[med-svn] [Git][med-team/prime-phylo][master] 7 commits: gcc-15.patch: new: fix build failures with gcc-15.

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Mon Sep 22 20:45:45 BST 2025 


Étienne Mollier pushed to branch master at Debian Med / prime-phylo


Commits:
1493140f by Étienne Mollier at 2025-09-22T21:02:46+02:00
gcc-15.patch: new: fix build failures with gcc-15.

Closes: #1097647

- - - - -
d786bbdd by Étienne Mollier at 2025-09-22T21:03:15+02:00
d/patches/*: normalize Last-Update timestamp.

- - - - -
62e4a937 by Étienne Mollier at 2025-09-22T21:05:37+02:00
d/control: declare compliance to standards version 4.7.2.

- - - - -
19011dfb by Étienne Mollier at 2025-09-22T21:33:12+02:00
cmake-4.patch: new: fix build failure past cmake 4.

Closes: #1113421

- - - - -
63816c9c by Étienne Mollier at 2025-09-22T21:42:50+02:00
d/watch: convert to v5 untrackable upstream.

- - - - -
e55b5089 by Étienne Mollier at 2025-09-22T21:43:43+02:00
d/control: R³ now defaults to no, thus redundant.

- - - - -
8a3d5bfb by Étienne Mollier at 2025-09-22T21:45:16+02:00
d/changelog: ready for upload to unstable.

- - - - -


8 changed files:

- debian/changelog
- debian/control
- debian/patches/0003-Fix-build-with-Boost-1.67.patch
- debian/patches/0004-fix-gcc10-build.patch
- + debian/patches/cmake-4.patch
- + debian/patches/gcc-15.patch
- debian/patches/series
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+prime-phylo (1.0.11-14) unstable; urgency=medium
+
+  * gcc-15.patch: new: fix build failures with gcc-15. (Closes: #1097647)
+  * cmake-4.patch: new: fix build failure past cmake 4. (Closes: #1113421)
+  * d/watch: convert to v5 untrackable upstream.
+  * d/control: R³ now defaults to no, thus redundant.
+  * d/patches/*: normalize Last-Update timestamp.
+  * d/control: declare compliance to standards version 4.7.2.
+
+ -- Étienne Mollier <emollier at debian.org>  Mon, 22 Sep 2025 21:44:48 +0200
+
 prime-phylo (1.0.11-13) unstable; urgency=medium
 
   * openmpi5.patch: new: fix build failure with openmpi 5. (Closes: #1086370)


=====================================
debian/control
=====================================
@@ -19,11 +19,10 @@ Build-Depends: debhelper-compat (= 13),
                libboost-mpi-dev,
                libboost-serialization-dev,
                zlib1g-dev
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/prime-phylo
 Vcs-Git: https://salsa.debian.org/med-team/prime-phylo.git
 Homepage: http://prime.sbc.su.se
-Rules-Requires-Root: no
 
 Package: prime-phylo
 Architecture: any


=====================================
debian/patches/0003-Fix-build-with-Boost-1.67.patch
=====================================
@@ -1,5 +1,5 @@
 From: Giovanni Mascellani <gio at debian.org>
-Date: Sat, 3 Nov 2018 21:50:48 +0100
+Last-Update: 2018-11-03
 Bug-Debian: https://bugs.debian.org/912781
 Subject: Fix build with Boost 1.67.
 


=====================================
debian/patches/0004-fix-gcc10-build.patch
=====================================
@@ -1,7 +1,7 @@
 Author: Nilesh Patra <npatra974 at gmail.com>
 Description: Append extern to prevent gcc-10 FTBFS
 Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?archive=no&bug=957708
-Last-Updated: July 26, 2020
+Last-Update: 2020-07-26
 
