[med-svn] [Git][med-team/python-py2bit][master] 5 commits: d/control: declare compliance to standards version 4.7.0.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / python-py2bit


Commits:
618b32c7 by Étienne Mollier at 2024-07-03T22:51:56+02:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
552fbf1f by Étienne Mollier at 2024-07-03T22:52:30+02:00
d/control: add myself to uploaders.

- - - - -
6ea97aca by Étienne Mollier at 2024-07-03T22:56:29+02:00
d/control: indicate that architecture-is-little-endian.

- - - - -
fefc9d02 by Étienne Mollier at 2024-07-03T23:22:26+02:00
gcc-14.patch: new: fix incompatible pointer type conversion.

Closes: #1075421

- - - - -
11aeb5cc by Étienne Mollier at 2024-07-03T23:23:19+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 +1,13 @@
+python-py2bit (0.3.1-3) unstable; urgency=medium
+
+  * d/control: declare compliance to standards version 4.7.0.
+  * d/control: add myself to uploaders.
+  * d/control: indicate that architecture-is-little-endian.
+  * gcc-14.patch: new: fix incompatible pointer type conversion.
+    (Closes: #1075421)
+
+ -- Étienne Mollier <emollier at debian.org>  Wed, 03 Jul 2024 23:22:55 +0200
+
 python-py2bit (0.3.1-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -2,10 +2,14 @@ Source: python-py2bit
 Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper-compat (= 13), dh-sequence-python3,
- python3-all-dev, python3-setuptools
-Standards-Version: 4.6.2
+Uploaders: Steffen Moeller <moeller at debian.org>,
+           Étienne Mollier <emollier at debian.org>
+Build-Depends: debhelper-compat (= 13),
+               architecture-is-little-endian,
+               dh-sequence-python3,
+               python3-all-dev,
+               python3-setuptools
+Standards-Version: 4.7.0
 Homepage: https://github.com/deeptools/py2bit/
 Vcs-Browser: https://salsa.debian.org/med-team/python-py2bit
 Vcs-Git: https://salsa.debian.org/med-team/python-py2bit.git
@@ -14,7 +18,7 @@ Rules-Requires-Root: no
 
 Package: python3-py2bit
 Section: python
-Architecture: any-amd64 ppc64el any-ia64 arm64 armel armhf any-i386 loong64 mips64el mipsel alpha riscv64 sh4 x32
+Architecture: any
 Depends: ${python3:Depends}, ${misc:Depends}, ${shlibs:Depends}
 Description: access to 2bit files
  From https://genome.ucsc.edu/FAQ/FAQformat.html#format7:


=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,30 @@
+Description: fix potential pointer bug flagged by gcc-14.
+ Since gcc 14, a whole range of warnings have become errors, notably the
+ casting from incompatible pointer types.  In the case of py2bit, this
+ seems to flag a real pointer arithmetic bug.  The symptom on build time
+ is:
+ .
+  py2bit.c:35:24: error: initialization of ‘pyTwoBit_t *’ from incompatible pointer type ‘TwoBit *’ [-Wincompatible-pointer-types]
+     35 |     pyTwoBit_t *pytb = self->tb;
+        |                        ^~~~
+ .
+ Transmitting the self pointer straight to the pytb pointer newly
+ created without referencing to the TwoBit_t pointer, fixes the issue.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075421
+Forwarded: https://github.com/deeptools/py2bit/pull/14
+Last-Update: 2024-07-03
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-py2bit.orig/py2bit.c
++++ python-py2bit/py2bit.c
+@@ -32,7 +32,7 @@
+ }
+ 
+ PyObject *py2bitEnter(pyTwoBit_t *self, PyObject *args) {
+-    pyTwoBit_t *pytb = self->tb;
++    pyTwoBit_t *pytb = self;
+ 
+     if(!pytb) {
+         PyErr_SetString(PyExc_RuntimeError, "The 2bit file handle is not open!");


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 enable-tests.patch
+gcc-14.patch



View it on GitLab: https://salsa.debian.org/med-team/python-py2bit/-/compare/237e62310cd9972b2e45e9114db2934c5109cd74...11aeb5cce0084a067580265ca579799f9e7f91e7

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