New Upstream Release - r-bioc-biocviews
Ready changes
Summary
Merged new upstream version: 1.68.1 (was: 1.66.2).
Diff
diff --git a/DESCRIPTION b/DESCRIPTION
index 28275de..38c4639 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -6,9 +6,9 @@ Description: Infrastructure to support 'views' used to classify
major classifications, corresponding to 'software', 'annotation',
and 'experiment data' packages.
biocViews: Infrastructure
-URL: http://bioconductor.org/packages/BiocViews
-BugReports: https://github.com/Bioconductor/BiocViews/issues
-Version: 1.66.2
+URL: http://bioconductor.org/packages/biocViews
+BugReports: https://github.com/Bioconductor/biocViews/issues
+Version: 1.68.1
License: Artistic-2.0
Author: VJ Carey <stvjc@channing.harvard.edu>,
BJ Harshfield <rebjh@channing.harvard.edu>,
@@ -26,9 +26,9 @@ Collate: AllClasses.R AllGenerics.R as-methods.R htmlDoc-methods.R
getPackageNEWS.R validation_tests.R recommendBiocViews.R
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/biocViews
-git_branch: RELEASE_3_16
-git_last_commit: ab81c4b
-git_last_commit_date: 2022-12-22
-Date/Publication: 2022-12-22
+git_branch: RELEASE_3_17
+git_last_commit: 2eaf0a0
+git_last_commit_date: 2023-05-09
+Date/Publication: 2023-05-14
NeedsCompilation: no
-Packaged: 2022-12-22 20:54:48 UTC; biocbuild
+Packaged: 2023-05-14 19:59:21 UTC; biocbuild
diff --git a/NEWS b/NEWS
index c46ddf2..6bc77f9 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,11 @@
+CHANGES IN VERSION 1.67.0
+-------------------------
+
+ENHANCEMENT
+
+ o (1.67.1) Add biocViews term WorkflowManagement
+ o (1.67.3) Add biocViews term LongRead
+
CHANGES IN VERSION 1.65.0
-------------------------
diff --git a/R/repository.R b/R/repository.R
index eb3b041..5d59aee 100644
--- a/R/repository.R
+++ b/R/repository.R
@@ -651,6 +651,7 @@ write_VIEWS <- function(reposRootPath, fields = NULL,
'source'=".tar.gz",
'win.binary'=".zip",
'mac.binary'=,
+ 'mac.binary.big-sur-x86_64'=,
'mac.binary.big-sur-arm64'=,
'mac.binary.mavericks'=,
'mac.binary.el-capitan'=".tgz",
diff --git a/build/vignette.rds b/build/vignette.rds
index b4e7a1d..ac7e48d 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/data/biocViewsVocab.rda b/data/biocViewsVocab.rda
index 36fb197..ef43a77 100644
Binary files a/data/biocViewsVocab.rda and b/data/biocViewsVocab.rda differ
diff --git a/debian/changelog b/debian/changelog
index d815466..1d56c60 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+r-bioc-biocviews (1.68.1-1) UNRELEASED; urgency=low
+
+ * New upstream release.
+
+ -- Debian Janitor <janitor@jelmer.uk> Mon, 05 Jun 2023 18:18:39 -0000
+
r-bioc-biocviews (1.66.2-1) unstable; urgency=medium
* Team Upload.
