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
[Bioc-devel] loadDb Arguments Mismatch
4 messages · Dario Strbenac, Marc Carlson
9 days later
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
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
2 days later
It turns out that the file wasn't properly copied to where it was being read from. After copying again, and making sure the file size was correct, the commands work.
1 day later
That makes sense since this metadata table is the very 1st thing that will be looked at when R wants to make an object. So when you have a bad .sqlite file and that table is missing or unreadable this is also the error you will see. Marc
On 01/20/2013 07:59 PM, Dario Strbenac wrote:
It turns out that the file wasn't properly copied to where it was being read from. After copying again, and making sure the file size was correct, the commands work.
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel