[med-svn] [Git][med-team/jellyfish][master] 3 commits: d/control: stop building on 32-bit architectures, as per upstream's wishes:...
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Mar 19 17:23:34 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / jellyfish
Commits:
0467ed34 by Michael R. Crusoe at 2024-03-19T17:20:48+01:00
d/control: stop building on 32-bit architectures, as per upstream's wishes: https://github.com/gmarcais/Jellyfish/pull/202#issuecomment- 2007544485
- - - - -
bcd3ed26 by Michael R. Crusoe at 2024-03-19T18:19:12+01:00
d/{control,rules}: undo the t64 migration, no longer needed.
- - - - -
4637e5fe by Michael R. Crusoe at 2024-03-19T18:21:25+01:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/libjellyfish-2.0-2t64.lintian-overrides → debian/libjellyfish-2.0-2.lintian-overrides
- − debian/patches/fix-32-bit.patch
- debian/patches/series
- debian/rules
- − debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,19 +1,18 @@
-jellyfish (2.3.1-3) UNRELEASED; urgency=medium
+jellyfish (2.3.1-3) unstable; urgency=medium
* Forwarded several patches upstream.
* debian/patches/fix_catch.patch is no longer used, remove it.
* Point to the Jellyfish 2.0 homepage
* d/control: simplify architecture specifications by build-dep'ing on
architecture-is-little-endian.
- * d/source/lintian-overrides: quiet false-positive from the t64
- transition.
- * d/patches/fix-32-bit.patch: forward upstream.
* d/patches/drop_distutils: upgrade to setuptools.
* d/control: s/pkg-config/pkgconf/g
- * debian/libjellyfish-2.0-2t64.lintian-overrides: silence another
- false-positive.
+ * d/control: stop building on 32-bit architectures, as per upstream's
+ wishes: https://github.com/gmarcais/Jellyfish/pull/202#issuecomment-
+ 2007544485
+ * d/control: undo the t64 migration, no longer needed.
- -- Michael R. Crusoe <crusoe at debian.org> Wed, 28 Feb 2024 14:57:36 +0100
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 19 Mar 2024 18:21:25 +0100
jellyfish (2.3.1-2.1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,9 +6,10 @@ Uploaders: Shaun Jackman <sjackman at debian.org>,
Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
-Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
+Build-Depends: debhelper-compat (= 13),
architecture-is-little-endian,
- d-shlibs (>= 0.106~),
+ architecture-is-64-bit,
+ d-shlibs,
autoconf-archive,
yaggo,
pkgconf,
@@ -34,7 +35,7 @@ Package: jellyfish
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libjellyfish-2.0-2t64 (= ${binary:Version})
+ libjellyfish-2.0-2 (= ${binary:Version})
Description: count k-mers in DNA sequences
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
@@ -50,10 +51,10 @@ Description: count k-mers in DNA sequences
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
-Package: libjellyfish-2.0-2t64
-Provides: ${t64:Provides}
-Replaces: libjellyfish-2.0-2
-Conflicts: libjellyfish-2.0-2 (<< ${source:Version})
+Package: libjellyfish-2.0-2
+Provides: libjellfish-2.0-2t64 (= ${binary:Version})
+Replaces: libjellyfish-2.0-2t64
+Conflicts: libjellyfish-2.0-2t64
Architecture: any
Multi-Arch: same
Section: libs
@@ -81,7 +82,7 @@ Package: libjellyfish-2.0-dev
Architecture: any
Section: libdevel
Depends: ${misc:Depends},
- libjellyfish-2.0-2t64 (= ${binary:Version})
+ libjellyfish-2.0-2 (= ${binary:Version})
Description: count k-mers in DNA sequences (development files of jellyfish)
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/libjellyfish-2.0-2t64.lintian-overrides → debian/libjellyfish-2.0-2.lintian-overrides
=====================================
@@ -1,4 +1,2 @@
# Upstream decided to use a dynamic library without really intending to make this a development package
-libjellyfish-2.0-2t64: no-symbols-control-file usr/lib/*/libjellyfish-*.so.*
-libjellyfish-2.0-2t64: package-name-doesnt-match-sonames libjellyfish-2.0-2
-libjellyfish-2.0-2t64: conflicts-with-version libjellyfish-2.0-2 (<< 2.3.1-3)
+libjellyfish-2.0-2: no-symbols-control-file usr/lib/*/libjellyfish-*.so.*
=====================================
debian/patches/fix-32-bit.patch deleted
=====================================
@@ -1,39 +0,0 @@
-Date: Thu, 3 Dec 2020 04:05:11 +0530
-From: Nilesh Patra <npatra974 at gmail.com>
-Bug-Debian: https://bugs.debian.org/962184
-Forwarded: https://github.com/gmarcais/Jellyfish/pull/202
-Description: Enable build on 32bit architectures
-
---- a/include/jellyfish/rectangular_binary_matrix.hpp
-+++ b/include/jellyfish/rectangular_binary_matrix.hpp
-@@ -118,7 +118,7 @@
- uint64_t *p = _columns;
- while(*p == 0 && p < _columns + _c)
- ++p;
-- return (p - _columns) == _c;
-+ return static_cast<unsigned int>(p - _columns) == _c;
- }
-
- // Randomize the content of the matrix
---- a/include/jellyfish/mer_dna.hpp
-+++ b/include/jellyfish/mer_dna.hpp
-@@ -693,7 +693,7 @@
-
- char buffer[mer.k() + 1];
- is.read(buffer, mer.k());
-- if(is.gcount() != mer.k())
-+ if(static_cast<unsigned int>(is.gcount()) != mer.k())
- goto error;
- buffer[mer.k()] = '\0';
- if(!mer.from_chars(buffer))
---- a/unit_tests/test_mer_dna.cc
-+++ b/unit_tests/test_mer_dna.cc
-@@ -466,7 +466,7 @@
-
- // Get bits by right-shifting
- typename TypeParam::Type cm(m);
-- for(unsigned int j = 1; j < start; j += 2)
-+ for(unsigned long int j = 1; start>=0 && j < static_cast<unsigned int>(start); j += 2)
- cm.shift_right(0); // Shift by 2 bits
- typename TypeParam::Type::base_type y = cm.word(0);
- if(start & 0x1)
=====================================
debian/patches/series
=====================================
@@ -3,4 +3,3 @@ manpage_whatis_entry.patch
portability.patch
test_needs_bash
python3
-fix-32-bit.patch
=====================================
debian/rules
=====================================
@@ -43,7 +43,6 @@ override_dh_auto_install:
chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so
dh_install
d-shlibmove --commit \
- --t64 \
--multiarch \
--devunversioned \
--movedev "debian/tmp/usr/include/$(DEB_SOURCE)*/$(DEB_SOURCE)/*.hpp" usr/include/$(DEB_SOURCE) \
=====================================
debian/source/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# this is fine, that "external" package used to come from this package
-jellyfish source: version-substvar-for-external-package Conflicts ${source:Version} libjellyfish-2.0-2t64 -> libjellyfish-2.0-2 [debian/control:56]
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/f0d0f8cd740ba13aa933ccc5cea9471b5e08f130...4637e5feadad3aaa0efce6be8f7c99b132555d6d
--
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/f0d0f8cd740ba13aa933ccc5cea9471b5e08f130...4637e5feadad3aaa0efce6be8f7c99b132555d6d
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240319/26cebbbe/attachment-0001.htm>
More information about the debian-med-commit
mailing list