[BioC] could not find function "makeProbePackage"

[James W. MacDonald]

Hi Merja,

On 6/9/2013 11:33 AM, Merja Heinäniemi wrote:
> Hi!
>
> I am trying to build a custom probe package using the AnnotationDBI library and the function makeProbePackage. The script worked earlier (with R.2.12 at least) but now I get an error.
> Error in eval(expr, envir, enclos) :
>    could not find function "makeProbePackage"
>
> I get the error with R2.15.2 and Biobase_2.18.0 (see more details in session info below)
>
> Did the function get replaced / removed ?  What should I do? Any other alternative than going back to earlier R and Bioconductor versions?

You want the AnnotationForge package.

Best,

Jim


>
> (in the same setting, building custom cdf worked but I would need the probe package for gcrma)
>
> kind regards,
> Merja
>
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-redhat-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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] AnnotationDbi_1.20.7 Biobase_2.18.0       BiocGenerics_0.4.0
> [4] makecdfenv_1.36.0    BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
>   [1] affy_1.36.1           affyio_1.26.0         DBI_0.2-7
>   [4] IRanges_1.16.6        parallel_2.15.2       preprocessCore_1.20.0
>   [7] RSQLite_0.11.4        stats4_2.15.2         tools_2.15.2
> [10] zlibbioc_1.4.0
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099