[med-svn] [Git][med-team/ea-utils][master] 2 commits: add gcc11.patch to fix ftbfs with gcc 11

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / ea-utils


Commits:
a4fee74e by Étienne Mollier at 2021-10-17T21:24:34+02:00
add gcc11.patch to fix ftbfs with gcc 11

Closes: #984043

- - - - -
c66b1706 by Étienne Mollier at 2021-10-17T21:41:52+02:00
ready to upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/gcc11.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+ea-utils (1.1.2+dfsg-9) unstable; urgency=medium
+
+  * Team upload.
+  * Add gcc11.patch to fix ftbfs with gcc 11.  (Closes: #984043)
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 17 Oct 2021 21:37:07 +0200
+
 ea-utils (1.1.2+dfsg-8) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/patches/gcc11.patch
=====================================
@@ -0,0 +1,41 @@
+Description: fix failure to build from source with gcc 11
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984043
+Forwarded: no
+Last-Update: 2021-10-17
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- ea-utils.orig/fastq-stats.cpp
++++ ea-utils/fastq-stats.cpp
+@@ -180,14 +180,14 @@
+ 	while ( (c = getopt (argc, argv, "?DdL:g:x:b:c:w:s:h")) != -1) {
+ 		switch (c) {
+ 			case 'c': cyclemax = atoi(optarg); break;
+-			case 'D': ++nodup; break;
+-			case 'd': ++debug; break;
++			case 'D': nodup=1; break;
++			case 'd': debug=1; break;
+ 			case 'w': window = atoi(optarg); break;
+ 			case 's': show_max = atoi(optarg); break;
+-			case 'x': fastx_outfile = optarg; ++fastx; break;
+-			case 'b': brkdown_outfile = optarg; ++brkdown; break;
+-			case 'L': ++len_hist; lenhist_outfile = optarg; break;
+-			case 'g': gc_outfile = optarg; ++gc; break;
++			case 'x': fastx_outfile = optarg; fastx=1; break;
++			case 'b': brkdown_outfile = optarg; brkdown=1; break;
++			case 'L': len_hist=1; lenhist_outfile = optarg; break;
++			case 'g': gc_outfile = optarg; gc=1; break;
+ 			case 'h': usage(stdout); return 0;
+ 			case '?':
+ 					  if (!optopt) {
+--- ea-utils.orig/sam-stats.cpp
++++ ea-utils/sam-stats.cpp
+@@ -226,7 +226,7 @@
+     while ( (c = getopt_long(argc, argv, "?BzArR:Ddx:MhS:", long_options, &long_index)) != -1) {
+                 switch (c) {
+                 case 'd': ++debug; break;                                       // increment debug level
+-                case 'D': ++trackdup; break;
++                case 'D': trackdup=1; break;
+                 case 'B': inbam=1; break;
+                 case 'A': max_chr=1000000; break;                               // max chrom
+                 case 'R': rnafile=optarg;                                       // pass through


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ hardening.patch
 name-space-conflict.patch
 cross.patch
 arm64.patch
+gcc11.patch



View it on GitLab: https://salsa.debian.org/med-team/ea-utils/-/compare/e3bf006d01905e2be8a4c2f69af7ad3f5ba37791...c66b17062823b4c4123f1ad5d4a77b259e602cc5

-- 
View it on GitLab: https://salsa.debian.org/med-team/ea-utils/-/compare/e3bf006d01905e2be8a4c2f69af7ad3f5ba37791...c66b17062823b4c4123f1ad5d4a77b259e602cc5
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