[med-svn] [Git][med-team/paml][master] 6 commits: fix ftbfs with gcc-10

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / paml


Commits:
2b50ab0b by Etienne Mollier at 2020-05-08T13:57:10+02:00
fix ftbfs with gcc-10

- - - - -
3fc00108 by Etienne Mollier at 2020-05-08T13:58:24+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
2424d210 by Etienne Mollier at 2020-05-08T13:58:28+02:00
routine-update: Add salsa-ci file

- - - - -
d2fa4a09 by Etienne Mollier at 2020-05-08T13:58:28+02:00
routine-update: Rules-Requires-Root: no

- - - - -
2cc5c75f by Etienne Mollier at 2020-05-08T13:58:29+02:00
Trim trailing whitespace.

Fixes: lintian: file-contains-trailing-whitespace
See-also: https://lintian.debian.org/tags/file-contains-trailing-whitespace.html

- - - - -
546184a1 by Etienne Mollier at 2020-05-08T14:00:44+02:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/patches/gcc10.patch
- debian/patches/series
- debian/rules
- + debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+paml (4.9j+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+  * Standards-Version: 4.5.0 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Trim trailing whitespace.
+
+ -- Etienne Mollier <etienne.mollier at mailoo.org>  Fri, 08 May 2020 13:58:34 +0200
+
 paml (4.9j+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -6,10 +6,11 @@ Uploaders: Pjotr Prins <pjotr.debian at thebird.nl>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12)
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/paml
 Vcs-Git: https://salsa.debian.org/med-team/paml.git
 Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
+Rules-Requires-Root: no
 
 Package: paml
 Architecture: any


=====================================
debian/patches/gcc10.patch
=====================================
@@ -0,0 +1,21 @@
+Description: fix ftbfs with gcc 10
+Author: Étienne Mollier <etienne.mollier at mailoo.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957659
+Forwarded: no
+Last-Update: 2020-05-08
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- paml.orig/src/paml.h
++++ paml/src/paml.h
+@@ -372,9 +372,9 @@
+ void printSptree(void);
+ 
+ 
+-enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
++extern enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
+ 
+-enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
++extern enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
+ 
+ 
+ /* use mean (0; default) for discrete gamma instead of median (1) */


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
+gcc10.patch
 hardening.patch
 add_clean_target.patch


=====================================
debian/rules
=====================================
@@ -43,4 +43,3 @@ override_dh_fixperms-arch:
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -f src/baseml src/basemlg src/chi2 src/codeml src/evolver src/infinitesites src/mcmctree src/pamp src/yn00
-


=====================================
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



View it on GitLab: https://salsa.debian.org/med-team/paml/-/compare/3eb602618251ca7de5fea6e246c37ad51357515a...546184a1ba86bfd328181baf33a0080c166fb18c

-- 
View it on GitLab: https://salsa.debian.org/med-team/paml/-/compare/3eb602618251ca7de5fea6e246c37ad51357515a...546184a1ba86bfd328181baf33a0080c166fb18c
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