[med-svn] [Git][med-team/probabel][master] 7 commits: Fix build with gcc-16 Closes: #1143692

Sat Sep 5 07:32:53 BST 2026


Andreas Tille pushed to branch master at Debian Med / probabel


Commits:
d5d0e489 by Andreas Tille at 2026-09-05T07:52:55+02:00
Fix build with gcc-16 Closes: #1143692

- - - - -
3ee2d127 by Andreas Tille at 2026-09-05T06:53:04+01:00
Reformat the Last-Update date as ISO YYYY-MM-DD.

Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/examples.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/ignore_failing_build_time_test.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html

- - - - -
fda6c181 by Andreas Tille at 2026-09-05T06:53:04+01:00
Remove redundant Priority: optional from source stanza.

Changes-By: lintian-brush
Fixes: lintian: source: redundant-priority-optional-field
See-also: https://lintian.debian.org/tags/redundant-priority-optional-field.html

- - - - -
dd94e225 by Andreas Tille at 2026-09-05T06:53:05+01:00
Update standards version to 4.7.4, no changes needed.

Upgrade checklist verified:
 4.6.1 → 4.6.2:
  * Package does not provide x-window-manager alternative
 4.6.2 → 4.7.0:
  * Package does not use dpkg-divert
 4.7.0 → 4.7.1:
  * Package does not install to non-/usr paths
 4.7.3 → 4.7.4:
  * Package is not in non-free-firmware

Changes-By: lintian-brush
Fixes: lintian: source: ancient-standards-version 4.6.0 (released 2021-08-18) (current is 4.7.4.1)
See-also: https://lintian.debian.org/tags/ancient-standards-version.html

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8b53019b by Andreas Tille at 2026-09-05T07:58:42+02:00
d/watch: version=5

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d2e2b85e by Andreas Tille at 2026-09-05T07:59:40+02:00
cme fix dpkg-control

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7993b69d by Andreas Tille at 2026-09-05T08:26:11+02:00
Upload to unstable

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6 changed files:

- debian/changelog
- debian/control
- debian/patches/examples.patch
- debian/patches/ignore_failing_build_time_test.patch
- debian/rules
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,20 @@
-probabel (0.5.0+dfsg-7) UNRELEASED; urgency=medium
+probabel (0.5.0+dfsg-7) unstable; urgency=medium
 
-  * Team upload.
+  [ Étienne Mollier ]
   * d/control: remove any-i386 support.
     This follows up on ftbfs bug #1091575 and removal request #1092275.
   * d/salsa-ci.yml: skip i386 CI build.
 
- -- Étienne Mollier <emollier at debian.org>  Mon, 06 Jan 2025 21:51:06 +0100
+  [ Andreas Tille ]
+  * Fix build with gcc-16
+    Closes: #1143692
+  * Reformat the Last-Update date as ISO YYYY-MM-DD.
+  * Remove redundant Priority: optional from source stanza.
+  * Update standards version to 4.7.4, no changes needed.
+  * d/watch: version=5
+  * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org>  Sat, 05 Sep 2026 07:59:45 +0200
 
 probabel (0.5.0+dfsg-6) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -1,19 +1,20 @@
 Source: probabel
+Standards-Version: 4.7.4
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
-           L.C. Karssen <lennart at karssen.org>,
-           Pranav Ballaney <ballaneypranav at gmail.com>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
+ L.C. Karssen <lennart at karssen.org>,
+ Pranav Ballaney <ballaneypranav at gmail.com>,
 Section: science
-Priority: optional
-Build-Depends: debhelper-compat (= 13),
-               libeigen3-dev,
-               texlive-latex-base,
-               texlive-latex-extra,
-               texlive-latex-recommended,
-               texlive-fonts-recommended,
-               r-cran-survival <!nocheck>,
-               debhelper
-Standards-Version: 4.6.0
+Build-Depends:
+ debhelper-compat (= 14),
+ libeigen3-dev,
+ texlive-latex-base,
+ texlive-latex-extra,
+ texlive-latex-recommended,
+ texlive-fonts-recommended,
+ r-cran-survival <!nocheck>,
+ debhelper,
 Vcs-Browser: https://salsa.debian.org/med-team/probabel
 Vcs-Git: https://salsa.debian.org/med-team/probabel.git
 Homepage: http://www.genabel.org
@@ -21,9 +22,11 @@ Rules-Requires-Root: no
 
 Package: probabel
 Architecture: any-amd64 m68k sh4 x32
-Depends: ${shlibs:Depends},
-         ${misc:Depends}
-Recommends: ${perl:Depends}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+Recommends:
+ ${perl:Depends},
 Description: Toolset for Genome-Wide Association Analysis
  The ProbABEL package is part of the GenABEL project for analysis of genome-wide
  data. ProbABEL is used to run GWAS. Using files in filevector/DatABEL format
@@ -31,10 +34,13 @@ Description: Toolset for Genome-Wide Association Analysis
 
 Package: probabel-examples
 Architecture: all
-Depends: ${misc:Depends}
-Recommends: probabel (= ${binary:Version})
-Enhances: probabel
 Multi-Arch: foreign
+Depends:
+ ${misc:Depends},
+Recommends:
+ probabel (= ${binary:Version}),
+Enhances:
+ probabel,
 Description: Example files for ProbABEL
  The ProbABEL package is part of the GenABEL project for analysis of genome-wide
  data. ProbABEL is used to run GWAS. Using files in filevector/DatABEL format


=====================================
debian/patches/examples.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Pranav Ballaney
-Last-Update: 2020-08-03 20:45:43 +0530
+Last-Update: 2020-08-03
 Description: Fix path in example scripts
 
 --- a/examples/example_bt.sh


=====================================
debian/patches/ignore_failing_build_time_test.patch
=====================================
@@ -2,7 +2,7 @@ Description: Build-time test issue reported at
      https://github.com/GenABEL-Project/ProbABEL/issues/47
  is failing and was patched out for the moment.
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 11 Oct 2021 11:36:55 +0200
+Last-Update: 2021-10-11
 
 --- a/checks/R-tests/run_models_in_R_palinear.R
 +++ b/checks/R-tests/run_models_in_R_palinear.R


=====================================
debian/rules
=====================================
@@ -6,8 +6,12 @@ BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
 
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
+# GCC removed operator>>(istream&, char*) for -std=c++20 and later (LWG 2499);
+# this package relies on it, so pin the C++ standard explicitly.
+export DEB_CXXFLAGS_MAINT_APPEND = -std=c++17
+
 ifeq ($(DEB_HOST_ARCH),arm64)
-  export DEB_CXXFLAGS_MAINT_APPEND = -march=armv8-a+nosimd
+  export DEB_CXXFLAGS_MAINT_APPEND += -march=armv8-a+nosimd
 endif
 
 include /usr/share/dpkg/default.mk


=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
 
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-   https://github.com/GenABEL-Project/ProbABEL/tags .*/v?@ANY_VERSION@@ARCHIVE_EXT@
+Template: Github
+Dist: https://github.com/GenABEL-Project/ProbABEL
+Dversion-Mangle: auto
+Repack-Suffix: +dfsg
+Custom-Version: v(\d[\d.]+)



View it on GitLab: https://salsa.debian.org/med-team/probabel/-/compare/4aa4b62c78a645c9c8e2e6da591de6d8a1a3089b...7993b69d17b7d38f86529824713bdeed4ab4fa73

-- 
View it on GitLab: https://salsa.debian.org/med-team/probabel/-/compare/4aa4b62c78a645c9c8e2e6da591de6d8a1a3089b...7993b69d17b7d38f86529824713bdeed4ab4fa73
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