[BioC] makePDpackage: Problem loading PD package in, oligo:read.celfiles function

[Matt Settles]

Hello,

I am trying to read and work with data from an Affymetrix tiling array. 
 (And appreciate the previous posts for working with such data)!  I am 
using the packages "makePlatformDesign" and "oligo".

I have successfully used the makePDpackage function to create the needed 
package (pd.at35b.mr.v04.2.tigrv5)
makePDpackage("At35b_MR_v04-2
_TIGRv5.bpmap", type="tiling", manufacturer="affymetrix")

However, when using oligo to read my CEL files, I run into a problem.
test<-read.celfiles("T1_R1.cel")

Gayla,

The oligo package and read.celfiles function retrieve the package name 
for the data from the header in the CEL files
and attaches a pd. to the front it of. Therefor when you create your 
package you must also name it the same thing. Here it is informing you 
that it is looking for the pd.at35b.mr.v04 package, simple name your 
package  pd.at35b.mr.v04 in the extra parameter when you use  
makePDpackage function

makePDpackage(designFile=designFile),
                file1=file1,
                file2= file2,
                manufacturer="affymetrix", type="tiling", 
genomebuild=genomebuild,
                extra = list("packagename"="pd.at35b.mr.v04", 
"cdf.path"=cde.path,
                "package.path"=pathtopackage, "author"="me", 
"maintainer"="me <me at wsu.edu>",
                "version"="1.0.0", "unlink"=TRUE, "verbose"=TRUE))

or simply

read.celfiles("T1_R1.cel",pkgname="pd.at35b.mr.v04.2.tigrv5")

Matt Settles
Bioinformatician
Bioinformatics Core
School of Molecular Biology
Department of Animal Sciences
Washington State University
Pullman, WA


 >I get the following Error message:
 >Loading required package: pd.at35b.mr.v04
 >Error: invalid version specification
 >
 >I've also tried installing the package directly
 >install.packages("pd.at35b.mr.v04.2.tigrv5", repos=NULL)
 >
 >And get the following errors:
 >Warning in 
install.packages("/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5",  :
 > argument 'lib' is missing: using '/home/server/uid/R_LIBS'
 >ERROR: cannot install to srcdir
 >Warning message:
 >In install.packages("/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5",  :
 >installation of package 
'/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5' had non-zero exit status
 >
 >One final thing I did notice is the package created by 
makePlatformDesign is pd.at35b.mr.v04.2.tigrv5, which is slightly 
different than the package it tries to load under the read.celfiles 
function >(pd.at35b.mr.v04).
 >
 >
 >Any ideas or suggestions for how I can use the package I created to 
read my cel files would be appreciated.  My sessionInfo() is pasted below.
 >
 >Thank you,
 >-Gayla Olbricht