[Bioc-devel] Vignette building fails

Fan, Jean jeanfan at fas.harvard.edu
Thu Jan 28 15:44:55 CET 2016

Hi Martin,

Ah, I didn’t realize the problems were connected. Yes, the vignettes do take quite a while to run. I’ll see what I can do. Thanks for the help.


> On Jan 28, 2016, at 9:28 AM, Morgan, Martin <Martin.Morgan at roswellpark.org> wrote:
> I tried to build your vignettes on my own computer, but they are taking too long. From
>  http://bioconductor.org/developers/package-guidelines/#correctness
> the time limit for checking a package (which includes running the vignette code, though not building the vignette) is 5 minutes. Do your vignettes take a lot of time to build?
> If so, you should first identify the slow portion of your code and attempt to vectorize it; ask here for help if needed.
> You should then construct examples for use in your vignette that are sufficiently realistic to shine a favorable light on the full richness of your software, but easily computed within the available time.
> Martin
> ________________________________________
> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Fan, Jean <jeanfan at fas.harvard.edu>
> Sent: Thursday, January 28, 2016 8:37 AM
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] Vignette building fails
> Hello,
> I recently updated my bioconductor package via svn. The package was built successfully on my computer via R CMD build scde and passed R CMD check scde and R CMD BiocCheck scde. But the build report on Bioconductor ran into the following errors when building the vignettes:
> * checking for file ‘scde/DESCRIPTION’ ... OK
> * preparing ‘scde’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> Loading required package: flexmix
> Loading required package: lattice
> Error: processing vignette 'diffexp.Rmd' failed with diagnostics:
> Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘diffexp’. The following files exist in directory ‘.’: ‘diffexp.R’, ‘diffexp.Rmd’, ‘diffexp.md’, ‘pagoda.Rmd’
> Execution halted
> I was able to build the vignettes locally using R CMD Sweave so I’m not sure what’s wrong. I haven’t been able to find any solutions by Googling around. Has anyone else encountered this error before?
> Thanks,
> Jean
> Jean Fan
> PhD Candidate
> Kharchenko Lab
> Harvard University
> 10 Shattuck St #3, Countway 336B
> Boston, MA 02115
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