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