I am trying to check a package for compliance with Bioconductor package guidelines with BiocCheck function from BiocCheck package. I have problem with vignettes compilation so I was about to skip that part of check and I wanted to pass further arguments to this function. I was following instructions from manual of BiocCheck function where there is a sentence
...
Run usage() to see the available options. When running BiocCheck interactively, options can be passed like so: BiocCheck(package, `no-check-vignettes`=TRUE)
but I failed with such an error:
Anyone knows how to fix this?
> usage()
Usage: R CMD BiocCheck [options] package
Options:
--no-check-vignettes
disable vignette checks
--new-package
enable checks specific to new packages
--no-check-bioc-views
disable biocViews-specific checks (for non-BioC packages)
-h, --help
Show this help message and exit
When running interactively, options can be passed like so:
BiocCheck(package, `no-check-vignettes`=TRUE)
> BiocCheck(package = getwd(), `no-check-vignettes`=TRUE)
* This is BiocCheck, version 1.4.0.
* BiocCheck is a work in progress. Output and severity of issues
may change.
* Installing package...
* CONSIDER: Clarifying how objects ‘., ., ., .’ (used in
availableDates, read.mutations, read.rnaseq,
whichDateToUse) were initialized. Maybe they are part of a
data set loaded with data(), or perhaps part of an object
referenced in with() or within().
Error in dots[["no-check-vignettes"]] : subscript out of bounds
> BiocCheck(package = getwd(), "no-check-vignettes"=TRUE)
* This is BiocCheck, version 1.4.0.
* BiocCheck is a work in progress. Output and severity of issues
may change.
* Installing package...
* CONSIDER: Clarifying how objects ‘., ., ., .’ (used in
availableDates, read.mutations, read.rnaseq,
whichDateToUse) were initialized. Maybe they are part of a
data set loaded with data(), or perhaps part of an object
referenced in with() or within().
Error in dots[["no-check-vignettes"]] : subscript out of bounds
My session info is:
> session_info()
Session info -----------------------------------------------------------------------
setting value
version R version 3.2.1 (2015-06-18)
system x86_64, mingw32
ui RStudio (0.99.441)
language (EN)
collate Polish_Poland.1250
tz Europe/Warsaw
Packages ---------------------------------------------------------------------------
package * version date source
assertthat 0.1 2013-12-06 CRAN (R 3.2.1)
Biobase 2.28.0 2015-04-17 Bioconductor
BiocCheck * 1.4.0 2015-04-17 Bioconductor
BiocGenerics 0.14.0 2015-04-17 Bioconductor
BiocInstaller * 1.18.4 2015-07-22 Bioconductor
biocViews 1.36.2 2015-06-19 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.2.1)
chron 2.3-47 2015-06-24 CRAN (R 3.2.1)
codetools 0.2-14 2015-07-15 CRAN (R 3.2.1)
curl 0.9.1 2015-07-04 CRAN (R 3.2.1)
data.table * 1.9.4 2014-10-02 CRAN (R 3.2.1)
devtools * 1.8.0 2015-05-09 CRAN (R 3.2.1)
digest 0.6.8 2014-12-31 CRAN (R 3.2.1)
getopt 1.20.0 2013-08-30 CRAN (R 3.2.1)
git2r 0.10.1 2015-05-07 CRAN (R 3.2.1)
graph 1.46.0 2015-04-17 Bioconductor
htmltools 0.2.6 2014-09-08 CRAN (R 3.2.1)
httr 1.0.0 2015-06-25 CRAN (R 3.2.1)
knitr 1.10.5 2015-05-06 CRAN (R 3.2.1)
knitrBootstrap 1.0.0 2015-08-05 Github (jimhester/knitrBootstrap@cdaa4a9)
magrittr 1.5 2014-11-22 CRAN (R 3.2.1)
markdown 0.7.7 2015-04-22 CRAN (R 3.2.1)
memoise 0.2.1 2014-04-22 CRAN (R 3.2.1)
optparse 1.3.0 2014-12-11 CRAN (R 3.2.1)
plyr 1.8.3 2015-06-12 CRAN (R 3.2.1)
R6 2.1.0 2015-07-04 CRAN (R 3.2.1)
RBGL 1.44.0 2015-04-17 Bioconductor
Rcpp 0.12.0 2015-07-25 CRAN (R 3.2.1)
RCurl 1.95-4.7 2015-06-30 CRAN (R 3.2.1)
reshape2 1.4.1 2014-12-06 CRAN (R 3.2.1)
rmarkdown 0.7.3 2015-08-05 Github (rstudio/rmarkdown@88afb8d)
RTCGA * 0.99.0 2015-08-05 Bioconductor (R 3.2.1)
RUnit 0.4.28 2015-01-06 CRAN (R 3.2.1)
rversions 1.0.2 2015-07-13 CRAN (R 3.2.1)
rvest * 0.2.0 2015-01-01 CRAN (R 3.2.1)
stringi 0.5-5 2015-06-29 CRAN (R 3.2.1)
stringr 1.0.0 2015-04-30 CRAN (R 3.2.1)
XML 3.98-1.3 2015-06-30 CRAN (R 3.2.1)
xml2 0.1.1 2015-06-02 CRAN (R 3.2.1)
yaml 2.1.13 2014-06-12 CRAN (R 3.2.1)
As @Dan suggested, one should add VignetteBuilder: knitr and Suggests: knitr