fix: formatting issues

DESCRIPTION

@@ -8,14 +8,13 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-3913-153X"))
   )
 Maintainer: Yabing Song <[email protected]>
-Description: The goal of 'ggcoverage' is to visualize coverage tracks from
-    genomics, transcriptomics or proteomics data. It contains functions to
-    load data from BAM, BigWig, BedGraph, txt, or xlsx files, create
-    genome/protein coverage plots, and add various annotations including
-    base and amino acid composition, GC content, copy number variation
-    (CNV), genes, transcripts, ideograms, peak highlights, HiC contact
-    maps, contact links and protein features. It is based on and
-    integrates well with 'ggplot2'.
+Description: Visualize coverage tracks from genomics, transcriptomics
+    or proteomics data. The package contains functions to load data from 'BAM',
+    'BigWig', 'BedGraph', 'txt', or 'xlsx' files, create genome/protein coverage
+    plots, and add various annotations including base and amino acid
+    composition, GC content, copy number variation (CNV), genes, transcripts,
+    ideograms, peak highlights, HiC contact maps, contact links and protein
+    features. It is based on and integrates well with 'ggplot2'.
 License: MIT + file LICENSE
 URL: https://showteeth.github.io/ggcoverage/,
     https://github.com/showteeth/ggcoverage
@@ -51,6 +50,7 @@ Suggests:
     HiCBricks,
     htmltools,
     knitr,
+    openxlsx,
     rmarkdown
 VignetteBuilder: 
     knitr

README.Rmd

@@ -446,10 +446,8 @@ THe default color scheme for base annotation is `Clustal-style`, more popular co
 nuc_color <- c(
   "A" = "#ff2b08", "C" = "#009aff", "G" = "#ffb507", "T" = "#00bc0d"
 )
-opar <- graphics::par()
 
 # create plot
-graphics::par(mar = c(1, 5, 1, 1))
 graphics::image(
   seq_along(nuc_color),
   1,
@@ -468,9 +466,6 @@ graphics::mtext(
   las = 1,
   side = 2
 )
-
-# reset par default
-graphics::par(opar)
 ```
 
 Default color scheme for amino acid annotation is from [Residual colours: a proposal for aminochromography](https://pubmed.ncbi.nlm.nih.gov/9342138/):
@@ -486,7 +481,6 @@ aa_color <- c(
   " " = "#FFFFFF"
 )
 
-graphics::par(mar = c(1, 5, 1, 1))
 graphics::image(
   1:5,
   1:5,
@@ -506,9 +500,6 @@ graphics::mtext(
   las = 1,
   side = 2
 )
-
-# reset par default
-graphics::par(opar)
 ```
 
 #### Add base and amino acid annotation

README.md

@@ -626,10 +626,8 @@ popular color schemes are available
 nuc_color <- c(
   "A" = "#ff2b08", "C" = "#009aff", "G" = "#ffb507", "T" = "#00bc0d"
 )
-opar <- graphics::par()
 
 # create plot
-graphics::par(mar = c(1, 5, 1, 1))
 graphics::image(
   seq_along(nuc_color),
   1,
@@ -652,12 +650,6 @@ graphics::mtext(
 
 <img src="man/figures/README-base_color_scheme-1.png" width="100%" style="display: block; margin: auto;" />
 
-``` r
-
-# reset par default
-graphics::par(opar)
-```
-
 Default color scheme for amino acid annotation is from [Residual
 colours: a proposal for
 aminochromography](https://pubmed.ncbi.nlm.nih.gov/9342138/):
@@ -673,7 +665,6 @@ aa_color <- c(
   " " = "#FFFFFF"
 )
 
-graphics::par(mar = c(1, 5, 1, 1))
 graphics::image(
   1:5,
   1:5,
@@ -697,12 +688,6 @@ graphics::mtext(
 
 <img src="man/figures/README-aa_color_scheme-1.png" width="100%" style="display: block; margin: auto;" />
 
-``` r
-
-# reset par default
-graphics::par(opar)
-```
-
 #### Add base and amino acid annotation
 
 **Use twill to mark position with SNV**:

cran-comments.md

@@ -1,6 +1,20 @@
 # Resubmission
 
-Update for current submission: 
+This package has been submitted previously (2023, v0.7.1) and was removed
+from CRAN due to several issues, which have been addressed now.
+
+## Issues
+
+### Update for current submission:
+
+- fixed DESCRIPTION abstract, added quotation marks for package names etc
+- examples that are running >5 sec were wrapped in `/donttest{}` instead of `/dontrun{}`
+- example in `ggcoverage.Rd` does not contain out-commented code as stated by the reviewer
+- changing of graphical parameters using `par(mfrow=c(2,2))` were removed from vignette
+- however the package does not contain any `par()` statement in any of the
+  functions (supposedly `R/geom_base.R`) as stated by the reviewer
+
+### Previously fixed issues
 
 - We have substantially removed the size of test files for the examples,
 reducing overall package size from ~30 Mb to only ~6 Mb. A further reduction
@@ -13,14 +27,6 @@ on the test environment -- this package never exceeds the threshold when
 tested locally on a 3 year old average laptop, or in 3 different github actions 
 workflows, but regularly fails on the CRAN server.
 
-Background information:
-
-This package has been submitted previously (2023, v0.7.1) and was removed from
-CRAN due to several issues. In the mean time many functions were re-factored,
-more than 10 dependencies were removed to make the package lighter, and other
-problems regarding documentation and style were fixed. Current version 1.4.0
-now builds fine on the tested platforms.
-
 ## Test environments
 
 ### Local

vignettes/ggcoverage.Rmd

@@ -475,10 +475,8 @@ THe default color scheme for base annotation is `Clustal-style`, more popular co
 nuc_color <- c(
   "A" = "#ff2b08", "C" = "#009aff", "G" = "#ffb507", "T" = "#00bc0d"
 )
-opar <- graphics::par()
 
 # create plot
-graphics::par(mar = c(1, 5, 1, 1))
 graphics::image(
   seq_along(nuc_color),
   1,
@@ -497,9 +495,6 @@ graphics::mtext(
   las = 1,
   side = 2
 )
-
-# reset par default
-graphics::par(opar)
 ```
 
 Default color scheme for amino acid annotation is from [Residual colours: a proposal for aminochromography](https://pubmed.ncbi.nlm.nih.gov/9342138/):
@@ -515,7 +510,6 @@ aa_color <- c(
   " " = "#FFFFFF"
 )
 
-graphics::par(mar = c(1, 5, 1, 1))
 graphics::image(
   1:5,
   1:5,
@@ -535,9 +529,6 @@ graphics::mtext(
   las = 1,
   side = 2
 )
-
-# reset par default
-graphics::par(opar)
 ```
 
 #### Add base and amino acid annotation