[BioC] Cannot find the package created by pdInfoBuilder package

[Dan Tenenbaum]

----- Original Message -----
> From: "dhivya [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, darasappan at gmail.com
> Sent: Friday, March 28, 2014 12:45:22 PM
> Subject: [BioC] Cannot find the package created by pdInfoBuilder package
> 
> 
> Hello,
> 
> I’ m a bioinformatician at UT Austin and I’m trying to do time
> series analysis of an arabidopsis tiling array.  I used the
> makePdInfoPackage function to create a pdinfpackage using my bpmap
> files.  It worked successfully and I can see a directory called
> pd.at35b.mr.v04:
> 
> ls pd.at35b.mr.v04/
> data  DESCRIPTION  inst  man  NAMESPACE  R
> 
> For further analysis, I need to provide the name of the "package
> containing the array probe and annotation information, as produces
> by the pdInfoBuilder-package".  Just providing the name of this
> directory does not seem to work (no such package error). Do I need
> to do some installation or additional step after creating this
> package, to use it?  I’m having difficulty finding this from the
> documentation and any help would be really appreciated.
> 

I think you just need to do this from the command line:

R CMD INSTALL pd.at35b.mr.v04

Dan


> thanks for any help
> dhivya arasappan
> Bioinformatician
> UT Austin
> 
>  -- output of sessionInfo():
> 
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets
>  methods
> [8] base
> 
> other attached packages:
>  [1] pdInfoBuilder_1.22.0                 affxparser_1.30.2
>  [3] BSgenome.Athaliana.TAIR.TAIR9_1.3.18 BSgenome_1.26.1
>  [5] GenomicRanges_1.10.7                 pd.atdschip.tiling_0.0.4
>  [7] RSQLite_0.11.4                       DBI_0.2-7
>  [9] waveTilingData_0.99.1                waveTiling_1.0.0
> [11] GenomeGraphs_1.18.0                  biomaRt_2.14.0
> [13] Biostrings_2.26.3                    IRanges_1.16.6
> [15] oligo_1.22.0                         Biobase_2.18.0
> [17] oligoClasses_1.20.0                  BiocGenerics_0.4.0
> [19] R.utils_1.29.8                       R.oo_1.18.0
> [21] R.methodsS3_1.6.1
> 
> loaded via a namespace (and not attached):
>  [1] affy_1.36.1           affyio_1.26.0         BiocInstaller_1.8.3
>  [4] bit_1.1-11            codetools_0.2-8       ff_2.2-12
>  [7] foreach_1.4.1         iterators_1.0.6       parallel_2.15.3
> [10] preprocessCore_1.20.0 RCurl_1.95-4.1        splines_2.15.3
> [13] stats4_2.15.3         waveslim_1.7.3        XML_3.98-1.1
> [16] zlibbioc_1.4.0
> 
> 
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