[med-svn] [Git][med-team/hisat2][debian/experimental] 12 commits: debian/patches/riscv5: fix compilation on riscv5
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sun Jan 22 17:05:09 GMT 2023
Michael R. Crusoe pushed to branch debian/experimental at Debian Med / hisat2
Commits:
4ef97c9b by Michael R. Crusoe at 2021-01-27T16:55:24+01:00
debian/patches/riscv5: fix compilation on riscv5
- - - - -
b3a001b6 by Michael R. Crusoe at 2021-01-27T17:34:03+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
5c4b14b9 by Michael R. Crusoe at 2021-01-27T17:34:32+01:00
routine-update: Ready to upload to unstable
- - - - -
455ae199 by Andreas Tille at 2021-09-28T10:28:28+02:00
routine-update: Fix watchfile to detect new versions on github
- - - - -
0c76c9e0 by Andreas Tille at 2021-09-28T10:28:42+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
5a11279e by Andreas Tille at 2021-09-28T10:35:37+02:00
Fix debian/source/lintian-overrides
- - - - -
a49e9e4c by Andreas Tille at 2021-09-28T10:38:50+02:00
Upload to unstable
- - - - -
877371e5 by Andreas Tille at 2022-10-14T18:55:00+02:00
Fix watch file
- - - - -
25015d77 by Andreas Tille at 2022-10-14T18:55:31+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
e2a7d4f0 by Andreas Tille at 2022-10-14T20:18:21+02:00
Update lintian-overrides
- - - - -
06425a54 by Andreas Tille at 2022-10-14T20:22:59+02:00
Upload to unstable
- - - - -
391f07ca by Michael R. Crusoe at 2023-01-22T18:03:28+01:00
Experimental rebuild with SIMDe 0.7.3~0git20230118123246.d1e75cd
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/riscv5
- debian/patches/series
- debian/source/lintian-overrides
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,34 @@
+hisat2 (2.2.1-5~0exp) experimental; urgency=medium
+
+ * Experimental rebuild with SIMDe 0.7.3~0git20230118123246.d1e75cd
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sun, 22 Jan 2023 18:01:28 +0100
+
+hisat2 (2.2.1-4) unstable; urgency=medium
+
+ * Team upload
+ * Fix watch file
+ * Standards-Version: 4.6.1 (routine-update)
+ * Update lintian-overrides
+
+ -- Andreas Tille <tille at debian.org> Fri, 14 Oct 2022 20:18:28 +0200
+
+hisat2 (2.2.1-3) unstable; urgency=medium
+
+ * Team upload.
+ * Fix watchfile to detect new versions on github (routine-update)
+ * Standards-Version: 4.6.0 (routine-update)
+ * Fix debian/source/lintian-overrides
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 Sep 2021 10:35:43 +0200
+
+hisat2 (2.2.1-2) unstable; urgency=medium
+
+ * debian/patches/riscv5: fix compilation on riscv5
+ * Standards-Version: 4.5.1 (routine-update)
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 27 Jan 2021 17:34:32 +0100
+
hisat2 (2.2.1-1) unstable; urgency=medium
[ Steffen Moeller ]
=====================================
debian/control
=====================================
@@ -4,11 +4,11 @@ Uploaders: Michael R. Crusoe <crusoe at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- libsimde-dev,
+ libsimde-dev (>= 0.7.3~0git20230118123246.d1e75cd),
help2man <!nodoc>,
pandoc <!nodoc>,
python3:any <!nodoc>
-Standards-Version: 4.5.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/hisat2
Vcs-Git: https://salsa.debian.org/med-team/hisat2.git
Homepage: https://daehwankimlab.github.io/hisat2/
=====================================
debian/patches/riscv5
=====================================
@@ -0,0 +1,35 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Fix compilation on riscv5
+--- hisat2.orig/alphabet.cpp
++++ hisat2/alphabet.cpp
+@@ -400,7 +400,7 @@
+
+ const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";
+
+-char mask2iupac[16] = {
++int mask2iupac[16] = {
+ -1,
+ 'A', // 0001
+ 'C', // 0010
+--- hisat2.orig/alphabet.h
++++ hisat2/alphabet.h
+@@ -65,7 +65,7 @@
+ /// corresponding 2-bit nucleotide
+ extern uint8_t nuccol2nuc[5][5];
+ /// Convert a 4-bit mask into an IUPAC code
+-extern char mask2iupac[16];
++extern int mask2iupac[16];
+
+ /// Convert an ascii color to an ascii dna char
+ extern char col2dna[];
+--- hisat2.orig/sstring.h
++++ hisat2/sstring.h
+@@ -3326,7 +3326,7 @@
+ */
+ char toChar(size_t idx) const {
+ assert_range((int)this->cs_[idx], 0, 15);
+- return mask2iupac[(int)this->cs_[idx]];
++ return (char)mask2iupac[(int)this->cs_[idx]];
+ }
+
+ /**
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ compilerflags
simde
python3
fix-manual
+riscv5
=====================================
debian/source/lintian-overrides
=====================================
@@ -1,2 +1,3 @@
# normal HTML
-hisat2 source: source-is-missing docs/_includes/share-buttons.html line length is 278 characters (>256)
+hisat2 source: source-is-missing [docs/_includes/share-buttons.html]
+hisat2 source: source-is-missing [docs_jhu/manual.inc.html]
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="filenamemangle=s%(?:.*?)?v(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/DaehwanKimLab/hisat2/releases .*/archive/v at ANY_VERSION@\.tar\.gz
+ https://github.com/DaehwanKimLab/hisat2/tags .*/v at ANY_VERSION@\.tar\.gz
View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/d6499b1debf00393658631c0b71edab12cff26dd...391f07cac26cfbb416d71671bc88316b62aa4310
--
View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/d6499b1debf00393658631c0b71edab12cff26dd...391f07cac26cfbb416d71671bc88316b62aa4310
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