[med-svn] [Git][med-team/trinityrnaseq][master] 5 commits: d/control: update homepage
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Sep 12 18:50:50 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq
Commits:
6aff8371 by Michael R. Crusoe at 2023-09-12T11:31:57+02:00
d/control: update homepage
- - - - -
c67af31d by Michael R. Crusoe at 2023-09-12T16:08:59+02:00
d/control: remove unused test-deps
- - - - -
153701bf by Michael R. Crusoe at 2023-09-12T16:09:33+02:00
d/source/lintian-overrides: note that we clean up the config.{log,status} automatically.
- - - - -
2e49a544 by Michael R. Crusoe at 2023-09-12T17:09:21+02:00
d/patches/R_4.2_fix: fix for R 4.2.x+.
Closes: #1006336, #100477
- - - - -
f2921728 by Michael R. Crusoe at 2023-09-12T17:12:31+02:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/R_4.2_fix
- debian/patches/extending_Function_in_jung.patch
- debian/patches/series
- debian/patches/update-paths
- + debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,58 +1,20 @@
-trinityrnaseq (2.15.1+dfsg-1) UNRELEASED; urgency=medium
+trinityrnaseq (2.15.1+dfsg-1) unstable; urgency=medium
[ Michael R. Crusoe ]
* d/watch: update for GitHub API breakage
[ 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
+
+ [ Michael R. Crusoe ]
+ * d/control: update homepage
+ * d/control: remove unused test-deps
+ * d/source/lintian-overrides: note that we clean up the
+ config.{log,status} automatically.
+ * d/patches/R_4.2_fix: fix for R 4.2.x+.
+ Closes: #1006336, #1004773
+
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 12 Sep 2023 17:12:30 +0200
trinityrnaseq (2.14.0+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -4,50 +4,19 @@ Uploaders: Michael R. Crusoe <crusoe at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- jellyfish,
libjung-free-java (>= 2.1.1),
javahelper,
libgetopt-java,
default-jdk,
- parafly,
libjs-jquery,
jaligner,
libhts-dev,
- bowtie2,
- salmon,
zlib1g-dev,
- cmake,
- r-bioc-edger,
- r-bioc-deseq2,
- r-bioc-rots,
- r-cran-fastcluster,
- liburi-perl,
- r-cran-ape,
- r-bioc-ctc,
- r-cran-gplots,
- r-cran-readr,
- r-bioc-biobase,
- r-bioc-qvalue,
- r-bioc-goseq,
- r-bioc-tximport,
- python3-htseq,
- rna-star,
- picard-tools,
- gmap,
- hisat2,
- subread,
- kallisto,
- python3-hisat2,
- r-cran-argparse,
- r-bioc-dexseq,
- tabix
-# r-cran-goplot,
-# r-bioc-glimma,
-# r-bioc-tximportdata
+ cmake
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/trinityrnaseq
Vcs-Git: https://salsa.debian.org/med-team/trinityrnaseq.git
-Homepage: https://trinityrnaseq.github.io/
+Homepage: https://github.com/trinityrnaseq/trinityrnaseq
Rules-Requires-Root: no
Package: trinityrnaseq
=====================================
debian/patches/R_4.2_fix
=====================================
@@ -0,0 +1,21 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Fix heatmap.3.R broken by R 4.2.x+
+Forwarded: https://github.com/trinityrnaseq/trinityrnaseq/issues/1337
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/R/heatmap.3.R
++++ trinityrnaseq/Analysis/DifferentialExpression/R/heatmap.3.R
+@@ -99,12 +99,12 @@
+ warning("Using scale=\"row\" or scale=\"column\" when breaks are",
+ "specified can produce unpredictable results.", "Please consider using only one or the other.")
+
+- if (is.null(Rowv) || is.na(Rowv))
++ if (all(is.null(Rowv)) || all(is.na(Rowv)))
+ Rowv <- FALSE
+
+- if (is.null(Colv) || is.na(Colv))
++ if (all(is.null(Colv)) || all(is.na(Colv)))
+ Colv <- FALSE
+- else if (Colv == "Rowv" && !isTRUE(Rowv))
++ else if (all(Colv == "Rowv") && !all(isTRUE(Rowv)))
+ Colv <- FALSE
+
+ if (length(di <- dim(x)) != 2 || !is.numeric(x))
=====================================
debian/patches/extending_Function_in_jung.patch
=====================================
@@ -4,8 +4,8 @@ Author: Pierre Gruet <pgt at debian.org>
Forwarded: not-needed
Last-Update: 2021-11-15
---- a/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java
-+++ b/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java
+--- trinityrnaseq.orig/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java
++++ trinityrnaseq/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java
@@ -9211,7 +9211,7 @@
HashMap<List<Integer>, Integer> gene_grouping = new HashMap<List<Integer>, Integer>();
@@ -24,8 +24,8 @@ Last-Update: 2021-11-15
int comp_counter = 0;
for (Set<SeqVertex> s : comps) {
---- a/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
-+++ b/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
+--- trinityrnaseq.orig/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
++++ trinityrnaseq/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
@@ -97,7 +97,7 @@
{
if (!w.equals(verToExclude) && !sd.distances.containsKey(w))
=====================================
debian/patches/series
=====================================
@@ -17,3 +17,4 @@ fix-gcc-10.patch
bamsifter_build
strip_m64
extending_Function_in_jung.patch
+R_4.2_fix
=====================================
debian/patches/update-paths
=====================================
@@ -5,7 +5,7 @@ Last-Updated: 2015-02-22
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -374,7 +374,7 @@
+@@ -381,7 +381,7 @@
# --bfly_algorithm <string> : assembly algorithm to use. Options: @BFLY_ALGORITHMS
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
@@ -14,7 +14,7 @@ Last-Updated: 2015-02-22
# (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here).
#
#
-@@ -1039,7 +1039,7 @@
+@@ -1074,7 +1074,7 @@
}
unless ($BFLY_JAR) {
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# these files are cleaned automatically
+configure-generated-file-in-source [trinity-plugins/ParaFly/config.log]
+configure-generated-file-in-source [trinity-plugins/ParaFly/config.status]
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/53ae410f54acd081ec35614a3fbcc7d6a1404a81...f29217285ea0f7de3276eeb05ab42f371117c437
--
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/53ae410f54acd081ec35614a3fbcc7d6a1404a81...f29217285ea0f7de3276eeb05ab42f371117c437
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