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List: bioconductor
Subject: [BioC] error: "'names' attribute [16] must be the same length as the vector [2]", using Making Organ
From: stefano romano <stfn.romano () gmail ! com>
Date: 2014-09-15 8:46:36
Message-ID: CAFL3zPat-NsuYpZWV=z7K1EhX6VVin2pKYcGQaGmkPMs6qf5Tw () mail ! gmail ! com
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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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