error: "'names' attribute [16] must be the same length as the vector [2]", using Making Organism packages use of makeOrgPackage()
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artur ▴ 80
@artur-6730
Last seen 6.3 years ago
Germany

I am creating my annotation package using makeOrgPackage().

I followed the instruction here: http://www.bioconductor.org/packages/release/bioc/vignettes/Annotation Forge/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 ", author="xxx ",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. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

annotationforge Annotation GO • 6.9k views
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Hi Artur,

Did you resolve the problem? I have the same problem as you, without strange the character in the species name...

Do you have the solution?
Thanks!

Bastien

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OK, I found the solution, the GID needs to be a vector of character and not a factor...

Cheers!

Bastien

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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.8 years ago
United States

The 1st thing I would do in troubleshooting this is to remove the whitespaces and hyphen characters from the species name you have provided here.  Those characters are not allowed for an R package name (which unfortunately is what this function is going to attempt to do with that string).

Hopefully that will speed you along your way,

  Marc

 

 

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