fix: attempt to fix various R CMD CHECK errors

.github/workflows/R-CMD-check.yaml

@@ -21,9 +21,7 @@ jobs:
         config:
           - {os: macos-latest, r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest, r: 'release'}
-          - {os: ubuntu-latest, r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

README.Rmd

@@ -10,7 +10,8 @@ knitr::opts_chunk$set(
   comment = "#>",
   fig.path = "man/figures/README-",
   out.width = "100%",
-  dpi = 60
+  dpi = 60,
+  crop = NULL
 )
 ```
 

vignettes/ggcoverage.Rmd

@@ -26,14 +26,12 @@ BiocStyle::markdown()
 ```
 
 ```{r setup, echo=FALSE, warning=FALSE}
-library(knitr)
-htmltools::tagList(rmarkdown::html_dependency_font_awesome())
-
-# set dpi
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
-  dpi = 60
+  dpi = 60,
+  fig.path = "png/",
+  crop = NULL
 )
 ```
 
@@ -256,18 +254,26 @@ basic_coverage +
 
 ### Add ideogram
 
-```{r ideogram_coverage_1, warning=FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+```{r ideogram_coverage_1, eval = FALSE}
 basic_coverage +
   geom_gene(gtf.gr = gtf_gr) +
   geom_ideogram(genome = "hg19", plot.space = 0)
 ```
 
-```{r ideogram_coverage_2, warning=FALSE, fig.height = 14, fig.width = 12, fig.align = "center"}
+```{r ideogram_coverage_1_plot, echo = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-ideogram_coverage_1-1.png")
+```
+
+```{r ideogram_coverage_2, eval = FALSE}
 basic_coverage +
   geom_transcript(gtf.gr = gtf_gr, label.vjust = 1.5) +
   geom_ideogram(genome = "hg19", plot.space = 0)
 ```
 
+```{r ideogram_coverage_2_plot, echo = FALSE, fig.height = 14, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-ideogram_coverage_2-1.png")
+```
+
 ## DNA-seq data
 
 ### CNV
@@ -311,14 +317,15 @@ basic_coverage <- ggcoverage(
   mark.region = NULL,
   range.position = "out"
 )
+
 basic_coverage
 ```
 
 ##### Add GC annotations
 
 Add **GC**, **ideogram** and **gene** annotaions.
 
-```{r gc_coverage, warning=FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+```{r gc_coverage, eval = FALSE}
 # load genome data
 library("BSgenome.Hsapiens.UCSC.hg19")
 
@@ -329,6 +336,11 @@ basic_coverage +
   geom_ideogram(genome = "hg19")
 ```
 
+
+```{r gc_coverage_plot, echo = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-gc_coverage-1.png")
+```
+
 #### Example 2
 
 ##### Load the data
@@ -384,7 +396,7 @@ head(cnv_df)
 
 Add **GC**, **ideogram** and **CNV** annotations.
 
-```{r cnv_gc_coverage}
+```{r cnv_gc_coverage, eval=FALSE}
 # create plot
 basic_coverage +
   geom_gc(bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19) +
@@ -398,6 +410,10 @@ basic_coverage +
   )
 ```
 
+```{r cnv_gc_coverage_plot, echo = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-cnv_gc_coverage-1.png")
+```
+
 
 ### Single-nucleotide level
 
@@ -506,13 +522,7 @@ graphics::par(opar)
 
 **Use twill to mark position with SNV**:
 
-```{r, echo = FALSE}
-# wait some time to avoid 'Too Many Requests' error
-Sys.sleep(60)
-```
-
-
-```{r base_aa_coverage, warning=FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+```{r base_aa_coverage, eval =FALSE}
 # create plot with twill mark
 ggcoverage(
   data = track_df,
@@ -527,14 +537,14 @@ ggcoverage(
   geom_ideogram(genome = "hg19", plot.space = 0)
 ```
 
-**Use star to mark position with SNV**:
 
-```{r, echo = FALSE}
-# wait some time to avoid 'Too Many Requests' error
-Sys.sleep(60)
+```{r base_aa_coverage_plot, echo = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-base_aa_coverage-1.png")
 ```
 
-```{r base_aa_coverage_star, warning=FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+**Use star to mark position with SNV**:
+
+```{r base_aa_coverage_star, eval = FALSE}
 # create plot with star mark
 ggcoverage(
   data = track_df,
@@ -549,14 +559,14 @@ ggcoverage(
   geom_ideogram(genome = "hg19", plot.space = 0)
 ```
 
-**Highlight position with SNV**:
 
