Question: Request: Annotate DESCRIPTION of 'extra' packages with 'biocViews' or other identifying tag
0
gravatar for Kevin Ushey
4.3 years ago by
Kevin Ushey10
United States
Kevin Ushey10 wrote:

Bioconductor hosts a couple of 'extra' packages, with the current set of 'release' packages annotated here:

    http://bioconductor.org/packages/release/extra/

It is rather nice that Bioconductor mirrors a subset of packages from external repositories. However, it appears to me that there is no content within the package / package DESCRIPTION that denotes such packages could be retrieved from Bioconductor.

This is a problem for 'shinyapps', as normally we infer whether a particular package came from Bioconductor based on the presence of a 'biocViews' tag within the package DESCRIPTION (which, IIUC, is mandatory for all packages submitted / hosted on Bioconductor, barring these 'extra' packages)

Would it be possible for Bioconductor to annotate these packages in some way that would allow a user to discover after-the-fact that the package was obtained from Bioconductor -- perhaps with 'biocViews: extra' or some other kind of metadata appended to the package DESCRIPTION? Of course, we can maintain our own list but from a reproducibility standpoint it would be useful to be able to infer the origin of a particular installed package.

Thanks,

Kevin

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Kevin Ushey10
Answer: Request: Annotate DESCRIPTION of 'extra' packages with 'biocViews' or other iden
1
gravatar for Dan Tenenbaum
4.3 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:

I'm not sure it would be appropriate for us to tag packages that come from other repositories with biocViews. 

Here's another way:

library(BiocInstaller)
isBioconductorPackage <- function(pkg)
{
     bioc_repos <- biocinstallRepos()
     bioc_repos <- bioc_repos[grep("^BioC", names(bioc_repos))]
     ap <- available.packages(contrib.url(bioc_repos))
     pkg %in% rownames(ap)
}

isBioconductorPackage(c("IRanges", "car"))
# [1]  TRUE FALSE

Does that help?

 

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Dan Tenenbaum8.2k
Answer: Request: Annotate DESCRIPTION of 'extra' packages with 'biocViews' or other iden
0
gravatar for Kevin Ushey
4.3 years ago by
Kevin Ushey10
United States
Kevin Ushey10 wrote:

Thanks Dan -- that will definitely suffice for us. Much appreciated!

ADD COMMENTlink written 4.3 years ago by Kevin Ushey10

Hervé pointed out a glaring flaw--biocInstallRepos() also returns CRAN repos. The answer has now been updated.

ADD REPLYlink written 4.3 years ago by Dan Tenenbaum8.2k
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