GitHub - r-lib/rcmdcheck: Run R CMD check from R and collect the results (original) (raw)

Run R CMD check from R and Capture Results

• rcmdcheck
  • Installation
  • Usage

rcmdcheck

Run R CMD check from R and Capture Results

Run R CMD check from R programmatically and capture the results of the individual checks.

Installation

Install the released version from CRAN

install.packages("rcmdcheck")

Or install the development version from GitHub:

install.packages("pak")

pak::pak("r-lib/rcmdcheck")

Usage

library(rcmdcheck) rcmdcheck("path/to/R/package")

Call rcmdcheck() on a source R package .tar.gz file, or on a folder containing your R package. Supply quiet = FALSE if you want to omit the output. The result of the check is returned, in a list with elementserrors, warnings, and notes. Each element is a character vector, and one element of the character vectors is a single failure.

Programmatic usage

rcmdcheck() returns an rcmdcheck object, which you can query and manipulate.

library(rcmdcheck) chk <- rcmdcheck("tests/testthat/bad1", quiet = TRUE) chk #> ── R CMD check results ─────────────────────────────────── badpackage 1.0.0 ──── #> Duration: 12.5s #> #> ❯ checking DESCRIPTION meta-information ... WARNING #> Non-standard license specification: #> Public domain #> Standardizable: FALSE #> #> 0 errors ✔ | 1 warning ✖ | 0 notes ✔

check_details() turns the check results into a simple lists with the following information currently:

names(check_details(chk)) #> [1] "package" "version" "notes" "warnings" "errors"
#> [6] "platform" "checkdir" "install_out" "description" "session_info" #> [11] "cran" "bioc"

• package: Package name.
• version: Package version number.
• notes: Character vector of check NOTEs.
• warnings: Character vector of check WARNINGs.
• errors: Character vector of check ERRORs.
• platform: Platform, e.g. x86_64-apple-darwin15.6.0.
• checkdir: Check directory.
• install_out: Output of the package installation.
• description: The text of the DESCRIPTION file.
• session_info: A sessioninfo::session_info object, session information from within the check process.
• cran: Flag, whether this is a CRAN package. (Based on theRepository field in DESCRIPTION, which is typically only set for published CRAN packages.)
• bioc: Flag, whether this is a Bioconductor package, based on the presence of the biocViews field in DESCRIPTION.

Note that if the check results were parsed from a file, some of these fields might be missing (NULL), as we don’t have access to the original DESCRIPTION, the installation output, etc.

Parsing check output

parse_check() parses check output from a file, parse_check_url()parses check output from a URL.

CRAN checks

rcmdcheck has a functions to access CRAN’s package check results.

cran_check_flavours() downloads the names of the CRAN platforms:

cran_check_flavours() #> [1] "r-devel-linux-x86_64-debian-clang" "r-devel-linux-x86_64-debian-gcc"
#> [3] "r-devel-linux-x86_64-fedora-clang" "r-devel-linux-x86_64-fedora-gcc"
#> [5] "r-devel-windows-x86_64" "r-patched-linux-x86_64"
#> [7] "r-release-linux-x86_64" "r-release-macos-arm64"
#> [9] "r-release-macos-x86_64" "r-release-windows-x86_64"
#> [11] "r-oldrel-macos-arm64" "r-oldrel-macos-x86_64"
#> [13] "r-oldrel-windows-x86_64"

cran_check_results() loads and parses all check results for a package.

