Question

R --vanilla and Annotation pkg

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SAURIN ★ 1.1k

@saurin-799

Last seen 9.6 years ago

Hi BioC, I just recently installed rae230a cdf, probe and rae230a pkg from bioconductor metadata website. When I run my script through R --vanilla < script1.R I have below problem. ------------------------------- chiptype <- rae230a; All_Annotations <- aafTableAnn(myGenes,chiptype,c("Symbol","Description","Function","GenB ank","UniGene")); [1] "You are missing rgu34a looking to see if it is available." Package rgu34a version 1.6.5 is available for download, would you like to install? [yes/y/no/n] All_Genes_Annotation <- merge(All_Genes_Annotation,All_Annotations); All_Genes_Annotation <- merge(All_Genes_Annotation,All_Annotations); is not a valid response, try again. ------------------------------- But WHEN.....I run my script1.R by copy and paste and then I do R --vanilla , I DON'T get above error. has anyone had this problem..? Thank you, Saurin

rae230a rgu34a cdf probe rae230a rgu34a cdf probe • 1.7k views

ADD COMMENT • link updated 19.3 years ago by Jeff Gentry ★ 3.9k • written 19.3 years ago by SAURIN ★ 1.1k

score 0 · Answer 1 · 2005-01-07

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Jeff Gentry ★ 3.9k

@jeff-gentry-12

Last seen 9.6 years ago

> But WHEN.....I run my script1.R by copy and paste and > then I do R --vanilla , I DON'T get above error. > has anyone had this problem..? Are you sure that you're getting the same .libPaths() between your interactive R session and the R --vanilla? That might very well not be the case, and if the package is installed in a directory that is in your interactive .libPaths but not in your vanilla session then you would see that behaviour.

ADD COMMENT • link 19.3 years ago Jeff Gentry ★ 3.9k

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Hi Jeff, When I install pkg. through my interactive session and then I do vanilla which is my different session , it works fine. that means I need to run my interactive session first in order to get going with vanilla. do you know how I can not set up my libpaths in my R script so, when ever I run my vanilla command, I just put that line before libraries so, all will have correct paths? Thank you for your time, Saurin --- Jeff Gentry <jgentry@jimmy.harvard.edu> wrote: > > But WHEN.....I run my script1.R by copy and paste > and > > then I do R --vanilla , I DON'T get above error. > > has anyone had this problem..? > > Are you sure that you're getting the same > .libPaths() between your > interactive R session and the R --vanilla? That > might very well not be > the case, and if the package is installed in a > directory that is in your > interactive .libPaths but not in your vanilla > session then you would see > that behaviour. > > ===== Saurin's WebWorld: http://hawkmail.monmouth.edu/~s0451884

ADD REPLY • link 19.3 years ago SAURIN ★ 1.1k