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

Ge Tan ge_tan at live.com
Wed Jan 27 15:26:25 CET 2016

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 on behalf of 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
>> biocLite()
>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
>	[[alternative HTML version deleted]]
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