[Bioc-devel] error message upon installing easyRNASeq

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Nov 14 01:02:46 CET 2012

Hi Richard,

Not that this really helps you, but I just installed R-devel from
r.research.att.com, and:

R> source("http://bioconductor.org/biocLite.R")
R> useDevel(TRUE)
Error: 'devel' version already in use ## great
R> biocLite("easyRNASeq")
... download muchos packages

R> library(easyRNASeq)
... this works...

One thing you should address before you continue is to perhaps start R
in --vanilla mode, or move the "saved data object" you are loading up
to somewhere that R won't find it.

I mean, see this message you get when starting R:

> [Workspace restored from /Users/friedman/.RData]
> [History restored from /Users/friedman/.Rapp.history]

Either move ~/.RData somewhere else, or start R from terminal like so:

$ R --vanilla

(among other ways)

Maybe you are loading something into your workspace that's unknowingly
tripping you up.

I'm not quite sure why RCurl is tripping you up -- but you can try
reinstalling just that package to see if it then works.

But, another thing you should be sure to *not* have done is to move
your "old" R-2.15.x packages into your R-2.16 search path.

You should always be sure to keep your libraries for R versions x.y.z
separate from x.(y+n).z (where n != 0).

You should be starting your R-2.devel adventure only with the packages
that it shipped with.

Also, the other difference between your setup and mine is that I'm
running OSX.8.2, but I'm not sure that this is too important as far as
R is concerned because I believe the build tools are quite similar (we
both should be able to run the latest versions of XCode, fore exmple)

Not sure if that helps at all ...


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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