[BioC] pdInfoBuilder for Niblegen 12x135k array, argument "posFile" is missing, with no default

[Benilton Carvalho]

for the archives: updating to the latest pdInfoBuilder solved the problem.

b

On Fri, Feb 5, 2010 at 2:00 PM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> The current version of the pdInfoBuilder package is 1.10.0.
>
> So, my first recommendation is to upgrade your R installation to the
> latest available version, so you can use the aforementioned
> pdInfoBuilder package.
>
> Once that's done, I'd suggest you to try the script again and I'll be
> able to help you out.
>
> Cheers,
>
> b
>
> On Fri, Feb 5, 2010 at 1:52 PM, Chris Fenton <chrisf at fagmed.uit.no> wrote:
>> Pretty much copied the code from
>> http://linusben.net/wiki/index.php/Oligo.bioconductor.
>>
>>
>> Something ala,
>>
>> """
>>> library(pdInfoBuilder)
>>> filename_ndf <- list.files('.',pattern='.ndf',full.names=T)
>>> filename_xys <- list.files('.',pattern=".xys",full.names=T)[1]
>>> seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile=filename_ndf, xysFile=filename_xys,
>>            author="Taejoon Kwon",email="email address",
>>            biocViews="AnnotationData", genomebuild="Unknown",
>>            url="http://www.marcottelab.org")
>>> makePdInfoPackage(seed, destDir = ".")
>> """
>>
>> I get the folling error in the seed <- new(...) line
>>
>> """
>> argument "posFile" is missing, with no default
>> """
>>
>>
>> Can't seem to find any documentation on this parameter.
>> Anyone run into this ?
>>
>> Chris
>>
>>
>>
>> sessionInfo()
>>
>> R version 2.7.2 (2008-08-25)
>> i686-pc-linux-gnu
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>> [1] pdInfoBuilder_1.4.0  oligo_1.4.0          oligoClasses_1.2.0
>> [4] AnnotationDbi_1.2.2  preprocessCore_1.2.1 affxparser_1.12.2
>> [7] RSQLite_0.7-1        DBI_0.2-4            Biobase_2.0.1
>>
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>>
>