-```{r, echo = FALSE}
-# wait some time to avoid 'Too Many Requests' error
-Sys.sleep(60)
+```{r base_aa_coverage_star_plot, echo = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-base_aa_coverage_star-1.png")
 ```
 
-```{r base_aa_coverage_highlight, warning=FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+**Highlight position with SNV**:
+
+```{r base_aa_coverage_highlight, eval = FALSE}
 # highlight one base
 ggcoverage(
   data = track_df,
@@ -571,6 +581,11 @@ ggcoverage(
   geom_ideogram(genome = "hg19", plot.space = 0)
 ```
 
+
+```{r base_aa_coverage_highlight_plot, echo = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-base_aa_coverage_highlight-1.png")
+```
+
 ## ChIP-seq data
 
 The ChIP-seq data used here are from [DiffBind](https://bioconductor.org/packages/release/bioc/html/DiffBind.html), I select four sample to use as example: Chr18_MCF7_input, Chr18_MCF7_ER_1, Chr18_MCF7_ER_3, Chr18_MCF7_ER_2, and all bam files are converted to bigwig file with [deeptools](https://deeptools.readthedocs.io/en/develop/).
@@ -638,12 +653,7 @@ basic_coverage
 
 Add **gene**, **ideogram** and **peak** annotations. To create peak annotation, we first **get consensus peaks** with [MSPC](https://github.com/Genometric/MSPC).
 
-```{r, echo = FALSE}
-# wait some time to avoid 'Too Many Requests' error
-Sys.sleep(60)
-```
-
-```{r peak_coverage, warning=FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+```{r peak_coverage, eval = FALSE}
 # get consensus peak file
 peak_file <- system.file("extdata",
                          "ChIP-seq",
@@ -656,6 +666,10 @@ basic_coverage +
   geom_ideogram(genome = "hg19", plot.space = 0)
 ```
 
+```{r peak_coverage_plot, echo = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-peak_coverage-1.png")
+```
+
 ## Hi-C data
 
 The Hi-C data are from [pyGenomeTracks: reproducible plots for multivariate genomic datasets](https://academic.oup.com/bioinformatics/article/37/3/422/5879987?login=false).
@@ -739,7 +753,7 @@ basic_coverage
 
 Add **link**, **contact map**annotations:
 
-```{r hic_coverage, warning=FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+```{r hic_coverage, eval = FALSE}
 basic_coverage +
   geom_tad(
     matrix = hic_mat,
@@ -755,6 +769,10 @@ basic_coverage +
             show.rect = TRUE)
 ```
 
+```{r hic_coverage_plot, echo = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-hic_coverage-1.png")
+```
+
 ## Mass spectrometry protein coverage
 
 [Mass spectrometry (MS) is an important method for the accurate mass determination and characterization of proteins, and a variety of methods and instrumentations have been developed for its many uses](https://en.wikipedia.org/wiki/Protein_mass_spectrometry). After MS, we can check the coverage of protein to check the quality of the data and find the reason why the segment did not appear and improve the experiment.
@@ -790,7 +808,7 @@ protein_set
 
 ### Protein coverage
 
-```{r basic_coverage_protein, warning=FALSE, fig.height = 6, fig.width = 12, fig.align = "center"}
+```{r basic_coverage_protein, eval = FALSE}
 protein_coverage <- ggprotein(
   coverage.file = coverage_file,
   fasta.file = fasta_file,
@@ -801,11 +819,15 @@ protein_coverage <- ggprotein(
 protein_coverage
 ```
 
+```{r basic_coverage_protein_plot, echo = FALSE, fig.height = 6, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-basic_coverage_protein-1.png")
+```
+
 ### Add annotation
 
 We can obtain features of the protein from [UniProt](https://www.uniprot.org/). For example, the above protein coverage plot shows that there is empty region in 1-24, and this empty region in [UniProt](https://www.uniprot.org/uniprotkb/P02769/entry) is annotated as Signal peptide and Propeptide peptide. When the protein is mature and released extracellular, these peptides will be cleaved. This is the reason why there is empty region in 1-24.
 
-```{r basic_coverage_protein_feature, warning=FALSE, fig.height = 6, fig.width = 12, fig.align = "center"}
+```{r basic_coverage_protein_feature, eval = FALSE}
 # protein feature obtained from UniProt
 protein_feature_df <- data.frame(
   ProteinID = "sp|P02769|ALBU_BOVIN",
@@ -820,6 +842,10 @@ protein_coverage +
                feature.color = c("#4d81be", "#173b5e", "#6a521d"))
 ```
 
+```{r basic_coverage_protein_feature_plot, echo = FALSE, fig.height = 6, fig.width = 12, fig.align = "center"}
+knitr::include_graphics("../man/figures/README-basic_coverage_protein_feature-1.png")
+```
+
 ## Code of Conduct
 
 Please note that the `ggcoverage` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.