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

Jiri Voller [guest] guest at bioconductor.org
Tue Mar 6 13:10:10 CET 2012

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

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)

[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

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