[med-svn] [Git][med-team/bedtools][master] 6 commits: Include patch from Bernhard Übelacker to fix 32-bit builds (Closes: #955403)
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Oct 28 11:28:58 GMT 2020
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 <michael.crusoe at gmail.com> Fri, 14 Feb 2020 16:50:58 +0100
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
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 <bernhardu at mailbox.org>
+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
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