Parse R and R package versions from session informations

Source: R/parsePkgVersions.R

The function parses the R version and R package versions from session information (created by sessionInfo(), tested with R 3.6) in files provided in infiles. Two types of files are currently supported:

Rout:

Files containing R console output (created by R CMD BATCH script.R output.Rout

md:

Files containing markdown output created by rmarkdown::render('input.Rmd', clean = FALSE), which will keep the intermediate .md file.

parsePkgVersions(infiles)

Arguments

infiles

Character vector with text files (extension must be either .Rout or .md), containing session information to parse out.

Value

A list of lists with one element in the outer list for each R version, contianing an innter list with elements files and packages.

Author

Michael Stadler

Examples

f <- list.files(system.file("extdata", "parsePkgVersions",
                            package = "swissknife"),
                full.names = TRUE)
parsePkgVersions(f)
#> $`R version 3.6.0 (2019-04-26)`
#> $`R version 3.6.0 (2019-04-26)`$files
#> [1] "/home/runner/work/_temp/Library/swissknife/extdata/parsePkgVersions/example.md"
#> 
#> $`R version 3.6.0 (2019-04-26)`$packages
#>  [1] "Biobase_2.44.0"              "BiocGenerics_0.30.0"        
#>  [3] "BiocParallel_1.18.0"         "DelayedArray_0.10.0"        
#>  [5] "DropletUtils_1.4.2"          "GenomeInfoDb_1.20.0"        
#>  [7] "GenomicRanges_1.36.0"        "IRanges_2.18.1"             
#>  [9] "RColorBrewer_1.1-2"          "S4Vectors_0.22.0"           
#> [11] "SingleCellExperiment_1.6.0"  "SummarizedExperiment_1.14.0"
#> [13] "dplyr_0.8.3"                 "ggplot2_3.2.0"              
#> [15] "matrixStats_0.54.0"          "scater_1.12.2"              
#> [17] "scran_1.12.1"                "sctransform_0.2.0"          
#> [19] "stringr_1.4.0"               "swissknife_0.12"            
#> [21] "tibble_2.1.3"                "tidyr_0.8.3"                
#> [23] "umap_0.2.2.0"               
#> 
#> 
#> $`R version 3.6.1 (2019-07-05)`
#> $`R version 3.6.1 (2019-07-05)`$files
#> [1] "/home/runner/work/_temp/Library/swissknife/extdata/parsePkgVersions/example.Rout"
#> 
#> $`R version 3.6.1 (2019-07-05)`$packages
#>  [1] "Biobase_2.44.0"              "BiocGenerics_0.30.0"        
#>  [3] "BiocParallel_1.18.1"         "DelayedArray_0.10.0"        
#>  [5] "GenomeInfoDb_1.20.0"         "GenomicRanges_1.36.1"       
#>  [7] "IRanges_2.18.3"              "Matrix_1.2-17"              
#>  [9] "RColorBrewer_1.1-2"          "S4Vectors_0.22.1"           
#> [11] "SingleCellExperiment_1.6.0"  "SummarizedExperiment_1.14.1"
#> [13] "dplyr_0.8.3"                 "matrixStats_0.55.0"         
#> [15] "tibble_2.1.3"                "tidyr_1.0.0"                
#> [17] "velocyto.R_0.6"             
#> 
#>