 --- a/src/cxx/libraries/sfile/gbread.c
 +++ b/src/cxx/libraries/sfile/gbread.c


=====================================
debian/patches/cmake-4.patch
=====================================
@@ -0,0 +1,41 @@
+Description: bump cmake requirement to v3.10.
+ This version bump allows fixing build failures with cmake 4 and later.
+ Strictly speaking a bump to 3.5 would be sufficient, but a bump to 3.10
+ would also get us rid of the warning caused by the ancient cmake
+ version.  The commented out CMakeLists.txt statement fails to configure
+ due to CMP0026, thankfully it does not look needed later on.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113421
+Forwarded: no
+Last-Update: 2025-09-22
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- prime-phylo.orig/CMakeLists.txt
++++ prime-phylo/CMakeLists.txt
+@@ -2,7 +2,7 @@
+ # Level: trunk/CMakeLists.txt
+ ################################################
+ 
+-cmake_minimum_required(VERSION 2.8)
++cmake_minimum_required(VERSION 3.5)
+ project(prime-phylo CXX)
+ 
+ SET(CMAKE_BUILD_TYPE Debug)
+@@ -132,4 +132,4 @@
+   file(MAKE_DIRECTORY "${vagrantdir}")
+   configure_file(excluded_from_release/packaging/debian/Vagrantfile.cmake "${vagrant_dir}/Vagrantfile" @ONLY)
+   configure_file(excluded_from_release/packaging/debian/provision.sh.cmake "${vagrant_dir}/provision.sh" @ONLY)
+-endif()
+\ No newline at end of file
++endif()
+--- prime-phylo.orig/src/cxx/CMakeLists.txt
++++ prime-phylo/src/cxx/CMakeLists.txt
+@@ -363,7 +363,7 @@
+ #===========================================================================
+ 
+ macro(prime_add_tests tests_dir)
+-  get_target_property(program_exe ${programname_of_this_subdir} LOCATION)
++#  get_target_property(program_exe ${programname_of_this_subdir} LOCATION)
+   file(GLOB tests RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} ${tests_dir}/test*[^~])
+   foreach(i ${tests})
+     get_filename_component(test ${i} NAME)


=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,28 @@
+Description: fix build failures with gcc-15.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097647
+Forwarded: no
+Last-Update: 2025-09-22
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- prime-phylo.orig/src/cxx/libraries/sfile/gb.y
++++ prime-phylo/src/cxx/libraries/sfile/gb.y
+@@ -25,7 +25,7 @@
+ 
+ extern int yylex (void);
+ unsigned linenumber();
+-static int yyerror();
++static int yyerror(char*);
+ 
+ #define YYDEBUG 1
+ extern int debug;
+--- prime-phylo.orig/src/cxx/libraries/sfile/entry.h
++++ prime-phylo/src/cxx/libraries/sfile/entry.h
+@@ -148,7 +148,6 @@
+    struct entry       *next;
+ };
+ 
+-struct entry       *new_entry();
+ struct featocc     *new_featocc();
+ struct reference   *new_reference();
+ struct author      *new_author();


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,5 @@ fix-ftbfs-with-gcc13.patch
 gcc-14.patch
 typos.patch
 openmpi5.patch
+gcc-15.patch
+cmake-4.patch


=====================================
debian/watch
=====================================
@@ -1,9 +1,6 @@
-version=4
+Version: 5
+Untrackable: upstream vanished
 
-opts=dversionmangle=s/.*/0.No-Site/ \
-  https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz
-
-# This used to be the download location but it vanished
-#  http://prime.sbc.su.se/download/prime-phylo-(.*)\.tar\.gz
+Source: http://prime.sbc.su.se/download/
+Matching-Pattern: prime-phylo-(.*)\.tar\.gz
 # see discussion at https://lists.debian.org/debian-med/2017/01/msg00028.html
-



View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/compare/6d15c097a90f8ca1414053c35eb3ca7c2f7b5993...8a3d5bfb2a2f5d007d4a84ad2071b0b07fd41f4a

-- 
View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/compare/6d15c097a90f8ca1414053c35eb3ca7c2f7b5993...8a3d5bfb2a2f5d007d4a84ad2071b0b07fd41f4a
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