various fixes

DESCRIPTION

@@ -30,7 +30,6 @@ Imports:
     rlang,
     scales
 License: GPL-2
-LazyData: true
 Suggests:
     Cairo,
     covr,
@@ -72,6 +71,6 @@ Collate:
     'stamp.R'
     'themes.R'
     'utils_ggplot2.R'
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8

R/cowplot.R

@@ -8,10 +8,9 @@
 #' hence the name (Claus O. Wilke's plot package). It has also been used
 #' extensively in the book Fundamentals of Data Visualization.
 #'
-#' @name cowplot
-#' @docType package
 #' @import ggplot2
 #' @import grid
 #' @import rlang
-NULL
+#' @keywords internal
+"_PACKAGE"
 

README.md

@@ -4,7 +4,7 @@
 
 <!-- badges: start -->
 [![R build status](https://github.com/wilkelab/cowplot/workflows/R-CMD-check/badge.svg)](https://github.com/wilkelab/cowplot/actions)
-[![Coverage Status](https://img.shields.io/codecov/c/github/wilkelab/cowplot/master.svg)](https://codecov.io/github/wilkelab/cowplot?branch=master)
+[![Coverage Status](https://img.shields.io/codecov/c/github/wilkelab/cowplot/master.svg)](https://app.codecov.io/github/wilkelab/cowplot?branch=master)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/cowplot)](https://CRAN.R-project.org/package=cowplot)
 [![CRAN\_Downloads\_Badge](https://cranlogs.r-pkg.org/badges/cowplot)](https://cranlogs.r-pkg.org/downloads/total/last-month/cowplot)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2533860.svg)](https://doi.org/10.5281/zenodo.2533860)

cran-comments.md

@@ -1,9 +1,9 @@
-Make sure tests don't fail just because vdiffr couldn't be installed, per request by Brian Ripley.
+Minor bug fixes
 
 ## Test environments
 
 * ubuntu 20.04, devel and release
-* windows, release
+* windows, devel and release
 * macOS, release
 
 ## R CMD check results

revdep/README.md

@@ -2,42 +2,55 @@
 
 |field    |value                        |
 |:--------|:----------------------------|
-|version  |R version 3.6.0 (2019-04-26) |
-|os       |macOS Mojave 10.14.5         |
-|system   |x86_64, darwin15.6.0         |
+|version  |R version 4.3.1 (2023-06-16) |
+|os       |macOS Ventura 13.6           |
+|system   |aarch64, darwin20            |
 |ui       |X11                          |
 |language |(EN)                         |
 |collate  |en_US.UTF-8                  |
 |ctype    |en_US.UTF-8                  |
 |tz       |America/Chicago              |
-|date     |2019-07-08                   |
+|date     |2023-12-14                   |
+|pandoc   |NA                           |
 
 # Dependencies
 
-|package |old   |new    |Δ  |
-|:-------|:-----|:------|:--|
-|cowplot |0.9.4 |0.9.99 |*  |
+|package |old   |new   |Δ  |
+|:-------|:-----|:-----|:--|
+|cowplot |1.1.1 |1.1.2 |*  |
+|ggplot2 |NA    |3.4.4 |*  |
+|scales  |NA    |1.3.0 |*  |
 
 # Revdeps
 
-## Failed to check (10)
-
-|package                            |version |error  |warning |note |
-|:----------------------------------|:-------|:------|:-------|:----|
-|BASiCS                             |1.6.0   |1      |        |     |
-|bigstatsr                          |0.9.1   |1      |        |     |
-|BPRMeth                            |1.10.0  |1      |        |     |
-|CaseBasedReasoning                 |0.1     |1      |        |     |
-|cytometree                         |1.3.0   |1      |        |     |
-|[foreSIGHT](failures.md#foresight) |0.9.6   |__+1__ |        |     |
-|graper                             |1.0.0   |1      |        |     |
-|MutationalPatterns                 |1.10.0  |1      |        |     |
-|poppr                              |2.8.3   |1      |        |     |
-|telefit                            |1.0.1   |1      |        |     |
-
-## New problems (1)
-
-|package                              |version |error  |warning |note |
-|:------------------------------------|:-------|:------|:-------|:----|
-|[AneuFinder](problems.md#aneufinder) |1.12.0  |__+1__ |        |1    |
+## Failed to check (18)
+
+|package             |version |error |warning |note |
+|:-------------------|:-------|:-----|:-------|:----|
+|ClassifyR           |3.6.2   |1     |1       |3    |
+|cola                |?       |      |        |     |
+|CoSMoS              |2.1.0   |1     |        |     |
+|fgsea               |?       |      |        |     |
+|GenomicPlot         |1.0.0   |1     |        |     |
+|HiLDA               |1.16.0  |1     |        |     |
+|mcmcabn             |0.6     |1     |        |     |
+|orthos              |1.0.1   |2     |1       |     |
+|pareg               |1.6.0   |1     |        |2    |
+|phemd               |1.18.0  |1     |        |     |
+|rliger              |?       |      |        |     |
+|scGPS               |?       |      |        |     |
+|seqArchRplus        |1.2.0   |1     |        |     |
+|simplifyEnrichment  |?       |      |        |     |
+|SpatialOmicsOverlay |1.2.1   |1     |        |     |
+|stppSim             |1.3.2   |1     |        |     |
+|TOmicsVis           |2.0.0   |1     |        |     |
+|valse               |0.1-0   |1     |        |     |
+
+## New problems (3)
+
+|package    |version |error  |warning |note |
+|:----------|:-------|:------|:-------|:----|
+|[dce](problems.md#dce)|1.10.0  |__+1__ |        |3    |
+|[multiWGCNA](problems.md#multiwgcna)|1.0.0   |__+1__ |        |1    |
+|[ORFik](problems.md#orfik)|1.22.1  |__+1__ |1       |4    |
 

revdep/cran.md

@@ -0,0 +1,16 @@
+## revdepcheck results
+
+We checked 363 reverse dependencies (250 from CRAN + 113 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 5 packages
+
+Issues with CRAN packages are summarised below.
+
+### Failed to check
+
+* CoSMoS    (NA)
+* mcmcabn   (NA)
+* stppSim   (NA)
+* TOmicsVis (NA)
+* valse     (NA)