[BioC] oligo and pdInfoBuilder

[Simon Melov]

That was it, Ben set me straight, sorry for the time waster!


On Jun 3, 2012, at 8:33 PM, Vincent Carey wrote:



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