[Debian-med-packaging] Bug#979681: soapaligner: FTBFS with GCC 10

[Logan Rosen]

Source: soapaligner
Version: 2.20-4
Severity: serious
Tags: patch ftbfs
Justification: fails to build from source (but built successfully in the past)
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu hirsute ubuntu-patch
X-Debbugs-Cc: logan at ubuntu.com

Hi,

soapaligner currently FTBFS with GCC 10 (which is now the default in
unstable). [1]

In Ubuntu, the attached patch was applied to achieve the following:

  * d/p/gcc-10.patch: Fix compilation with GCC 10.

Thanks for considering the patch.

Logan

[1] https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/soapaligner.html
-------------- next part --------------
diff -Nru soapaligner-2.20/debian/patches/gcc-10.patch soapaligner-2.20/debian/patches/gcc-10.patch
--- soapaligner-2.20/debian/patches/gcc-10.patch	1969-12-31 19:00:00.000000000 -0500
+++ soapaligner-2.20/debian/patches/gcc-10.patch	2021-01-09 18:46:50.000000000 -0500
@@ -0,0 +1,36 @@
+--- 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);
diff -Nru soapaligner-2.20/debian/patches/series soapaligner-2.20/debian/patches/series
--- soapaligner-2.20/debian/patches/series	2020-04-17 05:45:00.000000000 -0400
+++ soapaligner-2.20/debian/patches/series	2021-01-09 18:43:23.000000000 -0500
@@ -2,3 +2,4 @@
 linkerror.patch
 UsageDoublette.patch
 spelling.patch
+gcc-10.patch