[med-svn] [Git][med-team/jellyfish][master] 9 commits: d/watch: repair broken link to github
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Aug 28 20:20:55 BST 2021
Étienne Mollier pushed to branch master at Debian Med / jellyfish
Commits:
863be65e by Étienne Mollier at 2021-08-28T15:18:31+02:00
d/watch: repair broken link to github
- - - - -
02ca0890 by Étienne Mollier at 2021-08-28T19:56:53+02:00
add fix-autoreconf.patch; address ftbfs
This patch provides protection to a couple of macros in configure.ac
to avoid breakage of the script configure which is produced by the
autoconf 2.70.
Closes: #978843
- - - - -
2831b809 by Étienne Mollier at 2021-08-28T20:46:08+02:00
update changelog
- - - - -
0f6e0163 by Étienne Mollier at 2021-08-28T20:46:40+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
31d0371a by Étienne Mollier at 2021-08-28T20:46:50+02:00
Apply multi-arch hints.
+ libjellyfish-2.0-dev: Drop Multi-Arch: same.
+ jellyfish-examples: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
- - - - -
c67201e5 by Étienne Mollier at 2021-08-28T20:59:17+02:00
d/control: add myself to uploaders
- - - - -
aeb41686 by Étienne Mollier at 2021-08-28T21:00:48+02:00
update changelog
- - - - -
4623cfc1 by Étienne Mollier at 2021-08-28T21:10:28+02:00
routine-update: Ready to upload to unstable
- - - - -
ecd0fc03 by Étienne Mollier at 2021-08-28T21:19:06+02:00
fix-autoreconf.patch forwarded
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix-autoreconf.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,19 @@
-jellyfish (2.3.0-11) UNRELEASED; urgency=medium
+jellyfish (2.3.0-11) unstable; urgency=medium
+ [ Andreas Tille ]
* Fix Homepage
Closes: #983273
- -- Andreas Tille <tille at debian.org> Mon, 15 Mar 2021 19:28:29 +0100
+ [ Étienne Mollier ]
+ * d/watch: repair broken link to github
+ * add fix-autoreconf.patch; fix ftbfs with autoreconf 2.70 (Closes: #978843)
+ * Standards-Version: 4.6.0 (routine-update)
+ * Apply multi-arch hints.
+ + libjellyfish-2.0-dev: Drop Multi-Arch: same.
+ + jellyfish-examples: Add Multi-Arch: foreign.
+ * d/control: add myself to uploaders
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 28 Aug 2021 21:01:20 +0200
jellyfish (2.3.0-10) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -2,7 +2,8 @@ Source: jellyfish
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Shaun Jackman <sjackman at debian.org>,
Andreas Tille <tille at debian.org>,
- Michael R. Crusoe <crusoe at debian.org>
+ Michael R. Crusoe <crusoe at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -20,7 +21,7 @@ Build-Depends: debhelper-compat (= 13),
libhts-dev,
dos2unix,
samtools
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
Homepage: https://github.com/gmarcais/Jellyfish
@@ -74,7 +75,6 @@ Description: count k-mers in DNA sequences (dynamic library of jellyfish)
Package: libjellyfish-2.0-dev
Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
-Multi-Arch: same
Section: libdevel
Depends: ${misc:Depends},
libjellyfish-2.0-2 (= ${binary:Version})
@@ -148,6 +148,7 @@ Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends}
Recommends: jellyfish
+Multi-Arch: foreign
Description: count k-mers in DNA sequences (examples for testing)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
=====================================
debian/patches/fix-autoreconf.patch
=====================================
@@ -0,0 +1,25 @@
+Description: fix ftbfs with autoconf 2.70
+ This patch provides protection to a couple of macros in configure.ac
+ to avoid breakage of the script configure which is produced by the
+ autoconf 2.70.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978843
+Forwarded: https://github.com/gmarcais/Jellyfish/pull/178
+Last-Update: 2021-08-28
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- jellyfish.orig/configure.ac
++++ jellyfish/configure.ac
+@@ -41,9 +41,9 @@
+
+ # Check for md5 or md5sum
+ AC_ARG_VAR([MD5], [Path to md5 hashing program])
+-AS_IF([test "x$MD5" = "x"], AC_CHECK_PROG([MD5], [md5sum], [md5sum]), [])
+-AS_IF([test "x$MD5" = "x"], AC_CHECK_PROG([MD5], [md5], [md5 -r]), [])
+-AS_IF([test "x$MD5" = "x"], AC_MSG_ERROR([Could not find md5 hashing program in your path]), [])
++AS_IF([test "x$MD5" = "x"], [AC_CHECK_PROG([MD5], [md5sum], [md5sum])], [])
++AS_IF([test "x$MD5" = "x"], [AC_CHECK_PROG([MD5], [md5], [md5 -r])], [])
++AS_IF([test "x$MD5" = "x"], [AC_MSG_ERROR([Could not find md5 hashing program in your path])], [])
+
+ # Check for yaggo
+ AC_ARG_VAR([YAGGO], [Yaggo switch parser generator])
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ fix_replacement_of_-L_option.patch
test_needs_bash
python3
fix-32-bit.patch
+fix-autoreconf.patch
=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
version=4
-https://github.com/gmarcais/Jellyfish/releases .*/[jelyfishv]*\.*(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+https://github.com/gmarcais/Jellyfish/tags \
+ archive/refs/tags/[vV]?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/9098ae203ec441f4e3ea27558dec2e4a52d53b1f...ecd0fc033d5ff80d117177b8d098835ea7fe3cd4
--
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/9098ae203ec441f4e3ea27558dec2e4a52d53b1f...ecd0fc033d5ff80d117177b8d098835ea7fe3cd4
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