Check R package — checkPackage • gDRstyle

Used in gDR platform pacakges' CI/CD pipelines to 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.

Usage

checkPackage(
  pkgName,
  repoDir,
  subdir = NULL,
  fail_on = "warning",
  bioc_check = FALSE,
  run_examples = TRUE,
  skip_lint = FALSE,
  skip_tests = FALSE,
  build_vignettes = TRUE,
  check_vignettes = TRUE,
  as_cran = FALSE
)

Arguments

pkgName: String of package name.
repoDir: String of path to repository directory.
subdir: String of relative path to the R package root directory from the repoDir.
fail_on: String specifying the level at which check fail. Supported values: "note", "warning" (default) and "error".
bioc_check: Logical whether bioc check should be performed
run_examples: Logical whether examples check should be performed
skip_lint: skip lint checks
skip_tests: skip tests
build_vignettes: build vignettes
check_vignettes: check vignettes
as_cran: run with as_cran flag

Value

NULL invisibly.

Examples

checkPackage(
  pkgName = "fakePkg",
  repoDir = system.file(package = "gDRstyle", "tst_pkgs", "dummy_pkg"),
  fail_on = "error"
)
#> Lint
#> ##------ Wed Nov  6 07:46:05 2024 ------##
#> Linting file: /usr/local/lib/R/site-library/gDRstyle/tst_pkgs/dummy_pkg/R/test.R
#> Linting file: /usr/local/lib/R/site-library/gDRstyle/tst_pkgs/dummy_pkg/tests/testthat.R
#> Linting file: /usr/local/lib/R/site-library/gDRstyle/tst_pkgs/dummy_pkg/tests/testthat/test-pkg.R
#> All files OK!
#> Tests
#> ##------ Wed Nov  6 07:46:05 2024 ------##
#> ✔ | F W  S  OK | Context
#> 
#> ⠏ |          0 | pkg                                                            
#> ✔ |          1 | pkg
#> 
#> ══ Results ═════════════════════════════════════════════════════════════════════
#> [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
#> 
#> Way to go!
#> Check
#> ##------ Wed Nov  6 07:46:06 2024 ------##
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> pdflatex not found! Not building PDF manual.
#> * checking for file ‘.../DESCRIPTION’ ... OK
#> * preparing ‘fakePkg’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘fakePkg_1.0.tar.gz’
#> 
#> ── R CMD check ─────────────────────────────────────────────────────────────────
#> * using log directory ‘/tmp/RtmpD0Ow68/file17b81331f/fakePkg.Rcheck’
#> * using R version 4.3.0 (2023-04-21)
#> * using platform: x86_64-pc-linux-gnu (64-bit)
#> * R was compiled by
#>     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
#>     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
#> * running under: Ubuntu 22.04.3 LTS
#> * using session charset: UTF-8
#> * using options ‘--no-tests --no-manual’
#> * checking for file ‘fakePkg/DESCRIPTION’ ... OK
#> * checking extension type ... Package
#> * this is package ‘fakePkg’ version ‘1.0’
#> * checking package namespace information ... OK
#> * checking package dependencies ... OK
#> * checking if this is a source package ... OK
#> * checking if there is a namespace ... OK
#> * checking for executable files ... OK
#> * checking for hidden files and directories ... OK
#> * checking for portable file names ... OK
#> * checking for sufficient/correct file permissions ... OK
#> * checking whether package ‘fakePkg’ can be installed ... OK
#> * checking installed package size ... OK
#> * checking package directory ... OK
#> * checking DESCRIPTION meta-information ... NOTE
#> Malformed Description field: should contain one or more complete sentences.
#> Non-standard license specification:
#>   What license is it under?
#> Standardizable: FALSE
#> * checking top-level files ... OK
#> * checking for left-over files ... OK
#> * checking index information ... OK
#> * checking package subdirectories ... OK
#> * checking R files for non-ASCII characters ... OK
#> * checking R files for syntax errors ... OK
#> * checking whether the package can be loaded ... OK
#> * checking whether the package can be loaded with stated dependencies ... OK
#> * checking whether the package can be unloaded cleanly ... OK
#> * checking whether the namespace can be loaded with stated dependencies ... OK
#> * checking whether the namespace can be unloaded cleanly ... OK
#> * checking loading without being on the library search path ... OK
#> * checking dependencies in R code ... OK
#> * checking S3 generic/method consistency ... OK
#> * checking replacement functions ... OK
#> * checking foreign function calls ... OK
#> * checking R code for possible problems ... OK
#> * checking Rd files ... OK
#> * checking Rd metadata ... OK
#> * checking Rd cross-references ... OK
#> * checking for missing documentation entries ... OK
#> * checking for code/documentation mismatches ... OK
#> * checking Rd \usage sections ... OK
#> * checking Rd contents ... OK
#> * checking for unstated dependencies in examples ... OK
#> * checking examples ... NONE
#> * checking for unstated dependencies in ‘tests’ ... OK
#> * checking tests ... SKIPPED
#> * DONE
#> 
#> Status: 1 NOTE
#> See
#>   ‘/tmp/RtmpD0Ow68/file17b81331f/fakePkg.Rcheck/00check.log’
#> for details.
#> Deps
#> ##------ Wed Nov  6 07:46:16 2024 ------##
#> Finished
#> ##------ Wed Nov  6 07:46:16 2024 ------##