[Bioc-devel] loadDb Arguments Mismatch

[Marc Carlson]

Hi Dario,

This kind of error probably means that whatever is in your 
transcriptsHs19.db database is missing a metadata table with appropriate 
fields filled out.  In particular, there needs to be a field (in 
metadata) to define the "Db type" and also one to define the "Supporting 
package".  These two fields tell loadDb 1) what kind of object does it 
need to make to connect to this DB and 2) what package had that 
definition in it.

This is described in more detail in section 7 of the vignette here:

http://www.bioconductor.org/packages/2.12/bioc/vignettes/AnnotationForge/inst/doc/MakingNewAnnotationPackages.pdf

Hope that this helps,


   Marc



On 01/08/2013 11:00 PM, Dario Strbenac wrote:
> 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
>
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