[Bioc-devel] loadDb Arguments Mismatch

[Dario Strbenac]

Hello,

Using Sweave to compile a long report, I get 

tx19 <- loadDb("transcriptsHs19.db")

Error in loadDb(file, dbType, dbPackage, ...) : 
  error in evaluating the argument 'dbType' in selecting a method for function 'loadDb': Error: argument "dbType" is missing, with no default

The documentation says that dbType is optional. I have tried to make a minimal example and run it in a new session, but the minimal example always works without error.

Here are the sessionInfos :

Session with error :

 sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.10.0 AnnotationDbi_1.20.3   Biobase_2.18.0        
[4] moments_0.13           Rsamtools_1.10.1       Biostrings_2.26.1     
[7] GenomicRanges_1.10.1   IRanges_1.16.2         BiocGenerics_0.4.0    

loaded via a namespace (and not attached):
 [1] biomaRt_2.12.0     bitops_1.0-4.1     BSgenome_1.24.0    DBI_0.2-5         
 [5] parallel_2.15.1    RCurl_1.95-1.1     RSQLite_0.11.2     rtracklayer_1.18.0
 [9] stats4_2.15.1      tools_2.15.1       XML_3.95-0.1       zlibbioc_1.2.0 

Session without error :

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.10.0 AnnotationDbi_1.20.3   Biobase_2.18.0         GenomicRanges_1.10.1  
[5] IRanges_1.16.2         BiocGenerics_0.4.0     moments_0.13          

loaded via a namespace (and not attached):
 [1] biomaRt_2.12.0     Biostrings_2.26.1  bitops_1.0-4.1     BSgenome_1.24.0    DBI_0.2-5         
 [6] parallel_2.15.1    RCurl_1.95-1.1     Rsamtools_1.10.1   RSQLite_0.11.2     rtracklayer_1.18.0
[11] stats4_2.15.1      tools_2.15.1       XML_3.95-0.1       zlibbioc_1.2.0 

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia