Question

CMD check warning using Bioconductor as a source for the dependencies of an R package

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dong ▴ 10

@dong-19810

Last seen 2.1 years ago

Israel

I am writing an R package and one of my dependencies is a bioconductor package xcms. It can pass the CMD check in my local PC, while when I submit my package to CRAN, there is one warning:

>Found the following significant warnings:
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN

Here is part of my Description File:

> Depends:     
> R (>= 3.1.0).   
> biocViews:    
> Imports:    
> xcms.

The CRAN check result is here https://win-builder.r-project.org/incomingpretest/Miso0.2.020190210133229/Windows/00check.log

I don't know how to eliminate this warning, thanks a lot for your help.

Bioconductor CMD check warning • 1.3k views

ADD COMMENT • link updated 5.2 years ago by Martin Morgan 25k • written 5.2 years ago by dong ▴ 10

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provide more detail, e.g., the link to the CRAN check and to your package source.

ADD REPLY • link 5.2 years ago Martin Morgan 25k

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@Martin Morgan, Thanks for your suggestion. The CRAN check has been added here.

ADD REPLY • link 5.2 years ago dong ▴ 10

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You can find further details in https://win-builder.r-project.org/incomingpretest/Miso0.2.020190210133229/Windows//00install.out

I wonder if this is because the Windows builder is stuck with an outdated version of a Bioconductor package that still references BiocInstaller. Perhaps there's a way to find more details of the packages installed?

If this is the case then I'm not sure there's much you can do other than wait for the relevant package to be updated.

ADD REPLY • link 5.2 years ago Mike Smith ★ 6.5k

score 2 · Accepted Answer · 2019-02-10

One can discover dependencies by discovering the packages available for the platform in question

db <- available.packages(repos=BiocManager::repositories(), type = "win.binary")

and then finding reverse dependencies

deps <- tools::package_dependencies("xcms", db, recursive = TRUE)

For the 'devel' version of R, the repositories are

> BiocManager::repositories()
                                               BioCsoft
           "https://bioconductor.org/packages/3.9/bioc"
                                                BioCann
"https://bioconductor.org/packages/3.9/data/annotation"
                                                BioCexp
"https://bioconductor.org/packages/3.9/data/experiment"
                                          BioCworkflows
      "https://bioconductor.org/packages/3.9/workflows"
                                                   CRAN
                             "https://cran.rstudio.com"

where the 3.9 indicates Bioconductor 3.9. There are no dependencies on BiocInstaller

> "BiocInstaller" %in% unlist(deps)
[1] FALSE

so at least for xcms Mike Smiths' speculation (that stale packages are installed on win-builder) would be the most likely explanation. If there is no dependency on BiocInstaller in the other direct and indirect dependencies, this should be taken up with the win-builder team. Actually, since BiocInstaller is not available under R-devel

> "BiocInstaller" %in% rownames(db)
[1] FALSE

and since the WARNING comes when BiocInstaller is loaded, it follows that win-builder does not have a current installation.