[med-svn] [Git][med-team/wise][master] 8 commits: Packaging update

Lance Lin (@linqigang) gitlab at salsa.debian.org
Mon Mar 24 14:52:03 GMT 2025 


Lance Lin pushed to branch master at Debian Med / wise


Commits:
4bdc571e by Lance Lin at 2025-03-24T20:16:52+07:00
Packaging update

- - - - -
452e959e by Lance Lin at 2025-03-24T20:18:37+07:00
d/control: Recommend xpdf instead of xpdfreader

- - - - -
4181a72a by Lance Lin at 2025-03-24T20:19:22+07:00
Standards-Version: 4.7.2 (routine-update)

- - - - -
7cf8280b by Lance Lin at 2025-03-24T20:23:15+07:00
d/patches: Mark Forwarded as not-needed, since no upstream bug tracking

- - - - -
8cedf5f7 by Lance Lin at 2025-03-24T20:30:11+07:00
d/patches: Fix invalid Forwarded field in patch

- - - - -
51185e2a by Lance Lin at 2025-03-24T20:43:17+07:00
d/patches: Add missing author field

- - - - -
5989fecf by Lance Lin at 2025-03-24T20:59:34+07:00
d/patches: Update format on Last-Update field in patches

- - - - -
b7a4a50a by Lance Lin at 2025-03-24T21:46:59+07:00
d/patches: Add patch to fix BLHC

- - - - -


15 changed files:

- debian/changelog
- debian/control
- debian/patches/05_glib2.patch
- debian/patches/06_getline.patch
- debian/patches/07_ld--as-needed.patch
- debian/patches/08_mayhem.patch
- debian/patches/09_dnal-add-return-statement.patch
- debian/patches/10_fix_path_to_data_files.patch
- debian/patches/cross.patch
- debian/patches/executable-is-script.patch
- + debian/patches/fix_blhc.patch
- debian/patches/gcc-14.patch
- debian/patches/implicit-function-declaration.patch
- debian/patches/series
- debian/patches/spelling.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+wise (2.4.1-26) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * d/control: Recommend xpdf instead of xpdfreader
+  * Standards-Version: 4.7.2 (routine-update)
+  * d/patches: Mark Forwarded as not-needed, since no upstream bug tracking
+  * d/patches: Fix invalid Forwarded field in patch
+  * d/patches: Add missing author field
+  * d/patches: Update format on Last-Update field in patches
+  * d/patches: Add patch to fix BLHC
+
+ -- Lance Lin <lq27267 at gmail.com>  Mon, 24 Mar 2025 20:16:05 +0700
+
 wise (2.4.1-25) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
                docbook-to-man,
                libglib2.0-dev,
                libfl-dev
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/wise
 Vcs-Git: https://salsa.debian.org/med-team/wise.git
 Homepage: https://www.ebi.ac.uk/~birney/wise2/
@@ -53,7 +53,7 @@ Architecture: all
 Section: doc
 Depends: ${misc:Depends}
 Recommends: wise (= ${source:Version}),
-            xpdf-reader | pdf-viewer
+            xpdf | pdf-viewer
 Description: documentation for the wise package
  Wise2 is a package focused on comparisons of biopolymers, commonly DNA
  and protein sequences. There are many other packages which do


=====================================
debian/patches/05_glib2.patch
=====================================
@@ -1,6 +1,7 @@
 Author: Barry deFreese <bdefreese at debian.org>
 Description: To build wise2 with the Glib version 2.0 instead of 1.2.
-Forwarded: birney at sanger.ac.uk
+  Forwarded patch to birney at sanger.ac.uk.
+Forwarded: not-needed
 --- wise-2.4.1.orig/src/makefile
 +++ wise-2.4.1/src/makefile
 @@ -31,13 +31,13 @@


=====================================
debian/patches/06_getline.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Philipp Benner <philipp at debian.org>
-Last-Update: Sat, 31 Oct 2009 21:25:52 +0000
+Last-Update: 2009-10-31
 Bug-Debian: http://bugs.debian.org/552821
 Description: Fixed conflicting definitions of getline().
 Forwarded: not-needed


=====================================
debian/patches/07_ld--as-needed.patch
=====================================
@@ -1,4 +1,5 @@
 Description: Fix FTBFS with ld --as-needed.
+Author: Charles Plessy <plessy at debian.org>
 Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
 Forwarded: not-needed
 


