[R-pkg-devel] EXTERNAL: CRAN packages dependency on bioconductor packages
Hi Marcel, I appreciate your suggestion and clarification. It is worth mentioning that ?rmarkdown? is included in the Import filed, and I apologize for not stating it here. Interestingly, I was able to successfully upload StepReg version 1.5.0 to CRAN with BiocStyle listed in the Suggests field. However, I encountered this issue this time around. I attempted to address it by adding an empty `biocViews:` field in the DESCRIPTION, but unfortunately, it did not resolve the problem. It seems that there are some issues with CRAN check. Best, Junhui From: Ramos Perez, Marcel <Marcel.RamosPerez at RoswellPark.org> Date: Wednesday, May 15, 2024 at 17:50 To: Li, Junhui <Junhui.Li11 at umassmed.edu>, r-package-devel at r-project.org <r-package-devel at r-project.org> Subject: Re: EXTERNAL: [R-pkg-devel] CRAN packages dependency on bioconductor packages Hi Junhui, There are about 25 packages in CRAN that use BiocStyle, including yours. It seems that MetaIntegrator is also facing the same error. I have not looked too deeply into the issue but it seems that you should also include "rmarkdown" in the Suggests field. AFAIK, there is no need to include an empty `biocViews:` field in the DESCRIPTION. CRAN knows about Bioconductor repositories via setRepositories(). Note. Users should use BiocManager to resolve Bioconductor dependencies (rather than setRepositories). Best regards, Marcel
From: R-package-devel <r-package-devel-bounces at r-project.org> on behalf of Li, Junhui <Junhui.Li11 at umassmed.edu>
Sent: Tuesday, May 14, 2024 3:51 PM
To: r-package-devel at r-project.org <r-package-devel at r-project.org>
Subject: EXTERNAL: [R-pkg-devel] CRAN packages dependency on bioconductor packages
Sent: Tuesday, May 14, 2024 3:51 PM
To: r-package-devel at r-project.org <r-package-devel at r-project.org>
Subject: EXTERNAL: [R-pkg-devel] CRAN packages dependency on bioconductor packages
Hi everyone,
I recently developed an R package called 'StepReg' and used the Bioconductor R package 'BiocStyle' in my vignettes, as shown below:
output:
BiocStyle::html_document:
toc_float: true
BiocStyle::pdf_document: default
In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and included a new line 'biocViews:', as follows:
VignetteBuilder: knitr
biocViews:
Suggests:
knitr,
testthat,
BiocStyle,
kableExtra
You may find all those information here: https://github.com/JunhuiLi1017/StepReg/tree/dev
There were no error messages when checking with 'R CMD check' and on https://win-builder.r-project.org/upload.aspx. However, an error message occurred when I attempted to upload it to CRAN:
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'StepReg.Rmd' using rmarkdown
Error: processing vignette 'StepReg.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building 'StepReg.Rmd'
SUMMARY: processing the following file failed:
'StepReg.Rmd'
Error: Vignette re-building failed.
Execution halted
For version 1.5.0 (https://cran.r-project.org/web/packages/StepReg/index.html), I successfully uploaded it to CRAN without including 'biocViews:' in the DESCRIPTION file two months ago. However, I'm encountering difficulties this time. Any insights or suggestions on resolving this issue would be greatly appreciated.
Thanks,
Junhui
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