[Bioc-devel] Vignette building fails

Morgan, Martin Martin.Morgan at roswellpark.org
Thu Jan 28 15:28:12 CET 2016

I tried to build your vignettes on my own computer, but they are taking too long. From


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.


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


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?


Jean Fan
PhD Candidate
Kharchenko Lab
Harvard University
10 Shattuck St #3, Countway 336B
Boston, MA 02115

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