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

Yu Sun sunyu1357 at gmail.com
Wed Jan 27 15:20:06 CET 2016


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]]

More information about the Bioc-devel mailing list