[BioC] installation of Rsamtools

[Steve Lianoglou]

Hi again,

On Fri, Dec 30, 2011 at 5:39 AM, Conny [guest] <guest at bioconductor.org> wrote:
>
> I still have problems installing Rsamtools. The first idea was that my R version was too old - so I updated it to the latest version.

Ok, getting close ...

> still the installation does not work - any ideas?
> this is just the end of the list after:
>
>> biocLite("Rsamtools")
> Warning: S3 methods ‘[<-.CURLOptions’, ‘[[<-.CURLOptions’ were declared in NAMESPACE but not found
> Error in library.dynam(lib, package, package.lib) :
>  shared object ‘RCurl.so’ not found
> ERROR: lazy loading failed for package ‘Rsamtools’
> * removing ‘/home/lab/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
> * restoring previous ‘/home/lab/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’

[snip]

It seems that your RCurl installation is somehow hosed. Did you notice
any errors when you tried to install it into your new R-2.14.1
install?

Or maybe ... did you copy your old packages from your previous R
install's library folder to your new version of R? That can open a
whole can of worms. I think there are a few ways to go from here.

If that's what happened, maybe you can try this maneuver to update
your installed packages first. This will try to update all of your
installed packages w/o any further intervention from you:

R> library(BiocInstaller)
R> biocLite(character(), ask=FALSE)

If you didn't copy your old R packages to your new install, I'm not
sure what happened. You can try to install RCurl again, seeing as how
this is the first problem you are running into:

R> library(BiocInstaller)
R> biocLite('RCurl')

Then try Rsamtools again ... keep your eyes open for other packages
that are broken and reinstall until the dust settles.

If you're still having problems, feel free to reply back with any new
surprises you're running into.

HTH,

-steve

-- 
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