I am trying to run makeOrgPackageFromNCBI, as follows -
> makeOrgPackageFromNCBI(version="0.1", + author="otills <*******@*******>", + maintainer="otills <*******@*******>", + outputDir=".", + tax_id="582868", + genus="Mollusca", + species="Radix balthica")
However, after approx 30 mins I get the error -
Getting data for gene2pubmed.gz Loading required package: RCurl Loading required package: bitops extracting only data for our organism from : gene2pubmed Getting data for gene2accession.gz Error in sqliteSendQuery(con, statement, bind.data) : error in statement: duplicate column name: NA
I've tried re-running (including on different machines), but I get this error consistently. The file sizes (gene2accession.gz, gene2pubmed.gz and NCBI.sqlite) are always the same size at the time of crash.
Can anyone suggest what the problem might be?
> sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  RCurl_1.95-4.5 bitops_1.0-6 AnnotationForge_1.8.1 org.Hs.eg.db_3.0.0 RSQLite_1.0.0  DBI_0.3.1 AnnotationDbi_1.28.1 GenomeInfoDb_1.2.4 IRanges_2.0.1 S4Vectors_0.4.0  Biobase_2.26.0 BiocGenerics_0.12.1 BiocInstaller_1.16.1 loaded via a namespace (and not attached):  tools_3.1.2 >