[med-svn] [Git][med-team/trinityrnaseq][master] 2 commits: fix version

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq


Commits:
580942f9 by Michael R. Crusoe at 2023-08-09T18:58:24+02:00
fix version

- - - - -
53ae410f by Michael R. Crusoe at 2023-08-10T09:59:36+02:00
document error remaining in autopkgtests

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-trinityrnaseq (2.15.0+dfsg-1) UNRELEASED; urgency=medium
+trinityrnaseq (2.15.1+dfsg-1) UNRELEASED; urgency=medium
 
   [ Michael R. Crusoe ]
   * d/watch: update for GitHub API breakage
@@ -6,6 +6,51 @@ trinityrnaseq (2.15.0+dfsg-1) UNRELEASED; urgency=medium
   [ Andreas Tille ]
   * Standards-Version: 4.6.2 (routine-update)
   TODO: Fix autopkgtest
+    File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
+    touch test_voom
+    /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --heatmap --sample_cor_matrix --log2 --save
+    CMD: Rscript Trinity_trans.TMM.EXPR.matrix.R
+    Loading required package: BiocGenerics
+    
+    Attaching package: ‘BiocGenerics’
+    
+    The following objects are masked from ‘package:stats’:
+    
+        IQR, mad, sd, var, xtabs
+    
+    The following objects are masked from ‘package:base’:
+    
+        anyDuplicated, aperm, append, as.data.frame, basename, cbind,
+        colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
+        get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
+        match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
+        Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
+        table, tapply, union, unique, unsplit, which.max, which.min
+    
+    Welcome to Bioconductor
+    
+        Vignettes contain introductory material; view with
+        'browseVignettes()'. To cite Bioconductor, see
+        'citation("Biobase")', and for packages 'citation("pkgname")'.
+    
+    
+    Attaching package: ‘fastcluster’
+    
+    The following object is masked from ‘package:stats’:
+    
+        hclust
+    
+    [1] "Reading matrix file."
+    Error in is.null(Rowv) || is.na(Rowv) : 
+      'length = 2' in coercion to 'logical(1)'
+    Calls: heatmap.3
+    Execution halted
+    Error, cmd: Rscript Trinity_trans.TMM.EXPR.matrix.R died with ret 256 at /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR line 1702.
+    make[2]: Leaving directory '/tmp/autopkgtest.qGAqzM/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example'
+    make[2]: *** [Makefile:32: test_PtR_heatmap] Error 25
+    make[1]: *** [Makefile:5: test] Error 2
+    make[1]: Leaving directory '/tmp/autopkgtest.qGAqzM/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis'
+    make: *** [Makefile:18: test] Error 2
 
  -- Andreas Tille <tille at debian.org>  Thu, 02 Mar 2023 08:34:23 +0100
 


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                jellyfish,
-               libjung-free-java (>= 2.1.1-1),
+               libjung-free-java (>= 2.1.1),
                javahelper,
                libgetopt-java,
                default-jdk,



View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/94bbafebee1cbd078a73f46717c5308d82a4f06b...53ae410f54acd081ec35614a3fbcc7d6a1404a81

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/94bbafebee1cbd078a73f46717c5308d82a4f06b...53ae410f54acd081ec35614a3fbcc7d6a1404a81
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230810/caeb226e/attachment-0001.htm>