Dear All,
I am trying to make a TxDb package from the UCSC Macaca fascicularis annotation.
I run:
makeTxDbPackageFromUCSC( version="0.1", maintainer="UB", author="UB", destDir="/Library/Frameworks/R.framework/Versions/3.3/Resources/library", license="Artistic-2.0", genome="macFas5", tablename="refGene", transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS)
and I get this error message:
Error in .abbrevOrganismName(.getMetaDataValue(txdb, "Organism")) :
Organism should have a genus and species separated by a space,
How could I get around this problem?
Thank you very much for your help
Ugo
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.24.0 GenomicFeatures_1.26.2 AnnotationDbi_1.36.2 Biobase_2.34.0
[5] GenomicRanges_1.26.2 GenomeInfoDb_1.10.3 IRanges_2.8.1 S4Vectors_0.12.1
[9] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 mirbase.db_1.2.0 XVector_0.14.0
[4] zlibbioc_1.20.0 GenomicAlignments_1.10.0 BiocParallel_1.8.1
[7] lattice_0.20-34 tools_3.3.2 grid_3.3.2
[10] SummarizedExperiment_1.4.0 DBI_0.5-1 digest_0.6.12
[13] Matrix_1.2-8 rtracklayer_1.34.2 bitops_1.0-6
[16] RCurl_1.95-4.8 biomaRt_2.30.0 memoise_1.0.0
[19] RSQLite_1.1-2 Biostrings_2.42.1 Rsamtools_1.26.1
[22] XML_3.98-1.5
