Your message dated Thu, 14 Jan 2021 12:48:34 +0000
with message-id <[email protected]>
and subject line Bug#979681: fixed in soapaligner 2.20-5
has caused the Debian Bug report #979681,
regarding soapaligner: FTBFS with GCC 10
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
979681: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=979681
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: soapaligner
Version: 2.20-4
Severity: serious
Tags: patch ftbfs
Justification: fails to build from source (but built successfully in the past)
User: [email protected]
Usertags: origin-ubuntu hirsute ubuntu-patch
X-Debbugs-Cc: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: soapaligner
Source-Version: 2.20-5
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
soapaligner, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated soapaligner package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 14 Jan 2021 17:05:45 +0530
Source: soapaligner
Architecture: source
Version: 2.20-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 979681
Changes:
soapaligner (2.20-5) unstable; urgency=medium
.
* Team Upload.
* d/p/gcc-10.patch: Fix compilation with GCC 10.
- Thank you, Logan Rosen (Closes: #979681)
* Declare compliance with policy 4.5.1
* Bump debhelper-compat version to 13
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