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
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