[med-svn] [Git][med-team/bioperl-run][master] 3 commits: d/control: restrict some build-deps to amd64.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / bioperl-run


Commits:
86f8da57 by Étienne Mollier at 2024-03-12T20:35:10+01:00
d/control: restrict some build-deps to amd64.

Following 64-bit time_t transition, ncbi tools have been limited to
64-bit architectures.  This fixes package building aod one of the
autodep8 perl autopkgtests.  This change is intended to facilitate the
transition timely.

- - - - -
07f0299d by Étienne Mollier at 2024-03-12T21:03:40+01:00
d/control: demote several packages as suggestions.

This fixes autodep8 perl autopkgtest base checking the installability
of recommendations; it could have been better to skip it but the
mecanisme to proceed to the skip occurs after the failure to install
missing recommends on architectures not supporting them.

- - - - -
61a3a7a6 by Étienne Mollier at 2024-03-12T21:14:46+01:00
ready changelog for upload to unstable.

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+bioperl-run (1.7.3-10) unstable; urgency=medium
+
+  * d/control: restrict some build-deps to amd64.
+    Following 64-bit time_t transition, ncbi tools have been limited to
+    64-bit architectures.  This fixes package building aod one of the
+    autodep8 perl autopkgtests.  This change is intended to facilitate the
+    transition timely.
+  * d/control: demote several packages as suggestions.
+    This fixes autodep8 perl autopkgtest base checking the installability
+    of recommendations; it could have been better to skip it but the
+    mecanisme to proceed to the skip occurs after the failure to install
+    missing recommends on architectures not supporting them.
+
+ -- Étienne Mollier <emollier at debian.org>  Tue, 12 Mar 2024 21:05:23 +0100
+
 bioperl-run (1.7.3-9) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/control
=====================================
@@ -22,19 +22,22 @@ Build-Depends-Indep: perl,
                      libbio-cluster-perl,
                      libbio-featureio-perl,
                      libconfig-any-perl,
-                     libbio-tools-run-alignment-clustalw-perl,
+                     libbio-tools-run-alignment-clustalw-perl [any-amd64],
                      libbio-eutilities-perl,
                      libbio-tools-run-remoteblast-perl,
 # Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup.
                      amap-align,
-                     bedtools,
+# While bedtools does install on i386 and other non-amd64 architectures, lack
+# of python3-pybedtools is causing missing test data resulting in tests
+# failures in bioperl-run, so the package is excluded on !amd64 for now.
+                     bedtools [any-amd64],
                      bedtools-test,
                      ncbi-blast+-legacy,
-                     clustalw,
+                     clustalw [any-amd64],
                      emboss,
                      exonerate,
                      hmmer [any-amd64 any-i386 powerpc ppc64],
-                     hyphy-pt | hyphy-mpi,
+                     hyphy-pt | hyphy-mpi [any-amd64],
                      infernal [any-amd64 any-i386],
                      kalign,
                      mafft,
@@ -44,9 +47,9 @@ Build-Depends-Indep: perl,
                      phyml,
                      primer3,
                      probcons,
-                     python3-pybedtools,
+                     python3-pybedtools [any-amd64],
                      raxml,
-                     samtools,
+                     samtools [any-amd64],
                      sim4,
                      tigr-glimmer,
                      wise,
@@ -69,7 +72,6 @@ Depends: ${misc:Depends},
          ${perl:Depends},
          bioperl (>= 1.7.4),
          libbio-perl-run-perl (= ${source:Version}),
-         libbio-tools-run-alignment-clustalw-perl,
          libbio-featureio-perl,
          libbio-cluster-perl,
          libtest-requiresinternet-perl,
@@ -77,13 +79,9 @@ Depends: ${misc:Depends},
          libbio-tools-run-remoteblast-perl,
          libsoap-lite-perl,
          default-jdk-headless,
-         hyphy-pt | hyphy-mpi
 Recommends: amap-align,
-            bedtools,
             ncbi-blast+-legacy,
-            bowtie,
             bwa,
-            clustalw,
             emboss,
             exonerate,
             hmmer,
@@ -94,22 +92,27 @@ Recommends: amap-align,
             muscle,
             ncoils,
             phylip,
-            phyml,
             primer3,
             probalign,
             probcons,
             raxml,
-            samtools,
             sim4,
             t-coffee,
             tigr-glimmer,
             wise,
             lagan,
-            pal2nal,
-            pftools
+            pal2nal
 Suggests: gmap,
           fasta3,
-          trnascan-se
+          trnascan-se,
+          bedtools,
+          bowtie,
+          clustalw,
+          hyphy-pt | hyphy-mpi,
+          libbio-tools-run-alignment-clustalw-perl,
+          pftools,
+          phyml,
+          samtools
 # gmap, fasta3, and trnascan-se is non-free
 # Removed from Debian at all: molphy,
 # Removed from Debian but might be reintroduced: ensembl,



View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/3e8174116aa42ce22f24c51deac4aaf8753bd3f3...61a3a7a674a41b9de418b0015726615954aeecdf

-- 
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/3e8174116aa42ce22f24c51deac4aaf8753bd3f3...61a3a7a674a41b9de418b0015726615954aeecdf
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