[BioC] Error in makeOrgPackageFromNCBI

Chris Whelan whelanch at ohsu.edu
Mon Jun 10 20:41:38 CEST 2013

Hi All,

I tried to build an OrgDB package from NCBI for gibbon (nomascus leukogenys) and got the error below. Any thoughts on what the problem might be? I was hoping to annotate chip-seq peaks using ChipPeakAnno and GO annotations; I think there's probably ways for me to do this by hand using my data and GOStats, but thought I'd report this error here.

And just in case my Googling hasn't turned up something I should have seen: is there anywhere I could look for an example or specification of how to make an OrgDB package based on data from, say, Ensembl/BioMart?



> makeOrgPackageFromNCBI(                                                                                                                                                                     
+          version="0.1",                                                                                                                                                                     
+          maintainer="Chris Whelan <XXX at XXX>",                                                                                                                                     
+          author="Chris Whelan <XXX at XXX>",                                                                                                                                         
+          outputDir=".",                                                                                                                                                                     
+          tax_id=61853,                                                                                                                                                                      
+          genus="Nomascus",                                                                                                                                                                  
+          species="leucogenys")                                                                                                                                                              
Getting data for gene2pubmed.gz
Populating gene2pubmed table:
table gene2pubmed filled
Getting data for gene2accession.gz
Populating gene2accession table:
table gene2accession filled
Getting data for gene2refseq.gz
Populating gene2refseq table:
table gene2refseq filled
Getting data for gene2unigene
Populating gene2unigene table:
table gene2unigene filled
Getting data for gene_info.gz
Populating gene_info table:
No data available for table gene_info
Getting data for gene2go.gz
Populating gene2go table:
Getting blast2GO data as a substitute for gene2go
table metadata filled
table map_metadata filled
table gene2go filled
table metadata filled
table map_metadata filled
Populating genes table:
Error in sqliteExecStatement(con, statement, bind.data) :
  bind.data must have non-zero dimensions

> traceback()
8: stop("bind.data must have non-zero dimensions")
7: sqliteExecStatement(con, statement, bind.data)
6: sqliteQuickSQL(conn, statement, bind.data, ...)
5: dbGetPreparedQuery(con, sql, gene_id)
4: dbGetPreparedQuery(con, sql, gene_id)
3: .makeCentralTable(egs, con)
2: makeOrgDbFromNCBI(tax_id = tax_id, genus = genus, species = species)
1: makeOrgPackageFromNCBI(version = "0.1", maintainer = "Chris Whelan <XXX at XXX>",
       author = "Chris Whelan <cwhelan at gmail.com>", outputDir = ".",
       tax_id = 61853, genus = "Nomascus", species = "leucogenys")

> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-pc-linux-gnu (64-bit)

[1] C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] RCurl_1.95-4.1                      bitops_1.0-5
 [3] AnnotationForge_1.0.3               rtracklayer_1.18.2
 [5] ChIPpeakAnno_2.6.1                  limma_3.14.4
 [7] org.Hs.eg.db_2.8.0                  GO.db_2.8.0
 [9] RSQLite_0.11.4                      DBI_0.2-7
[11] AnnotationDbi_1.20.7                BSgenome.Ecoli.NCBI.20080805_1.3.17
[13] multtest_2.14.0                     Biobase_2.18.0
[15] biomaRt_2.14.0                      VennDiagram_1.6.0
[17] BSgenome_1.26.1                     Biostrings_2.26.3
[19] GenomicRanges_1.10.7                IRanges_1.16.6
[21] BiocGenerics_0.4.0                  BiocInstaller_1.8.3

loaded via a namespace (and not attached):
 [1] MASS_7.3-23      Rsamtools_1.10.2 XML_3.96-1.1     compiler_2.15.3
 [5] parallel_2.15.3  splines_2.15.3   stats4_2.15.3    survival_2.37-4
 [9] tools_2.15.3     zlibbioc_1.4.0

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