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[Bioc-devel] Missing knitcitations package on devel for PharmacoGx

3 messages · Eeles, Christopher, Mike Smith, Vincent Carey

Original
Eeles, Christopher
# 
Hello Bioc community,

I am the maintainer for PharmacoGx and have noticed that I have an error on all platforms of the devel branch related to the knitcitations package.


* checking for file ?PharmacoGx/DESCRIPTION? ... OK
* preparing ?PharmacoGx?:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ?CreatingPharmacoSet.Rmd? using rmarkdown
Quitting from lines 79-82 (CreatingPharmacoSet.Rmd)
Error: processing vignette 'CreatingPharmacoSet.Rmd' failed with diagnostics:
there is no package called 'knitcitations'
--- failed re-building ?CreatingPharmacoSet.Rmd?

--- re-building ?PharmacoGx.Rmd? using rmarkdown
Quitting from lines 79-82 (PharmacoGx.Rmd)
Error: processing vignette 'PharmacoGx.Rmd' failed with diagnostics:
there is no package called 'knitcitations'
--- failed re-building ?PharmacoGx.Rmd?

SUMMARY: processing the following files failed:
  ?CreatingPharmacoSet.Rmd? ?PharmacoGx.Rmd?

Error: Vignette re-building failed.
Execution halted

The package builds fine on the release branch with the same vignettes and knitcitations in the suggests field of the description.

Any advice on how I can fix this? It seems like my suggests aren't being installed on the devel branch.

Thanks for your assistance.

Best,
Christopher Eeles
Software Developer
Benjamin Haibe-Kains Lab
Princess Margaret Cancer Centre

This e-mail may contain confidential and/or privileged i...{{dropped:22}}
Mike Smith
# 
Hi Christopher,

It looks like the knitcitations package is no longer on CRAN.  Heading to
https://cran.r-project.org/web/packages/knitcitations/index.html results in:

  Package ?knitcitations? was removed from the CRAN repository.

  Formerly available versions can be obtained from the archive.

  Archived on 2020-10-27 as reauired archived package 'RefManageR'.

My guess is the release branch has a copy of knitcitations installed from
before it was removed from CRAN, so you don't see the error, but a fresh R
installation using either release or devel would throw the same problem.

The latest commit message to https://github.com/cboettig/knitcitations is
'prep for release', so it looks likely that the author of knitcitations is
addressing the CRAN issue.  I would hang tight for a while longer and hope
it gets smoothed out there.

Mike

On Thu, 26 Nov 2020 at 04:26, Eeles, Christopher <
Christopher.Eeles at uhnresearch.ca> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Vincent Carey
    

    

      
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This problem has been recognized:
https://github.com/cboettig/knitcitations/issues/107

In a few days it will likely clear.

On Wed, Nov 25, 2020 at 10:26 PM Eeles, Christopher <

        
Christopher.Eeles at uhnresearch.ca> wrote: