fix: preparation for CRAN submission

Author: m-jahn

DESCRIPTION

@@ -1,13 +1,13 @@
 Type: Package
 Package: ggcoverage
 Title: Visualize Genome/Protein Coverage with Various Annotations
-Version: 1.3.0
+Version: 1.4.0
 Authors@R: c(
     person("Yabing", "Song", , "songyb0519@gmail.com", role = c("aut", "cre", "cph")),
     person("Michael", "Jahn", , "jahn@mpusp.mpg.de", role = c("aut", "cph"),
            comment = c(ORCID = "0000-0002-3913-153X"))
   )
-Maintainer: Yabing Song <songyb0519@gmail.com>
+Maintainer: Michael Jahn <jahn@mpusp.mpg.de>
 Description: The goal of 'ggcoverage' is to simplify the process of
     visualizing genome/protein coverage. It contains functions to load
     data from BAM, BigWig, BedGraph or txt/xlsx files, create

NEWS.md

@@ -1,3 +1,15 @@
+# ggcoverage 1.4.0
+## Major changes
+* removed 11 strict dependencies, refactored many functions to work with basic solutions
+* formatted all R code with 'styler'
+* improved arrow style for genomic features
+
+## Minor changes
+* fixed overlapping gene arrows issue
+* dont run failing ideogram example check
+* fixed unavailable URLS
+* use tidy description
+
 # ggcoverage 1.3.0
 ## Major changes
 * Refactored `LoadTrack` function.

cran-comments.md

@@ -0,0 +1,37 @@
+# Resubmission
+
+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
+
+- Ubuntu 22.04
+
+### with Github Actions
+
+- windows-latest (release)
+- macOS-latest (release)
+- ubuntu-latest (release)
+
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+There was 1 NOTE:
+
+```
+❯ checking installed package size ... NOTE
+    installed size is 31.9Mb
+    sub-directories of 1Mb or more:
+      doc       2.2Mb
+      extdata  28.6Mb
+```
+
+## Downstream dependencies
+
+- There are currently no downstream dependencies for this package

vignettes/ggcoverage.Rmd

@@ -3,9 +3,11 @@ title: >
   ggcoverage User Guide
 author: 
 - name: Yabing Song
-  affiliation: 
-  - &id1 School of Life Sciences, Tsinghua University
+  affiliation: School of Life Sciences, Tsinghua University
   email: songyb18@mails.tsinghua.edu.cn
+- name: Michael Jahn
+  affiliation: Max Planck Unit for the Science of Pathogens, Berlin
+  email: jahn@mpusp.mpg.de
 date: "`r BiocStyle::doc_date()`"
 package: "`r BiocStyle::pkg_ver('ggcoverage')`"
 abstract: >