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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