[Bioc-devel] cTRAP: WARNINGS in package submission

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Tue Oct 9 17:05:53 CEST 2018

I'm sure your reviewer could offer additional advice as well, but first thought is are you downloading the data each time the package is run or each time a vignette or example is run?  Perhaps caching the file using  BiocFileCache would save some additional time (or be costly the first run but then be expedited on future runs)  See https://bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#cache-to-manage-package-data

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Nuno Agostinho <nunodanielagostinho using gmail.com>
Sent: Tuesday, October 9, 2018 10:51:56 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] cTRAP: WARNINGS in package submission

Dear all,

I am the developer of cTRAP <https://github.com/nuno-agostinho/cTRAP>, a package that I recently submitted for approval to Bioconductor: https://github.com/Bioconductor/Contributions/issues/906 <https://github.com/Bioconductor/Contributions/issues/906>.

The package makes use of ENCODE and L1000 datasets downloaded from the web and the examples for such functions include downloading some sample files. However, this makes R CMD check take more than 5 minutes and labels my package with WARNING. Should I simply mark the examples of "slow" functions with \dontrun? I do not think that is the optimal approach, but it is certainly the easiest solution to pass the 5 minute requirement of R CMD check.

Thank you for your time!

Best regards,
Nuno Agostinho
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