[med-svn] [Git][med-team/mrbayes][master] 7 commits: Avoid baseline violation by disabling AX_EXT

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / mrbayes


Commits:
b97f15d4 by Andreas Tille at 2020-07-18T14:31:34+02:00
Avoid baseline violation by disabling AX_EXT

- - - - -
613a233a by Andreas Tille at 2020-07-18T14:31:50+02:00
routine-update: debhelper-compat 13

- - - - -
993bc29b by Andreas Tille at 2020-07-18T14:31:55+02:00
routine-update: Add salsa-ci file

- - - - -
0472b78a by Andreas Tille at 2020-07-18T14:31:55+02:00
routine-update: Rules-Requires-Root: no

- - - - -
64b119f5 by Andreas Tille at 2020-07-18T14:32:06+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
074fbdbe by Andreas Tille at 2020-07-18T14:41:20+02:00
Override dh_missing with --list-missing

- - - - -
eea344b3 by Andreas Tille at 2020-07-18T14:44:26+02:00
Upload to unstable

- - - - -


7 changed files:

- debian/changelog
- debian/control
- + debian/patches/no_baseline_violation.patch
- debian/patches/series
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+mrbayes (3.2.7a-3) unstable; urgency=medium
+
+  * Avoid baseline violation by disabling AX_EXT
+    Closes: #958125, #964787
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+  * Override dh_missing with --list-missing since due to the duplicate
+    build some examples would be installed twice otherwise
+
+ -- Andreas Tille <tille at debian.org>  Sat, 18 Jul 2020 14:41:26 +0200
+
 mrbayes (3.2.7a-2) unstable; urgency=medium
 
   * Fix binary-all build


=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                libreadline-dev,
                mpi-default-dev,
                libhmsbeagle-dev,
@@ -14,6 +14,7 @@ Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/mrbayes
 Vcs-Git: https://salsa.debian.org/med-team/mrbayes.git
 Homepage: http://mrbayes.csit.fsu.edu/
+Rules-Requires-Root: no
 
 Package: mrbayes
 Architecture: any


=====================================
debian/patches/no_baseline_violation.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Avoid baseline violation by disabling AX_EXT
+Bug-Debian: https://bugs.debian.org/958125
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 18 Jul 2020 14:29:31 +0200
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -241,7 +241,7 @@ AX_CFLAGS_WARN_ALL
+ 
+ # Check for SIMD (etc.) extensions supported by hardware and compiler
+ # (-msse2 etc.)
+-AX_EXT
++# AX_EXT
+ 
+ AS_IF([test "x$enable_sse" = "xno"],
+     [AC_DEFINE([DISABLE_SSE], [1],


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 no_rpath.patch
 autoreconf.patch
+no_baseline_violation.patch


=====================================
debian/rules
=====================================
@@ -38,3 +38,6 @@ override_dh_installdeb:
 	    find debian/.debhelper/mrbayes-mpi/dbgsym-root/usr/lib/debug -name "*.debug" -delete ; \
 	fi
 	dh_installdeb
+
+override_dh_missing:
+	dh_missing --list-missing


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/NBISweden/MrBayes/issues
+Bug-Submit: https://github.com/NBISweden/MrBayes/issues/new
 Reference:
  - Author: >
     Fredrik Ronquist and Maxim Teslenko and Paul van der Mark and
@@ -47,3 +49,5 @@ Registry:
    Entry: OMICS_04237
  - Name: conda:bioconda
    Entry: mrbayes
+Repository: https://github.com/NBISweden/MrBayes.git
+Repository-Browse: https://github.com/NBISweden/MrBayes



View it on GitLab: https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e

-- 
View it on GitLab: https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e
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