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

[Yu Sun]

Thanks Jean! You solved my problem :)
Yu

On Wed, Jan 27, 2016 at 3:35 PM, Fan, Jean <jeanfan at fas.harvard.edu> wrote:

> 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
>
> Best,
> Jean
>
> Jean Fan
> PhD Candidate
> NSF GRFP
> 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> wrote:
>
> The error message explains the reason. Just install pandoc and
> pandoc-citeproc.
>
> Ge
>
>
>
>
> 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:
>
> Hi,
>
> 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
> command
>
> source("https://bioconductor.org/biocLite.R")
>
> 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!
>
> Best
> Yu
>
>
> --
> Yu Sun
> Department of Cell and Molecular Biology
> BMC, Uppsala University
> Sweden
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>


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

	[[alternative HTML version deleted]]