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

[Andrzej Oleś]

Hi Christian, Dan,

thank you for reporting your issues with using BiocStyle. I didn't
experience such problems before, I use "`r pkg_ver('EBImage')`" in my
package vignette and both R CMD build and R CMD check pass without errors,
without the need of prepending 'BiocStyle::' to the the pkg_ver.

Are you using BiocStyle::pdf_document as output format?

Cheers,
Andrzej

On Tue, Sep 22, 2015 at 10:25 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

>
>
> ----- 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
> > 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
> >
>
> I didn't have the exact same errors as you. But I was able to fix the
> errors I did have by changing this line (line #5) in the vignette:
>
> package: "`r pkg_ver('SNPhoodData')`"
>
> to:
>
> package: "`r BiocStyle::pkg_ver('SNPhoodData')`"
>
> I'm not sure if this indicates an issue with the BiocStyle package.
>
> Let me know if that fixes it for you. Make that change and then:
>
> R CMD build SNPhoodData
> R CMD check SNPhoodData_0.99.0.tar.gz
>
> Dan
>
>
>
> >
> > Any help is appreciated, thanks,
> > Christian
> >
> >
> > --
> > —————————————————————————
> > 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
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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>

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