diff --git a/inst/doc/HOWTO-BCV.html b/inst/doc/HOWTO-BCV.html
index 401354c..6c3557b 100644
--- a/inst/doc/HOWTO-BCV.html
+++ b/inst/doc/HOWTO-BCV.html
@@ -11,7 +11,7 @@
<meta name="author" content="S. Falcon and V.J. Carey" />
-<meta name="date" content="2022-12-22" />
+<meta name="date" content="2023-05-14" />
<title>HOWTO generate biocViews HTML</title>
@@ -509,6 +509,10 @@ code > span.paren { color: #000000;}
padding-left: 65px;
}
+.references {
+padding-right: 150px;
+}
+
.margin-toggle {
display: none;
}
@@ -523,6 +527,8 @@ p {
padding-left: 0;
padding-right: 0;
}
+.references { padding-right: 0;
+}
h1, h2, h3, h4, h5, h6 {
width: 100%;
padding-left: 0;
@@ -700,7 +706,7 @@ function toggle_visibility(id1) {
<h1 class="title toc-ignore">HOWTO generate biocViews HTML</h1>
<p class="author-name">S. Falcon and V.J. Carey</p>
-<h4 class="date">December 22, 2022</h4>
+<h4 class="date">May 14, 2023</h4>
</div>
@@ -861,13 +867,13 @@ all subterms should be returned. For a complete list use
## [29] "DenovoGenome" "TargetedResequencing"
## [31] "DenovoTranscriptome" "MicrobialStrain"
## [33] "HiC" "PooledScreens"
-## [35] "MNaseSeq" "MultiChannel"
-## [37] "OneChannel" "TwoChannel"
-## [39] "MethylationArray" "GenotypingArray"
-## [41] "MicroRNAArray" "mRNAMicroarray"
-## [43] "ChipOnChip" "ReversePhaseProteinArray"
-## [45] "TissueMicroarray" "ProprietaryPlatforms"
-## [47] "ImagingMassSpectrometry"</code></pre>
+## [35] "MNaseSeq" "LongRead"
+## [37] "MultiChannel" "OneChannel"
+## [39] "TwoChannel" "MethylationArray"
+## [41] "GenotypingArray" "MicroRNAArray"
+## [43] "mRNAMicroarray" "ChipOnChip"
+## [45] "ReversePhaseProteinArray" "TissueMicroarray"
+## [47] "ProprietaryPlatforms" "ImagingMassSpectrometry"</code></pre>
</div>
<div id="generating-html" class="section level1">
<h1><span class="header-section-number">4</span> Generating HTML</h1>
diff --git a/inst/doc/createReposHtml.html b/inst/doc/createReposHtml.html
index 19fddb0..b98fb4b 100644
--- a/inst/doc/createReposHtml.html
+++ b/inst/doc/createReposHtml.html
@@ -11,7 +11,7 @@
<meta name="author" content="S. Falcon" />
-<meta name="date" content="2022-12-22" />
+<meta name="date" content="2023-05-14" />
<title>HOWTO generate repository HTML</title>
@@ -509,6 +509,10 @@ code > span.paren { color: #000000;}
padding-left: 65px;
}
+.references {
+padding-right: 150px;
+}
+
.margin-toggle {
display: none;
}
@@ -523,6 +527,8 @@ p {
padding-left: 0;
padding-right: 0;
}
+.references { padding-right: 0;
+}
h1, h2, h3, h4, h5, h6 {
width: 100%;
padding-left: 0;
@@ -700,7 +706,7 @@ function toggle_visibility(id1) {
<h1 class="title toc-ignore">HOWTO generate repository HTML</h1>
<p class="author-name">S. Falcon</p>
-<h4 class="date">December 22, 2022</h4>
+<h4 class="date">May 14, 2023</h4>
</div>
diff --git a/inst/dot/biocViewsVocab.dot b/inst/dot/biocViewsVocab.dot
index 5153803..fed9172 100644
--- a/inst/dot/biocViewsVocab.dot
+++ b/inst/dot/biocViewsVocab.dot
@@ -52,6 +52,7 @@ Sequencing -> MicrobialStrain;
Sequencing -> HiC;
Sequencing -> PooledScreens;
Sequencing -> MNaseSeq;
+Sequencing -> LongRead;
Technology -> Microarray;
Microarray -> MultiChannel;
Microarray -> OneChannel;
diff --git a/inst/extdata/biocViewsVocab.sqlite b/inst/extdata/biocViewsVocab.sqlite
index d937845..8698672 100644
Binary files a/inst/extdata/biocViewsVocab.sqlite and b/inst/extdata/biocViewsVocab.sqlite differ