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-de...@lists.ubuntu.com
Usertags: origin-ubuntu hirsute ubuntu-patch
X-Debbugs-Cc: lo...@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
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
