Question

How to find all available packages on BioConductor

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mick.jordan • 0

@mickjordan-12462

Last seen 7.9 years ago

Is there a way to find all the available packages on BioConductor in an R program, as in utils::available.packages() to get all the CRAN packages? I searched for this and read the BiocInstaller docs but didn't see how to do it.

bioconductor • 2.3k views

ADD COMMENT • link 7.9 years ago mick.jordan • 0

score 3 · Answer 1 · 2017-02-27

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 1 hour ago

United States

library(BiocInstaller)

z <- available.packages(repos = biocinstallRepos()[1])

ADD COMMENT • link 7.9 years ago James W. MacDonald 67k

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EDIT:

z <- available.packages(repo = biocinstallRepos()[1])

ADD REPLY • link 7.9 years ago James W. MacDonald 67k

score 0 · Answer 2 · 2017-02-27

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mick.jordan • 0

@mickjordan-12462

Last seen 7.9 years ago

Thanks! FYI, this is for automated package testing for the FastR project: https://github.com/graalvm/fastr

ADD COMMENT • link 7.9 years ago mick.jordan • 0

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Package testing likely requires experiment and annotation packages, which is likely BiocInstaller::biocinstallRepos()[1:3], but maybe decide based on

> BiocInstaller:::biocinstallRepos()
                                               BioCsoft 
           "https://bioconductor.org/packages/3.5/bioc" 
                                                BioCann 
"https://bioconductor.org/packages/3.5/data/annotation" 
                                                BioCexp 
"https://bioconductor.org/packages/3.5/data/experiment" 
                                              BioCextra 
          "https://bioconductor.org/packages/3.5/extra" 
                                                   CRAN 
                             "https://cran.rstudio.com"

It will likely be more efficient to use mirror via rsync to maintain a local repository, rather than installing built binaries over http.

ADD REPLY • link 7.9 years ago Martin Morgan 25k

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Yes, I wondered about those other entries. I go back and forth on maintaining a local copy (of CRAN) which is what we test now, a few hundred packages a day on a rolling basis. We have to build everything from source anyway (at least those packages with native code) as FastR is not binary-compatible with the C code.

ADD REPLY • link 7.9 years ago mick.jordan • 0