Re: [Bioc-devel] Missing knitcitations package on devel for PharmacoGx
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.ee...@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}} > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [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.ee...@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}} > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Missing knitcitations package on devel for PharmacoGx
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}} ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel