[BioC] Bug in metaArray package

[Martin Morgan]

Hi Raffael --

No need to cross post; polite to include the package maintainer (e.g.,
packageDescription('metaArray')) when reporting package bugs.

The problem is that the C code is not loaded -- the NAMESPACE file
requires the line useDynLib('metaArray').

A workaround until this is fixed is to issue the command

  dyn.load('metaArray')

after loading the package.

Martin

rcaloger <raffaele.calogero at gmail.com> writes:

> Hi,
> I am the maintainer of oneChannleGUI. For data mining in my package I
> have an implementation of  IC coefficient derived from metaArray
> package.
> To run intcor function I use an Object of class mergeExpressionSet
> created with two expression sets and the function mergeExprs:
>  > metaData
> ExpressionSet (storageMode: list)
> assayData: 31 features, 200 samples
>   element names: exprs
> phenoData
>   sampleNames: GSM282373, GSM282374, ..., GSM282572  (200 total)
>   varLabels and varMetadata description:
>     Name: Name
>     FileName: FileName
>     Target: Target
> featureData
>   featureNames: 200737_at, 200738_s_at, ..., AFFX-HUMGAPDH/M33197_M_at
>   (31 total)
>   fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: hgu133a.db
> ExpressionSet (storageMode: list)
> assayData: 31 features, 204 samples
>   element names: exprs
> phenoData
>   sampleNames: GSM308256, GSM308257, ..., GSM308460  (204 total)
>   varLabels and varMetadata description:
>     FileName: FileName
>     Target: Target
> featureData
>   featureNames: 200737_at, 200738_s_at, ..., AFFX-HUMGAPDH/M33197_M_at
>   (31 total)
>   fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: 
>
> to run intcor I use the metaArray function intcor:
> merged.cor <- intcor(metaData)
> At this point I get the following error:
> Error in .C("intcor", as.double(unlist(expr)), as.integer(unlist(cl)),  :
>   C symbol name "intcor" not in DLL for package "metaArray"
>
> If I run intCor from the MergeMaid package:
> merged.cor <- intCor(metaData)
> No errors are encountered.
> It seems to me a problem in call of the C function.
> Cheers
> raffaele
>
>  >sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=Italian_Italy.1252;LC_CTYPE=Italian_Italy.1252;LC_MONETARY=Italian_Italy.1252;LC_NUMERIC=C;LC_TIME=Italian_Italy.1252
>
> attached base packages:
>  [1] splines   tools     tcltk     stats     graphics  grDevices utils
>  [8] datasets  methods   base    
>
> other attached packages:
>  [1] MergeMaid_2.16.0     MASS_7.2-47          survival_2.35-4    [4]
>  metaArray_1.20.0     oneChannelGUI_1.10.8 preprocessCore_1.6.0
>  [7] GOstats_2.10.0       RSQLite_0.7-1        DBI_0.2-4          [10]
>  graph_1.22.2         Category_2.10.1      AnnotationDbi_1.6.1
> [13] tkWidgets_1.22.0     DynDoc_1.22.0        widgetTools_1.22.0 [16]
> affylmGUI_1.18.0     affyio_1.12.0        affy_1.22.0        [19]
> limma_2.18.2         Biobase_2.4.1      
>
> loaded via a namespace (and not attached):
> [1] annotate_1.22.0   genefilter_1.24.2 GO.db_2.2.11
> GSEABase_1.6.1  [5] RBGL_1.20.0       XML_2.5-3         xtable_1.5-5 

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793