cran_check_results("igraph") #> $r-devel-linux-x86_64-debian-clang #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File ‘igraph/libs/igraph.so’: #> Found non-API call to R: ‘Rf_allocSExp’ #>
#> Compiled code should not call non-API entry points in R. #>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, #> and section ‘Moving into C API compliance’ for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-devel-linux-x86_64-debian-gcc #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File ‘igraph/libs/igraph.so’: #> Found non-API call to R: ‘Rf_allocSExp’ #>
#> Compiled code should not call non-API entry points in R. #>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, #> and section ‘Moving into C API compliance’ for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-devel-linux-x86_64-fedora-clang #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File ‘igraph/libs/igraph.so’: #> Found non-API call to R: ‘Rf_allocSExp’ #>
#> Compiled code should not call non-API entry points in R. #>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, #> and section ‘Moving into C API compliance’ for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-devel-linux-x86_64-fedora-gcc #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File ‘igraph/libs/igraph.so’: #> Found non-API call to R: ‘Rf_allocSExp’ #>
#> Compiled code should not call non-API entry points in R. #>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, #> and section ‘Moving into C API compliance’ for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-devel-windows-x86_64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File 'igraph/libs/x64/igraph.dll': #> Found non-API call to R: 'Rf_allocSExp' #>
#> Compiled code should not call non-API entry points in R. #>
#> See 'Writing portable packages' in the 'Writing R Extensions' manual, #> and section 'Moving into C API compliance' for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-patched-linux-x86_64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File ‘igraph/libs/igraph.so’: #> Found non-API call to R: ‘Rf_allocSExp’ #>
#> Compiled code should not call non-API entry points in R. #>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, #> and section ‘Moving into C API compliance’ for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-release-linux-x86_64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File ‘igraph/libs/igraph.so’: #> Found non-API call to R: ‘Rf_allocSExp’ #>
#> Compiled code should not call non-API entry points in R. #>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, #> and section ‘Moving into C API compliance’ for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-release-macos-arm64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File ‘igraph/libs/igraph.so’: #> Found non-API call to R: ‘Rf_allocSExp’ #>
#> Compiled code should not call non-API entry points in R. #>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, #> and section ‘Moving into C API compliance’ for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-release-macos-x86_64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File ‘igraph/libs/igraph.so’: #> Found non-API call to R: ‘Rf_allocSExp’ #>
#> Compiled code should not call non-API entry points in R. #>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, #> and section ‘Moving into C API compliance’ for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-release-windows-x86_64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking compiled code ... NOTE #> File 'igraph/libs/x64/igraph.dll': #> Found non-API call to R: 'Rf_allocSExp' #>
#> Compiled code should not call non-API entry points in R. #>
#> See 'Writing portable packages' in the 'Writing R Extensions' manual, #> and section 'Moving into C API compliance' for issues with the use of #> non-API entry points. #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-oldrel-macos-arm64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking installed package size ... NOTE #> installed size is 23.8Mb #> sub-directories of 1Mb or more: #> R 2.1Mb #> doc 1.2Mb #> help 2.9Mb #> libs 17.1Mb #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-oldrel-macos-x86_64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking installed package size ... NOTE #> installed size is 23.6Mb #> sub-directories of 1Mb or more: #> R 1.3Mb #> doc 1.2Mb #> help 2.0Mb #> libs 18.7Mb #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> $r-oldrel-windows-x86_64 #> ── R CMD check results ─────────────────────────────────────── igraph 2.1.4 ──── #> Duration: 0ms #> #> ❯ checking installed package size ... NOTE #> installed size is 10.7Mb #> sub-directories of 1Mb or more: #> R 1.3Mb #> doc 1.2Mb #> help 2.1Mb #> libs 5.7Mb #> #> 0 errors ✔ | 0 warnings ✔ | 1 note ✖ #> #> attr(,"package") #> [1] "igraph" #> attr(,"class") #> [1] "rmcdcheck_cran_results"

Comparing checks

compare_checks() can compare two or more rcmdcheck objects.compare_to_cran() compares an rcmdcheck object to the CRAN checks of the same package:

chk <- rcmdcheck(quiet = TRUE) compare_to_cran(chk) #> ── R CMD check comparison ──────────────────── rcmdcheck 1.4.0 / 1.4.0.9000 ──── #> Status: OK

Background processes

rcmdcheck_process is a processx::process class, that can runR CMD check in the background. You can also use this to run multiple checks concurrently. processx::process methods can be used to poll or manipulate the check processes.

chkpx <- rcmdcheck_process$new() chkpx #> PROCESS 'R', running, pid 74156.

chkpx$wait() chkpx$parse_results() #> ── R CMD check results ─────────────────────────────── rcmdcheck 1.4.0.9000 ──── #> Duration: 19.5s #> #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