Question

List of package names with versions

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nathan.watsonhaigh • 0

@nathanwatsonhaigh-9830

Last seen 8.7 years ago

I'd like to get an up-to-date list of all the bioconductor packages together with their version number for a particular BioC version.

I know all_group() will return the list of package names, but I also need the versions. Where can I get these from?

Cheers,

Nathan

packages • 2.4k views

ADD COMMENT • link updated 8.7 years ago by Sushant Pawar • 0 • written 8.7 years ago by nathan.watsonhaigh • 0

score 0 · Answer 1 · 2016-03-01

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Sushant Pawar • 0

@sushant-pawar-9287

Last seen 7.8 years ago

Nashik

you can try this

packinfo <- installed.packages(fields = c("Package", "Version"))
packinfo[,c("Package", "Version")]

ADD COMMENT • link 8.7 years ago Sushant Pawar • 0

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Is there a solution which doesn't first require installing everything? Will this only return BioC packages or also those installed via CRAN?

ADD REPLY • link 8.7 years ago nathan.watsonhaigh • 0

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See https://bioconductor.org/packages/3.3/bioc/src/contrib/PACKAGES . Substitute your bioconductor version of interest for 3.3.

You can read this within R with the read.dcf() function. Of course, for current release and devel versions, package versions can change over time.

ADD REPLY • link 8.7 years ago Dan Tenenbaum ★ 8.2k

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Thanks for this information. Please consider moving it from a comment to an answer.

ADD REPLY • link 8.7 years ago nathan.watsonhaigh • 0

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Specify the appropriate 'repos' argument to available.packages(). The appropriate url is from BiocInstaller::biocinstallRepos(), for instance

> biocVersion()
[1] '3.2'
> biocinstallRepos()
                                               BioCsoft 
           "https://bioconductor.org/packages/3.2/bioc" 
                                                BioCann 
"https://bioconductor.org/packages/3.2/data/annotation" 
                                                BioCexp 
"https://bioconductor.org/packages/3.2/data/experiment" 
                                              BioCextra 
          "https://bioconductor.org/packages/3.2/extra" 
                                                   CRAN 
                             "https://cran.rstudio.com" 
> nrow(available.packages(contriburl=contrib.url(biocinstallRepos()[1:4])))
[1] 2264
> nrow(available.packages(contriburl=contrib.url(biocinstallRepos())))
[1] 10259

ADD REPLY • link 8.7 years ago Martin Morgan 25k

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Thanks for this information. Please consider moving it from a comment to an answer.

ADD REPLY • link 8.7 years ago nathan.watsonhaigh • 0