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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