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Question: Error in makeOrgPackageFromNCBI
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gravatar for Chris Whelan
4.4 years ago by
Chris Whelan60
Chris Whelan60 wrote:
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? Thanks, Chris > 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) locale: [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
ADD COMMENTlink written 4.4 years ago by Chris Whelan60
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