[Bioc-devel] Issues with R CMD check and an ExperimentalData package
dtenenba at fredhutch.org
Tue Sep 22 22:06:02 CEST 2015
----- Original Message -----
> From: "Christian Arnold" <christian.arnold at embl.de>
> To: bioc-devel at r-project.org
> Sent: Tuesday, September 22, 2015 1:03:59 PM
> Subject: [Bioc-devel] Issues with R CMD check and an ExperimentalData package
> Hi all,
> I am sorry for writing again, but I didn't find anything in the
> 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:
> 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
> 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 ...
> Probably, 3 and 4 are just consequences of 2, but I don't understand
> in particular. The vignette is very short, and compiles fine in
> 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
Can you post a link to the package, either to the list or just to me offline?
> 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/
> Bioc-devel at r-project.org mailing list
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