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[Bioc-devel] Vignette building fails

6 messages · Martin Morgan, Fan, Jean, Paul Grosu +2 more

Original
Fan, Jean
# 
Hello,

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?

Thanks,
Jean

Jean Fan
PhD Candidate
NSF GRFP
Kharchenko Lab
Harvard University
10 Shattuck St #3, Countway 336B
Boston, MA 02115
Martin Morgan
# 
I tried to build your vignettes on my own computer, but they are taking too long. From

  http://bioconductor.org/developers/package-guidelines/#correctness

the time limit for checking a package (which includes running the vignette code, though not building the vignette) is 5 minutes. Do your vignettes take a lot of time to build?

If so, you should first identify the slow portion of your code and attempt to vectorize it; ask here for help if needed.

You should then construct examples for use in your vignette that are sufficiently realistic to shine a favorable light on the full richness of your software, but easily computed within the available time.

Martin
Fan, Jean
# 
Hi Martin,

Ah, I didn?t realize the problems were connected. Yes, the vignettes do take quite a while to run. I?ll see what I can do. Thanks for the help.

Best,
Jean
Paul Grosu
# 
Hi Jean,

I think you might need to update the required packages, so that they
install if you don't have them installed.  The test I usually run is by
keeping clean R installations and testing packages fresh as if I am a user
who just downloaded R.  You seem to need org.Hs.eg.db and GO.db for the
vignette, which I'm not sure the package automatically downloads, but those
can take some time.

And as always feel free to check with folks on this list :)

Hope it helps,
`p
On Thu, Jan 28, 2016 at 9:44 AM, Fan, Jean <jeanfan at fas.harvard.edu> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
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Also be sure you are using a recent version of R-devel.
Dan


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      Ludwig Geistlinger
    

    

      
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Dear Dan,

For some reason the citation on my package's landing page

http://bioconductor.org/packages/EnrichmentBrowser.html

is not displayed in agreement with my inst/CITATION file.

Furthermore, the version number is also not up to date here, although
displayed correctly at the bottom of the page (--> Package Archives).

How to resolve this?

Thx,
Ludwig