[R] Help with R and Bioconductor

[Ashok Veeraraghavan]

Hi Jeff,

First of all thanks for the response. But i still am encountering some
problems with installing bioconductor.

I did remove the directory 00Lock.
I ran getBioC("affy")

During the installation i get a warning several times.
chmod:/Library/Frameworks/R.framework/Version/2.0.1/Resources/library/R.css:Operation
Not Permitted
Is this warning message critical to the installation?

Moreover at the end of the Installation i also got this message. I
have appended that message to the end of this email.

Question 1.
Package Annotate was not updated. Why wasnt it updated. How can i update it?

Question 2.
Should i be worried abt the other warning messages?

Thanks
Regards
Ashok




Packages that were not updated:
        annotate

Warning messages: 
1: 
 Package annotate version 1.5.1 suggests zebrafish
Package annotate version 1.5.1 suggests xenopuslaevis 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib,
searchOptions = searchOptions,
2: Installation of package annaffy had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
3: 
 Package annotate version 1.5.1 suggests zebrafish
Package annotate version 1.5.1 suggests xenopuslaevis 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib,
searchOptions = searchOptions,
4: Installation of package Rgraphviz had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
5: Installation of package geneplotter had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
6: 
 Package annotate version 1.5.1 suggests zebrafish
Package annotate version 1.5.1 suggests xenopuslaevis 
 in: resolve.depends(pkgInfo, repEntry, force, lib = lib,
searchOptions = searchOptions,




On Thu, 27 Jan 2005 13:41:45 -0500 (EST), Jeff Gentry
<jgentry at jimmy.harvard.edu> wrote:
> > seemed successful. Then while attempting to getBioC() I had to force
> > quit the R application since I had to attend to something else
> > urgently. When i returned and tried to getBioC, I am getting errors
> 
> Why not just let it run?
> 
> > indicating that there is a lock on some files. So i would like to
> 
> The directory will likely be <path-to-R>/library/00LOCK (I say likely
> because the '<path-to-R>/library' part could be something else if you
> specified an alternate installation directory or your default .libPaths is
> different then standard), and removing that directory will solve your
> issues.
> 
>