[BioC] AnnotationDbi - makeOrgPackageFromNCBI - gene_info table is not populated

[Marc Carlson]

Thanks for the info and I will look into this, but if you want human 
data why would you not use the existing package here?

http://www.bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html


   Marc



On 03/06/2012 04:10 AM, Jiri Voller [guest] wrote:
> Hello.
> I would like to report the following error, maybe gene_info.gz has some new columns. It would also be nice, if the package could use a local NCBI copy.
> Thank you + regards. Jiri
>
>
>
> library("AnnotationDbi")
> makeOrgPackageFromNCBI(version = "0.1",+
>                         author = "JV<jv at gmail.com>",+
>                         maintainer = "JV<jv at gmail.com>",+
>                         outputDir = getwd(),+
>                         tax_id = "9606",+
>                         genus = "Homo",+
>                         species = "sapiens")
>
> I am getting the following error(no traceback) when gene_info.gz is converted into the table .
>
> (until this point Getting data and populating tables is OK)
> Getting data for gene_info.gz
> Populating gene_info table:
> Error in sqliteExecStatement(con, statement, bind.data) :
>    RS-DBI driver: (error in statement: table gene_info has 3 columns but 14 values were supplied)
>
>
>
>
>   -- output of sessionInfo():
>
> R version 2.14.1 (2011-12-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=Czech_Czech Republic.1250  LC_CTYPE=Czech_Czech Republic.1250    LC_MONETARY=Czech_Czech Republic.1250 LC_NUMERIC=C                          LC_TIME=Czech_Czech Republic.1250
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RCurl_1.91-1.1        bitops_1.0-4.1        GO.db_2.6.1           RSQLite_0.11.1        DBI_0.2-5             AnnotationDbi_1.16.18 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.12.6
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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