repositories2
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@christopher-albert-728
Last seen 9.6 years ago
Hi, Is there an easy way to override the built-in options()$repositories2 list from an .Rprofile file to use a locally mirrored repository? Thanks, Chris
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Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 9.6 years ago
> Is there an easy way to override the built-in options()$repositories2 > list from an .Rprofile file to use a locally mirrored repository? Currently what should happen is if you have 'repositories2' defined before loading reposTools, any value that reposTools wants to set will not be overwritten. For instance, if before loading reposTools you set: > options(repositories2=c(CRAN="http://cran.r-project.org", BIOCData="http://www.local.mirror.org")) Then upon loading reposTools you should see: getOption("repositories2") CRAN "http://cran.r-project.org" BIOCData "http://www.local.mirror.org" BIOCRel1.3 "http://www.bioconductor.org/repository/release1.3/package" BIOCDevel "http://www.bioconductor.org/repository/devel/package" BIOCDevData "http://www.bioconductor.org/data/metaData-devel" BIOCExdata "http://www.bioconductor.org/data/experimental/repos" BIOCCourses "http://www.bioconductor.org/repository/Courses" BIOCcdf "http://www.bioconductor.org/data/cdfenvs/repos" BIOCprobes "http://www.bioconductor.org/data/probes/Packages" BIOCOmegahat "http://www.bioconductor.org/repository/Omegahat" A good question is if this is the proper behavior, or should reposTools detect that a 'repositories2' option exists and simply not change anything in it instead of only leaving alone the similar entries. -J
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Jeff Gentry wrote: > Currently what should happen is if you have 'repositories2' defined before > loading reposTools, any value that reposTools wants to set will not be > overwritten. For instance, if before loading reposTools you set: > > >>options(repositories2=c(CRAN="http://cran.r-project.org", > > BIOCData="http://www.local.mirror.org")) This works fine from an .Rprofile file, although I used the named vector syntax of the options()$repositories2 structure. About the CRAN option in repositories2, when I use a plain vanilla CRAN mirror I get the error "does not seem to have a valid repository, skipping" . Is this because reposTools looks for a "repdatadesc.rda" file which is not found in general on CRAN repositories? Chris
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> About the CRAN option in repositories2, when I use a plain vanilla CRAN > mirror I get the error "does not seem to have a valid repository, > skipping" . > Is this because reposTools looks for a "repdatadesc.rda" file which is > not found in general on CRAN repositories? Yep. The two aren't compatable - reposTools repositories require their own data files (repdatadesc.rda and replisting) and the builtin R functions require their own (PACKAGES). The CRAN repository at www.bioconductor.org is the only one that I know of that provides a reposTools style repository for the CRAN packages. -J
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