New Upstream Release - r-bioc-gsva

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Maintainer email: r-pkg-team@alioth-lists.debian.net
Automatic publish policy: main: push-derived , pristine-tar: push-derived , upstream: push-derived
Last processed: 2023-06-06T02:06 (took 7m47s)
Branch URL: https://salsa.debian.org/r-pkg-team/r-bioc-gsva.git -b master (taken from version 1.50.0+ds-1)
Queue position: 114234 (a 48w5d wait)
Ready changes

Summary

Merged new upstream version: 1.48.1+ds (was: 1.46.0+ds).
Diff

diff --git a/DESCRIPTION b/DESCRIPTION
index 24879dd..524083a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: GSVA
-Version: 1.46.0
+Version: 1.48.1
 Title: Gene Set Variation Analysis for microarray and RNA-seq data
 Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"),
              person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"),
@@ -23,12 +23,12 @@ Encoding: latin1
 biocViews: FunctionalGenomics, Microarray, RNASeq, Pathways,
         GeneSetEnrichment
 git_url: https://git.bioconductor.org/packages/GSVA
-git_branch: RELEASE_3_16
-git_last_commit: 4036d9f
-git_last_commit_date: 2022-11-01
-Date/Publication: 2022-11-01
+git_branch: RELEASE_3_17
+git_last_commit: 9957f63
+git_last_commit_date: 2023-06-01
+Date/Publication: 2023-06-01
 NeedsCompilation: yes
-Packaged: 2022-11-01 21:46:53 UTC; biocbuild
+Packaged: 2023-06-01 20:59:46 UTC; biocbuild
 Author: Robert Castelo [aut, cre],
   Justin Guinney [aut],
   Alexey Sergushichev [ctb],
diff --git a/R/gsva.R b/R/gsva.R
index 1b50efa..1aa4001 100644
--- a/R/gsva.R
+++ b/R/gsva.R
@@ -54,6 +54,12 @@ setMethod("gsva", signature(expr="HDF5Array", gset.idx.list="list"),
   rval
 })
 
+setMethod("gsva", signature(expr="SingleCellExperiment", gset.idx.list="GeneSetCollection"),
+          function(expr, gset.idx.list, ...)
+{
+  gsva(expr, geneIds(gset.idx.list), ...)
+})
+
 setMethod("gsva", signature(expr="SingleCellExperiment", gset.idx.list="list"),
           function(expr, gset.idx.list, annotation,
   method=c("gsva", "ssgsea", "zscore", "plage"),
@@ -597,15 +603,15 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list"),
 	
   ## because we keep the argument 'parallel.sz' for backwards compatibility
   ## we need to harmonize it with the contents of BPPARAM
-  if (parallel.sz > 1L && class(BPPARAM) == "SerialParam") {
+  if (parallel.sz > 1L && inherits(BPPARAM, "SerialParam")) {
     BPPARAM=MulticoreParam(progressbar=verbose, workers=parallel.sz, tasks=100)
-  } else if (parallel.sz == 1L && class(BPPARAM) != "SerialParam") {
+  } else if (parallel.sz == 1L && !inherits(BPPARAM, "SerialParam")) {
     parallel.sz <- bpnworkers(BPPARAM)
-  } else if (parallel.sz > 1L && class(BPPARAM) != "SerialParam") {
+  } else if (parallel.sz > 1L && !inherits(BPPARAM, "SerialParam")) {
     bpworkers(BPPARAM) <- parallel.sz
   }
 
-  if (class(BPPARAM) != "SerialParam" && verbose)
+  if (!inherits(BPPARAM, "SerialParam") && verbose)
     cat(sprintf("Setting parallel calculations through a %s back-end\nwith workers=%d and tasks=100.\n",
                     class(BPPARAM), parallel.sz))
 
diff --git a/R/gsvaDelayedArray.R b/R/gsvaDelayedArray.R
index 09525a2..ef488d7 100644
--- a/R/gsvaDelayedArray.R
+++ b/R/gsvaDelayedArray.R
@@ -23,15 +23,15 @@
   
   ## because we keep the argument 'parallel.sz' for backwards compatibility
   ## we need to harmonize it with the contents of BPPARAM
-  if (parallel.sz > 1L && class(BPPARAM) == "SerialParam") {
+  if (parallel.sz > 1L && inherits(BPPARAM, "SerialParam")) {
     BPPARAM=MulticoreParam(progressbar=verbose, workers=parallel.sz, tasks=100)
-  } else if (parallel.sz == 1L && class(BPPARAM) != "SerialParam") {
+  } else if (parallel.sz == 1L && !inherits(BPPARAM, "SerialParam")) {
     parallel.sz <- bpnworkers(BPPARAM)
-  } else if (parallel.sz > 1L && class(BPPARAM) != "SerialParam") {
+  } else if (parallel.sz > 1L && !inherits(BPPARAM, "SerialParam")) {
     bpworkers(BPPARAM) <- parallel.sz
   }
   
-  if (class(BPPARAM) != "SerialParam" && verbose)
+  if (!inherits(BPPARAM, "SerialParam") && verbose)
     cat(sprintf("Setting parallel calculations through a %s back-end\nwith workers=%d and tasks=100.\n",
                 class(BPPARAM), parallel.sz))
   
diff --git a/build/vignette.rds b/build/vignette.rds
index 5091762..7596c52 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/debian/changelog b/debian/changelog
index 2bd69c3..6e5d215 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+r-bioc-gsva (1.48.1+ds-1) UNRELEASED; urgency=low
+
+  * New upstream release.
+
+ -- Debian Janitor <janitor@jelmer.uk>  Tue, 06 Jun 2023 01:58:49 -0000
+
 r-bioc-gsva (1.46.0+ds-1) unstable; urgency=medium
 
   * Team upload.
diff --git a/inst/CITATION b/inst/CITATION
index de5abd1..b65ebfa 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -9,7 +9,7 @@ citEntry(entry="Article",
   volume = "14",
   pages = "7",
   year = "2013",
-  url = "http://www.biomedcentral.com/1471-2105/14/7",
+  url = "https://doi.org/10.1186/1471-2105-14-7",
   doi = "10.1186/1471-2105-14-7",
   textVersion = paste("H�nzelmann, S., Castelo, R. and Guinney, A.",
                       "GSVA: gene set variation analysis for microarray and RNA-seq data.",
diff --git a/man/gsva.Rd b/man/gsva.Rd
index e37d99a..83ce87c 100644
--- a/man/gsva.Rd
+++ b/man/gsva.Rd
@@ -2,6 +2,7 @@
 \alias{gsva}
 \alias{gsva,HDF5Array,list-method}
 \alias{gsva,SingleCellExperiment,list-method}
+\alias{gsva,SingleCellExperiment,GeneSetCollection-method}
 \alias{gsva,dgCMatrix,list-method}
 \alias{gsva,SummarizedExperiment,list-method}
 \alias{gsva,SummarizedExperiment,GeneSetCollection-method}
diff --git a/src/register_cmethods.c b/src/register_cmethods.c
index afc2745..794c0d1 100644
--- a/src/register_cmethods.c
+++ b/src/register_cmethods.c
@@ -29,4 +29,5 @@ cMethods[] = {
 void
 R_init_GSVA(DllInfo *info) {
   R_registerRoutines(info, cMethods, NULL, NULL, NULL);
+  R_useDynamicSymbols(info, FALSE);
 }
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New Upstream Release - r-bioc-gsva

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