On Sun, Jun 3, 2012 at 11:08 PM, Simon Melov <smelov@buckinstitute.org>wrote:

> I've been beating my head against the wall for several hours trying to see
> why I cant build a library for a nimblegen expression array, using the
> oligo and pdInfoBuilder packages. I dont see any errors when building the
> library for a 12plex yeast genome expression array....
>
>  makePdInfoPackage(seed, destDir =
> "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/")
>
> ================================================================================
> Building annotation package for Nimblegen Expression Array
> NDF: 100718_Scer_EXP.ndf
> XYS: 532785A01_Chip6.330.2012.5.8_532.xys
>
> ================================================================================
> Parsing file: 100718_Scer_EXP.ndf... OK
> Parsing file: 532785A01_Chip6.330.2012.5.8_532.xys... OK
> Merging NDF and XYS files... OK
> Preparing contents for featureSet table... OK
> Preparing contents for bgfeature table... OK
> Preparing contents for pmfeature table... OK
> Creating package in
> /Library/Frameworks/R.framework/Versions/2.15/Resources/library//pd.100718.scer.exp
> Inserting 5777 rows into table featureSet... OK
> Inserting 137040 rows into table pmfeature... OK
> Counting rows in featureSet
> Counting rows in pmfeature
> Creating index idx_pmfsetid on pmfeature... OK
> Creating index idx_pmfid on pmfeature... OK
> Creating index idx_fsfsetid on featureSet... OK
> Saving DataFrame object for PM.
> Done.
> >
>
> but when I try to use the library in oligo, it fails for some reason
>
> library(pd.100718.scer.exp)
> Error in library(pd.100718.scer.exp) :
>  'pd.100718.scer.exp' is not a valid installed package
>

What happened when you ran R CMD INSTALL (or install.packages?)

sessionInfo()?


> >
>
> Can anyone help? I'm at my wits end...
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