : (long)_rightSlop; ++ CHRPOS left_slop = should_swap ? (CHRPOS)_rightSlop : (CHRPOS)_leftSlop; ++ CHRPOS right_slop = should_swap ? (CHRPOS)_leftSlop : (CHRPOS)_rightSlop; + + bed.start -= left_slop; + bed.end += right_slop; ===================================== debian/patches/series ===================================== @@ -10,3 +10,4 @@ fix_intersect_test.patch spelling hardening no-samtools +32-bit-fixes.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 ===================================== debian/upstream/metadata ===================================== @@ -1,4 +1,6 @@ Archive: GitHub +Bug-Database: https://github.com/arq5x/bedtools2/issues +Bug-Submit: https://github.com/arq5x/bedtools2/issues/new Reference: Author: Quinlan, Aaron R. and Hall, Ira M. Title: > View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b -- View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/compare/fdd468037455494cf27f2f0b6b8cdecb6f31441c...9889a387f292fabdb790f306a905cf805a56e55b You're receiving this email because of your account on salsa.debian.org.
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