Question

rationale behind getBioC script

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Adaikalavan Ramasamy ★ 1.8k

@adaikalavan-ramasamy-675

Last seen 10.2 years ago

What is the rationale behind using the getBioC script ? For example if I want to install all R packages, I would do the following : all <- CRAN.packages()[ ,1] got <- installed.packages()[ ,1] need <- setdiff(all, got) install.packages( need ) and then go for a really long coffee break. Is would be useful to have something similar to CRAN.packages, perhaps named BioC.packages() . Is it sensible to have BioC.packages() and install.packages2() (currently in reposTools) directly in the R base package itself ? Thank you. Regards, Adai

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ADD COMMENT • link updated 19.7 years ago by Jeff Gentry ★ 3.9k • written 19.7 years ago by Adaikalavan Ramasamy ★ 1.8k

score 0 · Answer 1 · 2005-03-11

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Jeff Gentry ★ 3.9k

@jeff-gentry-12

Last seen 10.2 years ago

> Is would be useful to have something similar to CRAN.packages, perhaps > named BioC.packages() . What is wrong with: CRAN.packages(CRAN=getOption("BIOC")) You'll find that you can utilize all of the standard R installation tools with that same 'CRAN=' flag above.

ADD COMMENT • link 19.7 years ago Jeff Gentry ★ 3.9k

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Nothing is wrong. I was not aware of it. Still it would be nice to have BioC.packages <- function() CRAN.packages( CRAN=getOption("BIOC") ) Because I think I will struggle to remember the full form. Thank you. Regards, Adai On Fri, 2005-03-11 at 10:07 -0500, Jeff Gentry wrote: > > Is would be useful to have something similar to CRAN.packages, perhaps > > named BioC.packages() . > > What is wrong with: > CRAN.packages(CRAN=getOption("BIOC")) > > You'll find that you can utilize all of the standard R installation tools > with that same 'CRAN=' flag above.

ADD REPLY • link 19.7 years ago Adaikalavan Ramasamy ★ 1.8k