[med-svn] [Git][med-team/sweed][master] 7 commits: added gcc10.patch to fix FTBFS with gcc 10
Étienne Mollier
gitlab at salsa.debian.org
Wed Jul 22 11:53:32 BST 2020
Étienne Mollier pushed to branch master at Debian Med / sweed
Commits:
2596f2b5 by Etienne Mollier at 2020-07-22T12:03:15+02:00
added gcc10.patch to fix FTBFS with gcc 10
- - - - -
86924645 by Etienne Mollier at 2020-07-22T12:10:58+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
71f21d44 by Etienne Mollier at 2020-07-22T12:10:58+02:00
routine-update: debhelper-compat 13
- - - - -
7b454c65 by Etienne Mollier at 2020-07-22T12:10:59+02:00
routine-update: Add salsa-ci file
- - - - -
b6bdd530 by Etienne Mollier at 2020-07-22T12:10:59+02:00
routine-update: Rules-Requires-Root: no
- - - - -
e3b18bec by Etienne Mollier at 2020-07-22T12:49:39+02:00
d/u/metadata: added repository information
This addresses lintian tag upstream-metadata-missing-repository.
- - - - -
16765a3c by Etienne Mollier at 2020-07-22T12:52:21+02:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/gcc10.patch
- debian/patches/series
- + debian/salsa-ci.yml
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+sweed (3.2.1+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * Added gcc10.patch to fix compilation issues related with the move to GCC 10
+ in Debian Bullseye. (Closes: #957851)
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Added repository informations in debian/upstream/metadata
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org> Wed, 22 Jul 2020 12:51:56 +0200
+
sweed (3.2.1+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #902960)
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,11 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11)
-Standards-Version: 4.1.5
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/sweed
Vcs-Git: https://salsa.debian.org/med-team/sweed.git
Homepage: https://sco.h-its.org/exelixis/web/software/sweed/
+Rules-Requires-Root: no
Package: sweed
Architecture: any
=====================================
debian/patches/gcc10.patch
=====================================
@@ -0,0 +1,95 @@
+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=957851
+Forwarded: no
+Last-Update: 2020-07-22
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- sweed.orig/SweeD.h
++++ sweed/SweeD.h
+@@ -114,18 +114,18 @@
+ #define MAXINT 2147483647
+
+
+-char bits_in_16bits [0x1u << 16];
++extern char bits_in_16bits [0x1u << 16];
+
+-int linkage_disequilibrium;
++extern int linkage_disequilibrium;
+
+-int borderTol;
++extern int borderTol;
+
+-int VCF_header_lines;
+-char VCF_alignment_name [MAX_CHROM_NAME_VCF];
+-int VCF_first_SNP;
+-int nxtVCFalignment;
++__attribute__((__common__)) int VCF_header_lines;
++__attribute__((__common__)) char VCF_alignment_name [MAX_CHROM_NAME_VCF];
++__attribute__((__common__)) int VCF_first_SNP;
++__attribute__((__common__)) int nxtVCFalignment;
+
+-char runName[INFILENAMESIZE];
++__attribute__((__common__)) char runName[INFILENAMESIZE];
+
+ typedef float cor_t;
+
+@@ -133,13 +133,13 @@
+
+ cor_t ABS (cor_t input);
+
+-double mainTime0;
++__attribute__((__common__)) double mainTime0;
+
+-int map[INTOKS];
++extern int map[INTOKS];
+
+-int nofTokens;
++extern int nofTokens;
+
+-int nofSamples;
++extern int nofSamples;
+
+ typedef int al_t;
+ typedef double t_sfs;
+@@ -222,17 +222,17 @@
+
+ } alignment_struct;
+
+-alignment_struct * alignment;
++__attribute__((__common__)) alignment_struct * alignment;
+
+-double * rv;
+-double ** rvLUT;
+-double ** rvLUT2;
++extern double * rv;
++__attribute__((__common__)) double ** rvLUT;
++extern double ** rvLUT2;
+
+
+ #define GRIDSIZE 300
+ #define LOCALGRIDSIZE 100
+
+-double div6;
++__attribute__((__common__)) double div6;
+
+
+ typedef struct
+@@ -242,7 +242,7 @@
+
+ } factorial_LUT;
+
+-factorial_LUT * factLUT;
++__attribute__((__common__)) factorial_LUT * factLUT;
+
+
+ typedef struct
+@@ -254,7 +254,7 @@
+
+ } clr_struct;
+
+-clr_struct * clr;
++__attribute__((__common__)) clr_struct * clr;
+
+ #ifdef _ANALYTICAL_SFS
+ typedef struct
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
+gcc10.patch
hardening.patch
=====================================
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 @@
+Repository: https://git.assembla.com/sweed.git
+Repository-Browse: https://app.assembla.com/spaces/sweed/git/source
Reference:
- Author: >
Pavlos Pavlidis and Daniel Živković and Alexandros Stamatakis and
View it on GitLab: https://salsa.debian.org/med-team/sweed/-/compare/04fb9d905e22cbed4e9f2869bc16ff9b44f2be47...16765a3c476beffae3c3d4c9b8c2132900c54f5e
--
View it on GitLab: https://salsa.debian.org/med-team/sweed/-/compare/04fb9d905e22cbed4e9f2869bc16ff9b44f2be47...16765a3c476beffae3c3d4c9b8c2132900c54f5e
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