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 <[email protected]> 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 <[email protected]> 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 <[email protected]>, Andreas Tille <[email protected]>, Carlos Borroto <[email protected]>, Ognyan Kulev <[email protected]>, - Michael R. Crusoe <[email protected]> + Michael R. Crusoe <[email protected]> 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 <[email protected]> +From: Andreas Tille <[email protected]> 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 <[email protected]> +Subject: Fix package to build with GCC-10 Bug-Debian: https://bugs.debian.org/957059 -Author: Nilesh Patra <[email protected]> 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 <[email protected]> +From: Michael R. Crusoe <[email protected]> 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 <[email protected]> +Author: Michael R. Crusoe <[email protected]> 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 <[email protected]> +From: Michael R. Crusoe <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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