[BioC] error: "'names' attribute [16] must be the same length as the vector [2]", using Making Organism packages use of makeOrgPackage()

stefano romano stfn.romano at gmail.com
Mon Sep 15 10:46:36 CEST 2014


I am creating my annotation package using makeOrgPackage().
I followed the instruction here:
http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.htm

This are the dataframes and the commands I used:

> test3
       GID Gene Name                                               Protein
Name
1 PSE_0724  PSE_0724                           GCN5-related
N-acetyltransferase
2 PSE_0725  PSE_0725                           GCN5-related
N-acetyltransferase
3 PSE_0726  PSE_0726                           GCN5-related
N-acetyltransferase
4 PSE_0727  PSE_0727                           GCN5-related
N-acetyltransferase
5 PSE_0728  PSE_0728                             Acetyltransferase, GNAT
family
6 PSE_0729  PSE_0729                             Acetyltransferase, GNAT
family
7 PSE_0730  PSE_0730 Protein containing GCN5-related N-acetyltransferase
domain
8 PSE_0731  PSE_0731                 Ribosomal-protein-serine
acetyltransferase

> test2
       GID         GO EVIDENCE
1 PSE_0724 GO:0008080      IEA
2 PSE_0725 GO:0008080      IEA
3 PSE_0726 GO:0008080      IEA
4 PSE_0727 GO:0008080      IEA
5 PSE_0728 GO:0008080      IEA
6 PSE_0729 GO:0008080      IEA
7 PSE_0730 GO:0008080      IEA
8 PSE_0731 GO:0008080      IEA

> makeOrgPackage( gene_info=test3, go=test2,
version="0.1",maintainer="xxxxx <xxxx at gmail.com>", author="xxx <xxxx at
gmail.com>",outputDir = ".",
tax_id="911405",genus="Pseudovibrio",species="sp. FO-BEG1",goTable="go")

Warning message:
In file.remove(dbFileName) :
  cannot remove file './org.Psp. FO-BEG1.eg.sqlite', reason 'Permission
denied'
Error in unique(unlist(unname(lapply(data, "[", "GID")))) :
  error in evaluating the argument 'x' in selecting a method for function
'unique': Error in structure(res, levels = lv, names = nm, class =
"factor") :
  'names' attribute [16] must be the same length as the vector [2]

Can someone help me to understand this error message?

Thank you very much in advance.

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