[med-svn] [Git][med-team/staden-io-lib][master] 4 commits: Fix build on non-x86 architectures

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / staden-io-lib


Commits:
6fee48ab by Andreas Tille at 2018-12-02T07:49:56Z
Fix build on non-x86 architectures

- - - - -
db1ade1e by Andreas Tille at 2018-12-02T07:50:21Z
Remove trailing whitespace in debian/changelog

- - - - -
263cd7bf by Andreas Tille at 2018-12-02T07:50:21Z
Remove trailing whitespace in debian/copyright

- - - - -
5c3fba39 by Andreas Tille at 2018-12-02T07:56:58Z
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/copyright
- + debian/patches/fix_non_x86.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+staden-io-lib (1.14.11-2) unstable; urgency=medium
+
+  * Fix build on non-x86 architectures (thanks to James Bonfield
+    <jkb at sanger.ac.uk>)
+    Closes: #912451
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/copyright
+
+ -- Andreas Tille <tille at debian.org>  Sun, 02 Dec 2018 08:50:21 +0100
+
 staden-io-lib (1.14.11-1) unstable; urgency=medium
 
   * New upstream version featuring SOVERSION bump
@@ -88,7 +98,7 @@ staden-io-lib (1.14.2-1) unstable; urgency=medium
 
   [ Charles Plessy ]
   * Removed debian/libstaden-read1.symbols_old (that is what VCSes
-    are for). 
+    are for).
 
   [ Andreas Tille ]
   * New upstream version
@@ -113,7 +123,7 @@ staden-io-lib (1.13.10-1) unstable; urgency=medium
   * cme fix dpkg-control
 
   [ Charles Plessy ]
-  * Multi-Arch: same. 
+  * Multi-Arch: same.
   * Unfuzzy debian/patches/pathmax.patch.
   * Update symbols file.
 
@@ -121,7 +131,7 @@ staden-io-lib (1.13.10-1) unstable; urgency=medium
 
 staden-io-lib (1.13.7-1) unstable; urgency=medium
 
-  * New upstream release. 
+  * New upstream release.
   * Removed debian/patches/fix-bam-read.patch, applied upstream.
   * debian/libstaden-read1.symbols: updated.  Some symbols are missing but
     it is in area of code that are considered beta (in my understanding).
@@ -156,7 +166,7 @@ staden-io-lib (1.13.5-1.1) unstable; urgency=medium
 
 staden-io-lib (1.13.5-1) unstable; urgency=medium
 
-  * New upstream release. 
+  * New upstream release.
   * debian/libstaden-read1.symbols: updated symbols.
   * debian/patches/pathmax.patch: refreshed.
   * debian/patches/fix_bufferoverflow.patch: removed (applied upstream).
@@ -186,7 +196,7 @@ staden-io-lib (1.13.3-1) unstable; urgency=low
  -- Charles Plessy <plessy at debian.org>  Sat, 30 Nov 2013 18:11:11 +0900
 
 staden-io-lib (1.13.2-3) unstable; urgency=low
- 
+
   * debian/patches: add patch to build on hurd_i386
   * no need to remove package from mips anymore (Closes: #726875)
 


=====================================
debian/copyright
=====================================
@@ -81,7 +81,7 @@ License: PD
 License: 454
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
  .
  IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
@@ -125,7 +125,7 @@ License: GRL
  OF THE POSSIBILITY OF SUCH DAMAGE.
 
 License: GRL-new
- Redistribution and use in source and binary forms, with or without 
+ Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions are met:
  .
     1. Redistributions of source code must retain the above copyright notice,


=====================================
debian/patches/fix_non_x86.patch
=====================================
@@ -0,0 +1,30 @@
+From: James Bonfield <jkb at sanger.ac.uk>
+Date: Wed, 28 Nov 2018 16:46:36 +0000
+Origin: https://github.com/jkbonfield/io_lib/commit/faa2a8a71129a94e4911f4d1231048aa259f8a1b
+Bug-Debian: https://bugs.debian.org/912451
+Subject: [PATCH] Bug fix to scramble on systems not defining ALLOW_UAC.
+
+(Mostly non-Intel platforms.)
+---
+ io_lib/bam.c | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/io_lib/bam.c b/io_lib/bam.c
+index 387dcec..55d0919 100644
+--- a/io_lib/bam.c
++++ b/io_lib/bam.c
+@@ -1751,11 +1751,11 @@ int bam_get_seq(bam_file_t *b, bam_seq_t **bsp) {
+ 	    return -1;
+     }
+ 
+-    if (!*bsp || blk_size+24 > (*bsp)->alloc) {
+-	if (!(bs = realloc(*bsp, blk_size+24)))
++    if (!*bsp || blk_size+44 > (*bsp)->alloc) {
++	if (!(bs = realloc(*bsp, blk_size+44)))
+ 	    return -1;
+ 	*bsp = bs;
+-	(*bsp)->alloc = blk_size+24;
++	(*bsp)->alloc = blk_size+44;
+ 	(*bsp)->blk_size = blk_size;
+     }
+     bs = *bsp;


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 pathmax.patch
 fix_fseeko.patch
+fix_non_x86.patch



View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/compare/8eb9196c924d649cb98b9e328fb7b4cf18518e42...5c3fba39f428259e4f47cbab4ecacf3d8a244854

-- 
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/compare/8eb9196c924d649cb98b9e328fb7b4cf18518e42...5c3fba39f428259e4f47cbab4ecacf3d8a244854
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/20181202/b58bcfb3/attachment-0001.html>