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[Bioc-devel] Bug in metaArray package

2 messages · rcaloger, Martin Morgan

Original
rcaloger
# 
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
# 
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: