[med-svn] [Git][med-team/maq][master] 5 commits: gcc-14.patch: new: fix improper uses of gzFile pointers.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / maq


Commits:
e78f2463 by Étienne Mollier at 2024-08-05T22:44:23+02:00
gcc-14.patch: new: fix improper uses of gzFile pointers.

Closes: #1075253

- - - - -
b3377254 by Étienne Mollier at 2024-08-05T22:46:44+02:00
d/*lintian-overrides: update mismatched overrides.

- - - - -
7f7a686e by Étienne Mollier at 2024-08-05T22:47:20+02:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
5d319057 by Étienne Mollier at 2024-08-05T22:48:04+02:00
d/control: add myself to uploaders.

- - - - -
1e9734ce by Étienne Mollier at 2024-08-05T22:50:33+02:00
ready to upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/maq.lintian-overrides
- + debian/patches/gcc-14.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+maq (0.7.1-10) unstable; urgency=medium
+
+  * gcc-14.patch: new: fix improper uses of gzFile pointers. (Closes: #1075253)
+  * d/*lintian-overrides: update mismatched overrides.
+  * d/control: declare compliance to standards version 4.7.0.
+  * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier at debian.org>  Mon, 05 Aug 2024 22:48:54 +0200
+
 maq (0.7.1-9) unstable; urgency=medium
 
   * Standards-Version: 4.5.0 (routine-update)


=====================================
debian/control
=====================================
@@ -1,12 +1,13 @@
 Source: maq
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>,
-           Charles Plessy <plessy at debian.org>
+           Charles Plessy <plessy at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                zlib1g-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/maq
 Vcs-Git: https://salsa.debian.org/med-team/maq.git
 Homepage: http://maq.sourceforge.net/


=====================================
debian/maq.lintian-overrides
=====================================
@@ -1,4 +1,3 @@
 # Maq ships `maq' and `maq.pl', it is therefore not possible to rename `maq.pl'.
-maq: script-with-language-extension usr/bin/maq.pl
-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-maq: script-with-language-extension usr/bin/*.*
+# also see https://lists.debian.org/debian-med/2018/06/msg00043.html
+maq: script-with-language-extension [usr/bin/*.pl]


=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,45 @@
+Description: fix improper variable declaration as a pointer.
+ On two occasions, a gzFile is declared as a pointer, except the type
+ mismatches with the expected type by the gz API, resulting in errors
+ like:
+ .
+ 	fastq2bfq.c:30:12: error: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
+ 	   30 |         fp = gzopen(str, "w");
+ 	      |            ^
+ 	fastq2bfq.c:36:28: error: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
+ 	   36 |                         fp = gzopen(str, "w");
+ 	      |                            ^
+ 	fastq2bfq.c:47:25: error: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types]
+ 	   47 |                 gzwrite(fp, &i, sizeof(int));
+ 	      |                         ^~
+ 	      |                         |
+ 	      |                         struct gzFile_s **
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075253
+Forwarded: no
+Last-Update: 2024-08-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- maq.orig/fastq2bfq.c
++++ maq/fastq2bfq.c
+@@ -15,7 +15,7 @@
+ 	char name[256], str[1024];
+ 	int l, is_new = 0, l_prefix = 0;
+ 	bit64_t n;
+-	gzFile *fp = 0;
++	gzFile fp = 0;
+ 	INIT_SEQ(seq); INIT_SEQ(qual);
+ 	seq_set_block_size(256);
+ 	n = 0;
+--- maq.orig/simulate.c
++++ maq/simulate.c
+@@ -74,7 +74,7 @@
+ {
+ 	fqc_t *fqc;
+ 	FILE *fp;
+-	gzFile *fpout;
++	gzFile fpout;
+ 	if (argc < 3) {
+ 		fprintf(stderr, "Usage: maq simutrain <simupars.dat> <known_reads.fastq>\n");
+ 		return 1;


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 10_prevent_-64_option.patch
 gcc-4.7.patch
 mayhem.patch
+gcc-14.patch



View it on GitLab: https://salsa.debian.org/med-team/maq/-/compare/b733545b3b5057e04f7a8297f53de090508cf52c...1e9734ce968e57bcf92985f7496fe090bedf8de8

-- 
View it on GitLab: https://salsa.debian.org/med-team/maq/-/compare/b733545b3b5057e04f7a8297f53de090508cf52c...1e9734ce968e57bcf92985f7496fe090bedf8de8
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