=====================================
debian/patches/08_mayhem.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Philipp Benner <philipp at debian.org>
-Last-Update: Sun, 07 Jul 2013 13:33:01 +0200
+Last-Update: 2013-07-07
 Description: Fix run time errors detected by Mayhem
 Forwarded: not-needed
 


=====================================
debian/patches/09_dnal-add-return-statement.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Dejan Latinovic <Dejan.Latinovic at imgtec.com>
-Last-Update: Mon, 4 Aug 2014 17:10:38 +0000
+Last-Update: 2014-08-04
 Bug-Debian: http://bugs.debian.org/751277
 Description: Make sure dnal has a valid return value
  This affects a bug reported against python-biopython.


=====================================
debian/patches/10_fix_path_to_data_files.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 04 Aug 2014 19:25:58 +0200
+Last-Update: 2014-08-04
 Forwarded: not-needed
 Description: Brute force patch to fix the PATH to the data files to make the
  tools finding the needed data for the test suite


=====================================
debian/patches/cross.patch
=====================================
@@ -1,4 +1,4 @@
-Date: Sat, 18 Apr 2020 11:59:09 +0200
+Date: 2020-04-18
 From: Helmut Grohne <helmut at subdivi.de>
 Bug-Debian: https://bugs.debian.org/958094
 Forwarded: not-needed


=====================================
debian/patches/executable-is-script.patch
=====================================
@@ -1,7 +1,7 @@
 Description: Fix perl binary location for
  executable-not-elf-or-script lintian warning
 Author: Lance Lin <lq27267 at gmail.com>
-Last-Update: 15 Mar 2024
+Last-Update: 2024-03-15
 Forwarded: not-needed
 
 --- a/src/test/testman.pl


=====================================
debian/patches/fix_blhc.patch
=====================================
@@ -0,0 +1,21 @@
+Description: Pass missing flags to fix BLHC
+Author: Lance Lin <lq27267 at gmail.com>
+Last-Update: 2025-03-24
+Forwarded: not-needed
+
+--- a/src/dyc/makefile
++++ b/src/dyc/makefile
+@@ -24,11 +24,11 @@
+ 
+ 
+ CC = cc
+-CFLAGS = -pthread -c -g  -DUNIX  -I../base/
++CFLAGS = $(CPPFLAGS) -pthread -c -g  -DUNIX  -I../base/
+ #CFLAGS = -c -g  -DUNIX -DNOERROR -DLINUX -I../base/
+ #CFLAGS = -c -DNOERROR
+ INCFLAGS = -I../base/
+-LFLAGS =  -g  -lm -L../base/ -lpthread
++LFLAGS = $(LDFLAGS) -g  -lm -L../base/ -lpthread
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0


=====================================
debian/patches/gcc-14.patch
=====================================
@@ -1,7 +1,7 @@
 Description: fix multiple issues gone fatal with gcc 14.
 Author: Étienne Mollier <emollier at debian.org>
 Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075638
-Forwarded: no
+Forwarded: not-needed
 Last-Update: 2024-08-15
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/


=====================================
debian/patches/implicit-function-declaration.patch
=====================================
@@ -1,6 +1,6 @@
 Description: Fix implicit-function-declaration build errors
 Author: Lance Lin <lq27267 at gmail.com>
-Last-Update: 14 Mar 2024
+Last-Update: 2024-03-14
 Forwarded: not-needed
 
 --- a/src/HMMer2/prior.c


=====================================
debian/patches/series
=====================================
@@ -14,3 +14,4 @@ cross.patch
 implicit-function-declaration.patch
 executable-is-script.patch
 gcc-14.patch
+fix_blhc.patch


=====================================
debian/patches/spelling.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 22 Sep 2017 09:18:47 +0200
+Last-Update: 2017-09-22
 Description: Fix spelling issues
 Forwarded: not-needed
 



View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/c23e9d1e3dfab17cf025d6ff6a193bf4623e804d...b7a4a50a3c46e9ca05a514bf2f0aa10332686948

-- 
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/c23e9d1e3dfab17cf025d6ff6a193bf4623e804d...b7a4a50a3c46e9ca05a514bf2f0aa10332686948
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