[med-svn] [Git][med-team/berkeley-express][master] 7 commits: cxx14.patch: new: bump to standard gnu++14.

Sun Jan 4 20:52:07 GMT 2026


Étienne Mollier pushed to branch master at Debian Med / berkeley-express


Commits:
07ae9782 by Étienne Mollier at 2026-01-04T21:47:07+01:00
cxx14.patch: new: bump to standard gnu++14.

This is necessary to fix build failures with boost1.88, older levels
like gnu++11 are now too old and incompatible.

Closes: #1110628

- - - - -
77b438ee by Étienne Mollier at 2026-01-04T21:48:17+01:00
d/rules: canonically populate CPPFLAGS.

- - - - -
f97f0c85 by Étienne Mollier at 2026-01-04T21:48:51+01:00
d/control: drop redundant Priority: optional.

- - - - -
8d0f4fbd by Étienne Mollier at 2026-01-04T21:49:06+01:00
d/control: drop redundant Rules-Requires-Root: no.

- - - - -
673bd861 by Étienne Mollier at 2026-01-04T21:49:21+01:00
d/control: declare compliance to standards version 4.7.3.

- - - - -
1ecd3b5f by Étienne Mollier at 2026-01-04T21:50:29+01:00
d/patches/*: normalize Last-Update timestamp.

- - - - -
4f30e380 by Étienne Mollier at 2026-01-04T21:51:45+01:00
d/changelog: ready for upload to unstable.

- - - - -


8 changed files:

- debian/changelog
- debian/control
- + debian/patches/cxx14.patch
- debian/patches/fix-bamtools-path
- debian/patches/privacy-breach.patch
- debian/patches/series
- debian/patches/spelling-fixes
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+berkeley-express (1.5.3+dfsg-5) unstable; urgency=medium
+
+  * Team upload.
+  * cxx14.patch: new: bump to standard gnu++14.
+    This is necessary to fix build failures with boost1.88, older levels
+    like gnu++11 are now too old and incompatible. (Closes: #1110628)
+  * d/rules: canonically populate CPPFLAGS.
+  * d/control: drop redundant Priority: optional.
+  * d/control: drop redundant Rules-Requires-Root: no.
+  * d/control: declare compliance to standards version 4.7.3.
+  * d/patches/*: normalize Last-Update timestamp.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 04 Jan 2026 21:50:53 +0100
+
 berkeley-express (1.5.3+dfsg-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -1,10 +1,9 @@
 Source: berkeley-express
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders:
  Michael R. Crusoe <crusoe at debian.org>,
 Section: science
-Priority: optional
 Build-Depends:
  debhelper-compat (= 13),
  libboost-thread-dev,
@@ -21,7 +20,6 @@ Build-Depends:
 Vcs-Browser: https://salsa.debian.org/med-team/berkeley-express
 Vcs-Git: https://salsa.debian.org/med-team/berkeley-express.git
 Homepage: http://bio.math.berkeley.edu/eXpress/index.html
-Rules-Requires-Root: no
 
 Package: berkeley-express
 Architecture: any


=====================================
debian/patches/cxx14.patch
=====================================
@@ -0,0 +1,20 @@
+Description: bump C++ standard to version 2014.
+ This change is necessary to support boost1.88 and beyond, because C++
+ 2014 becomes the minimum supported version.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1110628
+Forwarded: no
+Last-Update: 2026-01-04
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- berkeley-express.orig/CMakeLists.txt
++++ berkeley-express/CMakeLists.txt
+@@ -6,7 +6,7 @@
+ set(${PROJECT_NAME}_VERSION_MINOR 5)
+ set(${PROJECT_NAME}_VERSION_PATCH 1)
+ 
+-set(CMAKE_CXX_STANDARD 11)
++set(CMAKE_CXX_STANDARD 14)
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
+ 
+ #set(CMAKE_CXX_FLAGS "-Wall")


=====================================
debian/patches/fix-bamtools-path
=====================================
@@ -1,5 +1,5 @@
 Author: Michael R. Crusoe <mcrusoe at msu.edu>
-Last-Update: Thu, 12 Feb 2015 09:21:09 +0100
+Last-Update: 2015-02-12
 Description: Fix path to Debian packaged bamtools
 
 --- berkeley-express.orig/CMakeLists.txt


=====================================
debian/patches/privacy-breach.patch
=====================================
@@ -1,6 +1,6 @@
 Description: avoid privace breach JS in html doc
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
+Last-Update: 2018-04-07
 
 --- berkeley-express.orig/html/faq.html
 +++ berkeley-express/html/faq.html


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ fix-bamtools-path
 drop-zlib
 correct-debug-flags.patch
 privacy-breach.patch
+cxx14.patch


=====================================
debian/patches/spelling-fixes
=====================================
@@ -1,5 +1,5 @@
 Author: Michael R. Crusoe <crusoe at ucdavis.edu>
-Last-Update: Fri, 21 Aug 2015 09:21:09 +0100
+Last-Update: 2015-08-21
 Description: Correct upstream typos
 
 --- express.orig/src/lengthdistribution.cpp


=====================================
debian/rules
=====================================
@@ -1,9 +1,7 @@
 #!/usr/bin/make -f
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-CPPFLAGS += -D__FILE__=\"\"
-export CPPFLAGS
+export DEB_CPPFLAGS_MAINT_APPEND = -D__FILE__=\"\"
 DH_VERBOSE := 1
 
 %:



View it on GitLab: https://salsa.debian.org/med-team/berkeley-express/-/compare/de97848bf31661e9455312a35c252d97aa54c1a8...4f30e38005e8416b9f706f610b2204af32872f81

-- 
View it on GitLab: https://salsa.debian.org/med-team/berkeley-express/-/compare/de97848bf31661e9455312a35c252d97aa54c1a8...4f30e38005e8416b9f706f610b2204af32872f81
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