[Bioc-devel] Vignette building fails

Fan, Jean jeanfan at fas.harvard.edu
Thu Jan 28 14:37:13 CET 2016


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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