[med-svn] [Git][med-team/soapaligner][master] 4 commits: d/p/gcc-10.patch: Fix compilation with GCC 10.

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / soapaligner


Commits:
4bebafbf by Nilesh Patra at 2021-01-14T17:05:02+05:30
d/p/gcc-10.patch: Fix compilation with GCC 10.

- - - - -
8aa02802 by Nilesh Patra at 2021-01-14T17:05:22+05:30
Declare compliance with policy 4.5.1

- - - - -
b5b05003 by Nilesh Patra at 2021-01-14T17:05:35+05:30
Bump debhelper-compat version to 13

- - - - -
45420b63 by Nilesh Patra at 2021-01-14T17:06:28+05:30
Update changelog

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/gcc-10.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+soapaligner (2.20-5) unstable; urgency=medium
+
+  * Team Upload.
+  * d/p/gcc-10.patch: Fix compilation with GCC 10.
+    - Thank you, Logan Rosen
+  * Declare compliance with policy 4.5.1
+  * Bump debhelper-compat version to 13
+
+ -- Nilesh Patra <npatra974 at gmail.com>  Thu, 14 Jan 2021 17:05:45 +0530
+
 soapaligner (2.20-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -3,8 +3,8 @@ 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-compat (= 12)
-Standards-Version: 4.5.0
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.1
 Vcs-Browser: https://salsa.debian.org/med-team/soapaligner
 Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git
 Homepage: https://web.archive.org/web/20190127081222/http://soap.genomics.org.cn/soapaligner.html


=====================================
debian/patches/gcc-10.patch
=====================================
@@ -0,0 +1,40 @@
+Description: Use extern to fix gcc-10 FTBFS
+Author: Logan Rosen <logan at ubuntu.com>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=979681
+Last-Update: 2021-01-14
+--- a/extratools.h
++++ b/extratools.h
+@@ -59,12 +59,12 @@
+ 	HITITEM *itemList;
+ }HITTABLE;
+ 
+-BWT * occBwt;
+-HASHTABLE * occHashtable;
+-unsigned int * occCollector;
+-unsigned int occCollected;
++extern BWT * occBwt;
++extern HASHTABLE * occHashtable;
++extern unsigned int * occCollector;
++extern unsigned int occCollected;
+ 
+-FILE * textPositionFile;
++extern FILE * textPositionFile;
+ void registerTPFile(FILE * filePtr,unsigned int searchMode);
+ 
+ void registerQIndex(unsigned int queryIndex);
+--- a/extratools.c
++++ b/extratools.c
+@@ -5,6 +5,13 @@
+ //     Hash Table
+ //     All things like those
+ 
++BWT * occBwt;
++HASHTABLE * occHashtable;
++unsigned int * occCollector;
++unsigned int occCollected;
++
++FILE * textPositionFile;
++
+ void LoadLookupTable(LOOKUPTABLE * lookupTable, const char * fileName, const int tableSize)  {
+     (*lookupTable).tableSize = tableSize;
+ 	unsigned long long NR_TOP = 1 << (tableSize * 2);


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ compiler_options.patch
 linkerror.patch
 UsageDoublette.patch
 spelling.patch
+gcc-10.patch



View it on GitLab: https://salsa.debian.org/med-team/soapaligner/-/compare/331cf08ce13bd48a121c95fe5e7b0fb4273b08a0...45420b6339098b64e3755be40fdc7d8c65a87f22

-- 
View it on GitLab: https://salsa.debian.org/med-team/soapaligner/-/compare/331cf08ce13bd48a121c95fe5e7b0fb4273b08a0...45420b6339098b64e3755be40fdc7d8c65a87f22
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210114/96b77dfc/attachment-0001.html>