v1.21.10 -- as predicted v1.21.9 failed on R CMD check instead of bui…

…ld. Now use crop = NULL
leekgroup · Apr 24, 2020 · c7b2fc8 · c7b2fc8
1 parent c63ec2c
commit c7b2fc8
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Showing 5 changed files with 23 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: regionReport
 Type: Package
 Title: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
-Version: 1.21.9
+Version: 1.21.10
 Date: 2020-04-23
 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
     = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")),
@@ -38,8 +38,7 @@ Imports:
     rmarkdown (>= 0.9.5),
     S4Vectors,
     SummarizedExperiment,
-    utils,
-    magick
+    utils
 Suggests:
     BiocManager,
     biovizBase,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,21 @@
+# regionReport 1.21.10
+
+BUG FIXES
+
+* Add `crop = NULL` to all template Rmarkdown files. Drop `magick` as a
+depencency since cropping is not used on the reports (as done through
+`BiocStyle` by default). This is again related to responding to
+https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html.
+
+# regionReport 1.21.9
+
+BUG FIXES
+
+* Ran another test in preparation for 
+https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html after the 
+test in version 1.21.8 failed. The code will now be run in the example of
+`derfinderReport()` instead of the vignette.
+
 # regionReport 1.21.8
 
 BUG FIXES

diff --git a/inst/DESeq2Exploration/DESeq2Exploration.Rmd b/inst/DESeq2Exploration/DESeq2Exploration.Rmd
@@ -33,7 +33,7 @@ This section contains the code for setting up the rest of the report.
 ```{r docSetup, bootstrap.show.code = FALSE, dev = device, bootstrap.show.message=FALSE}
 ## knitrBoostrap and device chunk options
 library('knitr')
-opts_chunk$set(bootstrap.show.code = FALSE, dev = device)
+opts_chunk$set(bootstrap.show.code = FALSE, dev = device, crop = NULL)
 if(!outputIsHTML) opts_chunk$set(bootstrap.show.code = FALSE, dev = device, echo = FALSE)
 ```
 

diff --git a/inst/basicExploration/basicExploration.Rmd b/inst/basicExploration/basicExploration.Rmd
@@ -33,7 +33,7 @@ Most plots were made with using `ggplot2` `r citep(bib[['ggplot2']])`.
 ```{r docSetup, bootstrap.show.code = FALSE, dev = device, bootstrap.show.message=FALSE}
 ## knitrBoostrap and device chunk options
 library('knitr')
-opts_chunk$set(bootstrap.show.code = FALSE, dev = device)
+opts_chunk$set(bootstrap.show.code = FALSE, dev = device, crop = NULL)
 if(!outputIsHTML) opts_chunk$set(bootstrap.show.code = FALSE, dev = device, echo = FALSE)
 ```
 

diff --git a/inst/regionExploration/regionExploration.Rmd b/inst/regionExploration/regionExploration.Rmd
@@ -33,7 +33,7 @@ Most plots were made with using `ggplot2` `r citep(bib[['ggplot2']])`.
 ```{r docSetup, bootstrap.show.code = FALSE, dev = device, bootstrap.show.message=FALSE}
 ## knitrBoostrap and device chunk options
 library('knitr')
-opts_chunk$set(bootstrap.show.code = FALSE, dev = device)
+opts_chunk$set(bootstrap.show.code = FALSE, dev = device, crop = NULL)
 if(!outputIsHTML) opts_chunk$set(bootstrap.show.code = FALSE, dev = device, echo = FALSE)
 ```