Search
Question: List of package names with versions
0
gravatar for nathan.watsonhaigh
20 months ago by
nathan.watsonhaigh0 wrote:

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

ADD COMMENTlink modified 20 months ago by Sushant Pawar0 • written 20 months ago by nathan.watsonhaigh0
0
gravatar for Sushant Pawar
20 months ago by
Nashik
Sushant Pawar0 wrote:

you can try this

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

 

ADD COMMENTlink written 20 months ago by Sushant Pawar0

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

ADD REPLYlink written 20 months ago by nathan.watsonhaigh0
2

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 REPLYlink written 20 months ago by Dan Tenenbaum ♦♦ 8.2k

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

ADD REPLYlink written 20 months ago by nathan.watsonhaigh0
1

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 REPLYlink written 20 months ago by Martin Morgan ♦♦ 20k

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

ADD REPLYlink written 20 months ago by nathan.watsonhaigh0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 135 users visited in the last hour