[Bioc-devel] Issues with R CMD check and an ExperimentalData package

Christian Arnold christian.arnold at embl.de
Tue Sep 22 22:03:59 CEST 2015

Hi all,

I am sorry for writing again, but I didn't find anything in the internet 
and I hope someone can help me here.

Maybe I am doing something stupid, but I am having troubles running R 
CMD check for an ExperimentalData package (biocViews: ExperimentData). 
it has no actual code, only a few files in inst/extdata. And one 
vignette located in "vignettes" (Rmd, knitr)

  I receive the following warnings:
1. * checking for unstated dependencies in examples ... WARNING
no parsed files found
2. * checking re-building of vignette outputs ...Warning in 
file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
3 . * checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
4. * checking PDF version of manual without hyperrefs or index ... ERROR

Probably, 3 and 4 are just consequences of 2, but I don't understand 2 
in particular. The vignette is very short, and compiles fine in RStudio.
How do I fix this, what is wrong? How do I fix 1?

R CMD BiocCheck --new-package runs without errors(required), only a 
recommendation to remove vignette sources from inst/doc

Any help is appreciated, thanks,

Christian Arnold, PhD
Staff Bioinformatician

SCB Unit - Computational Biology
Joint appointment Genome Biology
Joint appointment European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory (EMBL)
Meyerhofstrasse 1; 69117, Heidelberg, Germany

Email: christian.arnold at embl.de
Phone: +49(0)6221-387-8472
Web: http://www.zaugg.embl.de/

More information about the Bioc-devel mailing list