[Bioc-devel] fail to build a package after updating Bioconductor packages

Fan, Jean jeanfan at fas.harvard.edu
Wed Jan 27 15:35:42 CET 2016

Hi Yu,

It looks like you’re using R Markdown v2 instead of R Markdown v1 so you will have to change your vignette engine.
Your vignette likely contains %\VignetteEngine{knitr::knitr}
You will need to change this to %\VignetteEngine{knitr::rmarkdown}
And you will need to add both knitr and rmarkdown to your DESCRIPTION Suggestions if they are not present already


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

On Jan 27, 2016, at 9:26 AM, Ge Tan <ge_tan at live.com<mailto:ge_tan at live.com>> wrote:

The error message explains the reason. Just install pandoc and pandoc-citeproc.


On 27/01/2016, 14:20, "Bioc-devel on behalf of Yu Sun" <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org> on behalf of sunyu1357 at gmail.com<mailto:sunyu1357 at gmail.com>> wrote:


I am very new in developing bioconductor packages, and had an annoying
problem yesterday afternoon. I wrote a package named sscu and it used to
have no problem to build a tarball, and I plan to submit it to Bioconductor
very soon. But yesterday after I updated my bioconductor packages using the


I got errors when building my package

yu at molev32-23:~/r_packages> R CMD build sscu
* checking for file ‘sscu/DESCRIPTION’ ... OK
* preparing ‘sscu’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... ERROR
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
 Pandoc (>= 1.12.3) and/or pandoc-citeproc is not available. Please
install both.
Warning in readLines(con) : incomplete final line found on 'sscu.Rmd'
Error: processing vignette 'sscu.Rmd' failed with diagnostics:
It seems you should call rmarkdown::render() instead of knitr::knit2html()
because sscu.Rmd appears to be an R Markdown v2 document.
Execution halted

Is there someone can explain what is the problem here? Thanks!


Yu Sun
Department of Cell and Molecular Biology
BMC, Uppsala University

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