1 Overview

The gDRstyle package is intended to be used during development of packages within the gDR platform. It has 3 primary uses: (1)to set a style guide with functions that check that the style is upheld, (2) during CI to ensure code passes R CMD check to maintain the state of the code in high quality, and (3) for package dependency installation during gDR platform image building.

2 Use Cases

2.1 Style guide

See the written Style guide. The function lintPkgDirs can be used to ensure the package is appropriately linted.

2.2 CI/CD

The checkPackage function will check that the package abides by gDRstyle stylistic requirements, passes rcmdcheck, and ensures that the dependencies.yml file used to build gDR platform’s docker image is kept up-to-date with the dependencies listed in the package’s DESCRIPTION file. This is called in gDR platform packages’ CI/CD.

2.3 Package installation

The function installAllDeps assists in installing package dependencies. For example, it’s used in gdrplatform packages (see e.g. link).

SessionInfo

sessionInfo()
## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] gDRstyle_1.5.0   BiocStyle_2.35.0
## 
## loaded via a namespace (and not attached):
##  [1] jsonlite_1.8.9      compiler_4.5.0      BiocManager_1.30.25
##  [4] crayon_1.5.3        xml2_1.3.6          callr_3.7.6        
##  [7] jquerylib_0.1.4     yaml_2.3.10         fastmap_1.2.0      
## [10] R6_2.5.1            knitr_1.48          backports_1.5.0    
## [13] tibble_3.2.1        lintr_3.1.2         bookdown_0.41      
## [16] desc_1.4.3          cyclocomp_1.1.1     bslib_0.8.0        
## [19] pillar_1.9.0        rlang_1.1.4         utf8_1.2.4         
## [22] cachem_1.1.0        xfun_0.48           sass_0.4.9         
## [25] lazyeval_0.2.2      rex_1.2.1           cli_3.6.3          
## [28] withr_3.0.2         magrittr_2.0.3      ps_1.8.1           
## [31] digest_0.6.37       processx_3.8.4      remotes_2.5.0      
## [34] lifecycle_1.0.4     vctrs_0.6.5         data.table_1.16.2  
## [37] evaluate_1.0.1      glue_1.8.0          fansi_1.0.6        
## [40] rmarkdown_2.28      pkgconfig_2.0.3     tools_4.5.0        
## [43] htmltools_0.5.8.1