[med-svn] [Git][med-team/rsem][master] 7 commits: Fix FTBFS with Boost 1.90. Closes: #1129855.

[Santiago Vila (@sanvila)]

Santiago Vila pushed to branch master at Debian Med / rsem


Commits:
22a76005 by Adrian Bunk at 2026-03-26T23:44:00+01:00
Fix FTBFS with Boost 1.90. Closes: #1129855.

- - - - -
dcdbc323 by Santiago Vila at 2026-03-26T23:45:00+01:00
Reword and rename patch for C++ 2014.

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e059c6c5 by Santiago Vila at 2026-03-26T23:46:00+01:00
d/control: Drop "Rules-Requires-Root: no" (default).

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ad3d7c6d by Santiago Vila at 2026-03-26T23:47:00+01:00
d/control: Drop "Priority: optional" (default).

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8ab01399 by Santiago Vila at 2026-03-26T23:48:00+01:00
d/control: Update standards-version.

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65d56ff5 by Santiago Vila at 2026-03-26T23:49:00+01:00
d/salsa-ci.yml: Disable redundant/duplicate jobs.

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c79e6d48 by Santiago Vila at 2026-03-26T23:50:00+01:00
Upload for unstable as 1.3.3+dfsg-4

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5 changed files:

- debian/changelog
- debian/control
- debian/patches/series
- debian/patches/stdgnu++11.patch → debian/patches/stdgnu++14.patch
- debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+rsem (1.3.3+dfsg-4) unstable; urgency=medium
+
+  * Team upload.
+
+  [ Adrian Bunk ]
+  * Fix FTBFS with Boost 1.90. Closes: #1129855.
+
+  [ Santiago Vila ]
+  * Drop "Rules-Requires-Root: no" (default).
+  * Drop "Priority: optional" (default).
+  * Update standards-version.
+  * Disable redundant/duplicate jobs in salsa-ci.yml.
+
+ -- Santiago Vila <sanvila at debian.org>  Thu, 26 Mar 2026 23:50:00 +0100
+
 rsem (1.3.3+dfsg-3) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -3,7 +3,6 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Michael R. Crusoe <crusoe at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
-Priority: optional
 Build-Depends: debhelper-compat (= 13),
                zlib1g-dev,
                libncurses-dev,
@@ -16,11 +15,10 @@ Build-Depends: debhelper-compat (= 13),
 # bowtie is a run-time dependency available on only a few systems, not actually
 # needed for building but it prevents the creation of uninstallable packages
                bowtie | bowtie2
-Standards-Version: 4.6.2
+Standards-Version: 4.7.3
 Vcs-Browser: https://salsa.debian.org/med-team/rsem
 Vcs-Git: https://salsa.debian.org/med-team/rsem.git
 Homepage: https://deweylab.github.io/RSEM/
-Rules-Requires-Root: no
 
 Package: rsem
 Architecture: any


=====================================
debian/patches/series
=====================================
@@ -1,4 +1,4 @@
 hardening
 use_debian_packaged_samtools.patch
 2to3.patch
-stdgnu++11.patch
+stdgnu++14.patch


=====================================
debian/patches/stdgnu++11.patch → debian/patches/stdgnu++14.patch
=====================================
@@ -1,7 +1,7 @@
-Description: port codebase to gnu++11.
- Since boost 1.83, it is necessary to build rsem with C++ 2011 standard.  This
- patch bumps the -std=gnu++98 passed by upstream Makefil to -std=gnu++11.  It
- should become unnecessary once upstream bumped to C++ 2011 or later, or when
+Description: port codebase to gnu++14.
+ Since boost 1.90, it is necessary to build rsem with C++ 2014 standard.  This
+ patch bumps the -std=gnu++98 passed by upstream Makefile to -std=gnu++14.  It
+ should become unnecessary once upstream bumped to C++ 2014 or later, or when
  the package will not depend on boost anymore, in case this is in upstream's
  agenda; there is a merge request open upstream to bump to -std=gnu++17 in the
  meantime.
@@ -9,7 +9,7 @@ Description: port codebase to gnu++11.
 Author: Étienne Mollier <emollier at debian.org>
 Bug: https://github.com/deweylab/RSEM/pull/96
 Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1056010
-Last-Update: 2023-12-18
+Last-Update: 2026-03-26
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- rsem.orig/Makefile
@@ -19,7 +19,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  # Compilation variables
  CXX = g++
 -CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST)
-+CXXFLAGS += -std=gnu++11 -Wall -I. -I$(BOOST)
++CXXFLAGS += -std=gnu++14 -Wall -I. -I$(BOOST)
  CPPFLAGS ?=
  
  LDFLAGS ?=


=====================================
debian/salsa-ci.yml
=====================================
@@ -6,3 +6,5 @@ include:
 # i386 is explicitly excluded by Build-Depends: bowtie2
 variables:
   SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1
+  SALSA_CI_DISABLE_BUILD_PACKAGE_ALL: 1
+  SALSA_CI_DISABLE_BUILD_PACKAGE_ANY: 1



View it on GitLab: https://salsa.debian.org/med-team/rsem/-/compare/7d77511a9b2e955a9f35904b1c7dc8ce1806a289...c79e6d48492dee7248271a0f72289643ad46644b

-- 
View it on GitLab: https://salsa.debian.org/med-team/rsem/-/compare/7d77511a9b2e955a9f35904b1c7dc8ce1806a289...c79e6d48492dee7248271a0f72289643ad46644b
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