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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor