[R-pkg-devel] EXTERNAL: CRAN packages dependency on bioconductor packages

[Ramos Perez, Marcel]

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 using r-project.org> on behalf of Li, Junhui <Junhui.Li11 using umassmed.edu>
Sent: Tuesday, May 14, 2024 3:51 PM
To: r-package-devel using r-project.org <r-package-devel using 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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