[med-svn] [Git][med-team/bwa][master] 6 commits: Build libbwa.a with -fPIC for uncalled
Michael R. Crusoe
gitlab at salsa.debian.org
Thu Feb 4 15:19:15 GMT 2021
Michael R. Crusoe pushed to branch master at Debian Med / bwa
Commits:
a64ea8c1 by Michael R. Crusoe at 2021-02-04T16:01:01+01:00
Build libbwa.a with -fPIC for uncalled
- - - - -
72cf731a by Michael R. Crusoe at 2021-02-04T16:15:13+01:00
Forward many patches upstream
- - - - -
8f5ee216 by Michael R. Crusoe at 2021-02-04T16:15:56+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
946d62a9 by Michael R. Crusoe at 2021-02-04T16:15:56+01:00
routine-update: debhelper-compat 13
- - - - -
c7111406 by Michael R. Crusoe at 2021-02-04T16:16:01+01:00
routine-update: watch file standard 4
- - - - -
5accb966 by Michael R. Crusoe at 2021-02-04T16:16:02+01:00
routine-update: Ready to upload to unstable
- - - - -
9 changed files:
- debian/changelog
- debian/control
- debian/patches/fix_build_on_freebsd.patch
- debian/patches/gcc10.patch
- debian/patches/hurd
- debian/patches/simde
- debian/patches/spelling
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,14 +1,21 @@
-bwa (0.7.17-6) UNRELEASED; urgency=medium
+bwa (0.7.17-6) unstable; urgency=medium
[ Michael R. Crusoe ]
* debian/patches/hurd: define PATH_MAX, if needed (fixes FTBFS on hurd-*)
* Switch to libsimde-dev from our code copy
+ * Build libbwa.a with -fPIC for uncalled
[ Andreas Tille ]
* Drop redundant debian/gbp.conf
- * Demote perl fro Depends to Recommends
+ * Demote perl from Depends to Recommends
- -- Andreas Tille <tille at debian.org> Mon, 22 Jun 2020 09:54:01 +0200
+ [ Michael R. Crusoe ]
+ * Forward many patches upstream
+ * Standards-Version: 4.5.1 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * watch file standard 4 (routine-update)
+
+ -- Michael R. Crusoe <crusoe at debian.org> Thu, 04 Feb 2021 16:16:02 +0100
bwa (0.7.17-5) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -4,13 +4,13 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>,
Carlos Borroto <carlos.borroto at gmail.com>,
Ognyan Kulev <ogi at debian.org>,
- Michael R. Crusoe <michael.crusoe at gmail.com>
+ Michael R. Crusoe <crusoe at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
libsimde-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/bwa
Vcs-Git: https://salsa.debian.org/med-team/bwa.git
Homepage: http://bio-bwa.sourceforge.net/
=====================================
debian/patches/fix_build_on_freebsd.patch
=====================================
@@ -1,6 +1,7 @@
-Author: Andreas Tille <tille at debian.org>
+From: Andreas Tille <tille at debian.org>
Last-Update: Fri, 10 Jul 2015 18:23:26 +0200
-Description: -lrt does not help only for Linux but also for freebsd
+Subject: -lrt does not help only for Linux but also for freebsd
+Forwarded: https://github.com/lh3/bwa/pull/312
Index: bwa/Makefile
===================================================================
=====================================
debian/patches/gcc10.patch
=====================================
@@ -1,7 +1,8 @@
-Description: Fix package to build with GCC-10
+From: Nilesh Patra <npatra974 at gmail.com>
+Subject: Fix package to build with GCC-10
Bug-Debian: https://bugs.debian.org/957059
-Author: Nilesh Patra <npatra974 at gmail.com>
Last-Update: Sat, 18 Apr 2020 20:19:30 +0530
+Origin: upstream, https://github.com/lh3/bwa/pull/267/commits/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284
--- a/rle.h
+++ b/rle.h
@@ -30,7 +30,7 @@
=====================================
debian/patches/hurd
=====================================
@@ -1,5 +1,6 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
Subject: Enable building on GNU/Hurd
+Forwarded: https://github.com/lh3/bwa/pull/312
--- bwa.orig/bwashm.c
+++ bwa/bwashm.c
@@ -9,6 +9,10 @@
=====================================
debian/patches/simde
=====================================
@@ -1,5 +1,6 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
Description: use the simde header library for greater compatibility
+Forwarded: https://github.com/lh3/bwa/pull/283
--- bwa.orig/ksw.c
+++ bwa/ksw.c
@@ -26,7 +26,8 @@
=====================================
debian/patches/spelling
=====================================
@@ -1,5 +1,6 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
Subject: Fix some typos
+Forwarded: https://github.com/lh3/bwa/pull/311
--- bwa.orig/NEWS.md
+++ bwa/NEWS.md
@@ -1198,7 +1198,7 @@
=====================================
debian/rules
=====================================
@@ -1,7 +1,7 @@
#!/usr/bin/make -f
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-export DEB_CFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
+export DEB_CFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC
export DEB_CXXFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
%:
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
-version=3
+version=4
opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/bwa-$1\.tar\.gz/ \
https://github.com/lh3/bwa/tags .*/v?(\d\S*)\.tar\.gz
View it on GitLab: https://salsa.debian.org/med-team/bwa/-/compare/e3fef43e17a26dd0c1c7d7ac81333a0e9c6367b3...5accb96674fdf42bcceb85d3e9dc3e824e2cca9c
--
View it on GitLab: https://salsa.debian.org/med-team/bwa/-/compare/e3fef43e17a26dd0c1c7d7ac81333a0e9c6367b3...5accb96674fdf42bcceb85d3e9dc3e824e2cca9c
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