R/safe_rcmdcheck.R
safe_rcmdcheck.Rddeal with errors at build stage when attempting to check
safe_rcmdcheck(x, error = "never", ...)character(1) path to source package folder for a package (not a tarball)
character() passed to rcmdcheck::rcmdcheck
passed to rcmdcheck::rcmdcheck, should not include 'error'
a list, see note.
If rcmdcheck succeeds without returning try-error, this function returns
the result of rcmdcheck. Otherwise it build a list with elements 'package',
'errors', 'warnings', 'notes', 'install_out', 'description' and 'version',
in which the 'errors' component includes data from capture.output on
rcmdcheck attempt.
chk = safe_rcmdcheck(system.file("demo_srcs/parody", package="BiocQE"))
str(chk)
#> List of 21
#> $ stdout : chr "* using log directory ‘/private/var/folders/n4/p9th81md60s8nv12yv40sv8m0000gp/T/RtmpvJ2ckE/file168b6029d550/par"| __truncated__
#> $ stderr : chr ""
#> $ status : int 0
#> $ duration : num 12.3
#> $ timeout : logi FALSE
#> $ rversion : chr(0)
#> $ platform : chr "aarch64-apple-darwin20.6.0"
#> $ errors : chr(0)
#> $ warnings : chr(0)
#> $ notes : chr(0)
#> $ description : chr "Package: parody\nTitle: Parametric And Resistant Outlier DYtection\nVersion: 1.49.10\nAuthors@R: \n person(g"| __truncated__
#> $ package : chr "parody"
#> $ version : chr "1.49.10"
#> $ cran : logi FALSE
#> $ bioc : logi TRUE
#> $ checkdir : chr "/private/var/folders/n4/p9th81md60s8nv12yv40sv8m0000gp/T/RtmpvJ2ckE/file168b6029d550/parody.Rcheck"
#> $ test_fail : Named list()
#> $ test_output :List of 1
#> ..$ test: chr "> library(parody)\nLoading required package: tools\n> library(testthat)\n> \n> test_check(\"parody\")\n[ FAIL 0"| __truncated__
#> $ install_out : chr "* installing *source* package ‘parody’ ...\n** using staged installation\n** R\n** data\n** inst\n** byte-compi"| __truncated__
#> $ session_info:List of 2
#> ..$ platform:List of 10
#> .. ..$ version : chr "R Under development (unstable) (2021-11-10 r81171)"
#> .. ..$ os : chr "macOS Monterey 12.1"
#> .. ..$ system : chr "aarch64, darwin20.6.0"
#> .. ..$ ui : chr "X11"
#> .. ..$ language: chr "en"
#> .. ..$ collate : chr "C"
#> .. ..$ ctype : chr "en_US.UTF-8"
#> .. ..$ tz : chr "America/New_York"
#> .. ..$ date : chr "2021-12-29"
#> .. ..$ pandoc : chr "2.13 @ /usr/local/bin/pandoc"
#> .. ..- attr(*, "class")= chr [1:2] "platform_info" "list"
#> ..$ packages:Classes ‘packages_info’ and 'data.frame': 1 obs. of 11 variables:
#> .. ..$ package : chr "parody"
#> .. ..$ ondiskversion: chr "1.49.10"
#> .. ..$ loadedversion: chr NA
#> .. ..$ path : chr "/private/var/folders/n4/p9th81md60s8nv12yv40sv8m0000gp/T/RtmpvJ2ckE/file168b6029d550/parody.Rcheck/parody"
#> .. ..$ loadedpath : chr NA
#> .. ..$ attached : logi FALSE
#> .. ..$ is_base : logi FALSE
#> .. ..$ date : chr "2021-12-29"
#> .. ..$ source : chr "Bioconductor"
#> .. ..$ md5ok : logi NA
#> .. ..$ library : Factor w/ 3 levels "/private/var/folders/n4/p9th81md60s8nv12yv40sv8m0000gp/T/RtmpvJ2ckE/file168b6029d550/parody.Rcheck",..: 1
#> ..- attr(*, "class")= chr [1:2] "session_info" "list"
#> $ cleaner :<environment: 0x11a85a058>
#> - attr(*, "class")= chr "rcmdcheck"