[med-svn] [Git][med-team/velvet][master] 3 commits: gcc-14.patch: new: fix incompatible pointer types.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / velvet


Commits:
43692f90 by Étienne Mollier at 2024-08-07T11:23:02+02:00
gcc-14.patch: new: fix incompatible pointer types.

Closes: #1075617

- - - - -
d51b4ef1 by Étienne Mollier at 2024-08-07T11:24:45+02:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
4294d426 by Étienne Mollier at 2024-08-07T11:31:22+02:00
Ready to upload to unstable.

- - - - -


4 changed files:

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


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+velvet (1.2.10+dfsg1-9) unstable; urgency=medium
+
+  * Team upload.
+  * gcc-14.patch: new: fix incompatible pointer types. (Closes: #1075617)
+  * d/control: declare compliance to standards version 4.7.0.
+
+ -- Étienne Mollier <emollier at debian.org>  Wed, 07 Aug 2024 11:25:01 +0200
+
 velvet (1.2.10+dfsg1-8) unstable; urgency=medium
 
   * Apply multi-arch hints.


=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),
                zlib1g-dev,
                texlive-latex-base,
                texlive-latex-recommended
-Standards-Version: 4.6.1
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/velvet
 Vcs-Git: https://salsa.debian.org/med-team/velvet.git
 Homepage: https://github.com/dzerbino/velvet


=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,46 @@
+Description: fix incompatible pointer types.
+ Incompatible pointer types are now fatal with gcc 14 by default.
+ This change fixes the following issues:
+ .
+ 	src/readSet.c:641:21: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
+ 	  641 |         file.gzFile = file.autoFile = NULL;
+ 	      |                     ^
+ 	src/readSet.c: In function ‘readFastXPair’:
+ 	src/readSet.c:680:22: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
+ 	  680 |         file1.gzFile = file1.autoFile = NULL;
+ 	      |                      ^
+ 	src/readSet.c:681:22: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
+ 	  681 |         file2.gzFile = file2.autoFile = NULL;
+ 	      |                      ^
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075617
+Forwarded: no
+Last-Update: 2024-08-07
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- velvet.orig/src/readSet.c
++++ velvet/src/readSet.c
+@@ -638,7 +638,8 @@
+ 	FileGZOrAuto file;
+ 	IDnum counter = 0;
+ 
+-        file.gzFile = file.autoFile = NULL;
++	file.autoFile = NULL;
++        file.gzFile = (gzFile)file.autoFile;
+         if (fileType == AUTO) {
+         	file.autoFile = openFileAuto(filename);
+                 if (!file.autoFile)
+@@ -677,8 +678,10 @@
+ 	if (cat==REFERENCE)
+ 		exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence in 'separate' read mode");
+ 
+-        file1.gzFile = file1.autoFile = NULL;
+-        file2.gzFile = file2.autoFile = NULL;
++        file1.autoFile = NULL;
++        file2.autoFile = NULL;
++        file1.gzFile = (gzFile)file1.autoFile;
++        file2.gzFile = (gzFile)file2.autoFile;
+         if (fileType == AUTO) {
+         	file1.autoFile = openFileAuto(filename1);
+                 if (!file1.autoFile)


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ fix-perl-path.patch
 hardening.patch
 spelling.patch
 2to3.patch
+gcc-14.patch



View it on GitLab: https://salsa.debian.org/med-team/velvet/-/compare/735e1f3e5d8d099dd7fafe8475516807c17eadc2...4294d426eda3586d9e18ac66c3fa5997a5e014fc

-- 
View it on GitLab: https://salsa.debian.org/med-team/velvet/-/compare/735e1f3e5d8d099dd7fafe8475516807c17eadc2...4294d426eda3586d9e18ac66c3fa5997a5e014fc
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