[BioC] Rsamtools installation

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Nov 8 15:54:54 CET 2011


On Tue, Nov 8, 2011 at 9:33 AM, John Coulthard <bahhab at hotmail.com> wrote:
> Hi
> I'm trying to install Rsamtools and getting errors!  I've tried...
>     install.packages("/home/ann/downloads/Rsamtools_1.6.0.tar.gz")
> and
>     biocLite("Rsamtools")
> (see below)
> Why doesn't  biocLite() install the current version?

It's trying to :-)

> I'm almost sure the dependencies are all up-to-date using  install.packages().

Correct me if I'm wrong, but `install.packages` doesn't update the
bioconductor packages, does it?

> So if it's not an out of date dependent what could the problem be?
> If is it an out of date dependent how do I get R to tell me which one?

Let's start with IRanges .. what version of that do you have installed?

You can also just:

R> library(BiocInstaller)
R> biocLite() ## maybe set ask=FALSE

to update your already installed packages (did you happen to move your
old R-2.13 library to R-2.14?) ...


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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