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

[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 using uhnresearch.ca> wrote:

> 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}}
>
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