[med-svn] [Git][med-team/trinityrnaseq][master] 5 commits: Fix build with CMake 4
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Oct 20 16:08:21 BST 2025
Andreas Tille pushed to branch master at Debian Med / trinityrnaseq
Commits:
51893f19 by Andreas Tille at 2025-10-20T16:15:38+02:00
Fix build with CMake 4
Closes: #1113587
- - - - -
6a858f89 by Andreas Tille at 2025-10-20T16:17:19+02:00
d/watch: version=5
- - - - -
0bb19d6d by Andreas Tille at 2025-10-20T16:17:30+02:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
c15b13fa by Andreas Tille at 2025-10-20T16:18:44+02:00
debputy lint --auto-fix (routine-update)
- - - - -
b7326d71 by Andreas Tille at 2025-10-20T17:00:14+02:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+trinityrnaseq (2.15.2+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * Fix build with CMake 4
+ Closes: #1113587
+ * d/watch: version=5
+ * Standards-Version: 4.7.2 (routine-update)
+ * debputy lint --auto-fix (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Mon, 20 Oct 2025 16:18:48 +0200
+
trinityrnaseq (2.15.2+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -1,19 +1,21 @@
Source: trinityrnaseq
+Standards-Version: 4.7.2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <crusoe at debian.org>
+Uploaders:
+ Michael R. Crusoe <crusoe at debian.org>,
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 13),
- libjung-free-java (>= 2.1.1),
- javahelper,
- libgetopt-java,
- default-jdk,
- libjs-jquery,
- jaligner,
- libhts-dev,
- zlib1g-dev,
- cmake
-Standards-Version: 4.6.2
+Build-Depends:
+ debhelper-compat (= 13),
+ libjung-free-java,
+ javahelper,
+ libgetopt-java,
+ default-jdk,
+ libjs-jquery,
+ jaligner,
+ libhts-dev,
+ zlib1g-dev,
+ cmake,
Vcs-Browser: https://salsa.debian.org/med-team/trinityrnaseq
Vcs-Git: https://salsa.debian.org/med-team/trinityrnaseq.git
Homepage: https://github.com/trinityrnaseq/trinityrnaseq
@@ -21,59 +23,62 @@ Rules-Requires-Root: no
Package: trinityrnaseq
Architecture: amd64 arm64 ppc64el riscv64 loong64
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${perl:Depends},
- ${java:Depends},
- bowtie,
- bowtie2,
- libwww-perl,
- default-jre-headless,
- samtools,
- jellyfish,
- r-base-core,
- rsem,
- berkeley-express,
- trimmomatic,
- parafly,
- ncbi-blast+,
- python3,
- liburi-perl,
- python3-htseq,
- subread,
- kallisto
-Recommends: ${java:Recommends},
- curl,
- trinityrnaseq-examples,
- picard-tools,
- tabix,
- gmap,
- salmon,
- rna-star,
- hisat2,
- r-cran-tidyverse,
- r-cran-readr,
- r-bioc-edger,
- r-bioc-deseq2,
- r-bioc-rots,
- r-cran-cluster,
- r-cran-fastcluster,
- r-bioc-ctc,
- r-bioc-goseq,
- r-cran-goplot,
- r-cran-gplots,
- r-bioc-dexseq,
- r-cran-ape,
- r-bioc-biobase,
- r-bioc-qvalue,
- r-cran-argparse,
- r-cran-kernsmooth,
- python3-numpy,
- python3-hisat2
-Suggests: collectl,
- transdecoder,
- r-bioc-tximport,
- r-bioc-tximportdata
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${perl:Depends},
+ ${java:Depends},
+ bowtie,
+ bowtie2,
+ libwww-perl,
+ default-jre-headless,
+ samtools,
+ jellyfish,
+ r-base-core,
+ rsem,
+ berkeley-express,
+ trimmomatic,
+ parafly,
+ ncbi-blast+,
+ python3,
+ liburi-perl,
+ python3-htseq,
+ subread,
+ kallisto,
+Recommends:
+ ${java:Recommends},
+ curl,
+ trinityrnaseq-examples,
+ picard-tools,
+ tabix,
+ gmap,
+ salmon,
+ rna-star,
+ hisat2,
+ r-cran-tidyverse,
+ r-cran-readr,
+ r-bioc-edger,
+ r-bioc-deseq2,
+ r-bioc-rots,
+ r-cran-cluster,
+ r-cran-fastcluster,
+ r-bioc-ctc,
+ r-bioc-goseq,
+ r-cran-goplot,
+ r-cran-gplots,
+ r-bioc-dexseq,
+ r-cran-ape,
+ r-bioc-biobase,
+ r-bioc-qvalue,
+ r-cran-argparse,
+ r-cran-kernsmooth,
+ python3-numpy,
+ python3-hisat2,
+Suggests:
+ collectl,
+ transdecoder,
+ r-bioc-tximport,
+ r-bioc-tximportdata,
Description: RNA-Seq De novo Assembly
Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
@@ -86,11 +91,13 @@ Description: RNA-Seq De novo Assembly
Package: trinityrnaseq-examples
Architecture: amd64 arm64 ppc64el riscv64 loong64
-Depends: ${perl:Depends},
- ${java:Depends},
- ${misc:Depends},
- r-base-core
-Recommends: trinityrnaseq
+Depends:
+ ${perl:Depends},
+ ${java:Depends},
+ ${misc:Depends},
+ r-base-core,
+Recommends:
+ trinityrnaseq,
Description: RNA-Seq De novo Assembly common example and testing files
Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
=====================================
debian/rules
=====================================
@@ -26,7 +26,7 @@ override_dh_autoreconf:
override_dh_auto_configure:
rm -f Chrysalis/Makefile
for target in ${SOURCE_DIRECTORIES_CMAKE}; do dh_auto_configure \
- --sourcedirectory=$${target} --builddirectory=$${target}_build; done
+ --sourcedirectory=$${target} --builddirectory=$${target}_build -- -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ; done
override_dh_auto_build:
for target in ${SOURCE_DIRECTORIES_CMAKE}; do dh_auto_build \
=====================================
debian/watch
=====================================
@@ -1,12 +1,7 @@
-version=4
+Version: 5
-opts=\
-repack,\
-compression=xz,\
-repacksuffix=+dfsg,\
-dversionmangle=auto,\
-searchmode=plain \
- https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases \
- https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v[\d\.]+/trinityrnaseq-v at ANY_VERSION@(?:\.FULL_with_extendedTestData)@ARCHIVE_EXT@
-
-# the ?: means the grouping is non-capturing, so the wExtSampleData or with_extendedTestData part isn't included in the version number
+Template: Github
+Owner: trinityrnaseq
+Project: trinityrnaseq
+Repack-Suffix: +dfsg
+Dversion-Mangle: auto
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/27538d9c4f7409b8ce246a71f4c620a4c2457b8a...b7326d7126bfb1f03cbe299e91ab3642ef7b764a
--
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/27538d9c4f7409b8ce246a71f4c620a4c2457b8a...b7326d7126bfb1f03cbe299e91ab3642ef7b764a
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