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 <[email protected]> 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 <[email protected]> Uploaders: Michael R. Crusoe <[email protected]>, 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 <[email protected]> +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 <[email protected]> -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 <[email protected]> -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 <[email protected]> -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 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
