Hello,

 

I encounter problems generating an org.Oc.eg.db using the function
'makeOrgPackageFromNCBI()' from the AnnotationDbi  package version
1.18.1 (under R 2.15.1 / Bioconductor 2.10)  for the organism
'Oryctolagus cuniculus' (Rabbit - NCBI taxonomy id 9986). Please, see
transcript below for the details. 

Can anyone assist in building this database ?

 

Thanks,

Steven Osselaer

 

TRANSCRIPT : 

 

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"

Copyright (C) 2012 The R Foundation for Statistical Computing

ISBN 3-900051-07-0

Platform: x86_64-unknown-linux-gnu (64-bit)

 

R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.

 

  Natural language support but running in an English locale

 

R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.

 

Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.

 

> sessionInfo()

R version 2.15.1 (2012-06-22)

Platform: x86_64-unknown-linux-gnu (64-bit)

 

locale:

[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=C                 LC_NAME=C

[9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

> library(AnnotationDbi)

Loading required package: BiocGenerics

 

Attaching package: BiocGenerics

 

The following object(s) are masked from package:stats:

 

    xtabs

 

The following object(s) are masked from package:base:

 

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,

    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,

    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,

    rownames, sapply, setdiff, table, tapply, union, unique

 

Loading required package: Biobase

Welcome to Bioconductor

 

    Vignettes contain introductory material; view with

    'browseVignettes()'. To cite Bioconductor, see

    'citation("Biobase")', and for packages 'citation("pkgname")'.

 

> makeOrgPackageFromNCBI(

+    version    = "0.1",

+    author     = "Steven Osselaer <sosselae@its.jnj.com>",

+    maintainer = "Steven Osselaer <sosselae@its.jnj.com>",

+    outputDir  = "/dvl/bix/current/chip/docs/R_repository/src/contrib",

+    tax_id     = "9986",

+    genus      = "Oryctolagus",

+    species    = "cuniculus"

+ )

Loading required package: RSQLite

Loading required package: DBI

Loading required package: GO.db

 

Getting data for gene2pubmed.gz

Loading required package: RCurl

Loading required package: bitops

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:

table gene_info filled

Getting data for gene2go.gz

Populating gene2go table:

Getting blast2GO data as a substitute for gene2go

Error in file(file, "rt") : invalid 'description' argument

In addition: Warning message:

In unzip(tmp) : error 1 in extracting from zip file

> traceback()

8: file(file, "rt")

7: read.table(file = file, header = header, sep = sep, quote = quote,

       dec = dec, fill = fill, comment.char = comment.char, ...)

6: read.delim(unzip(tmp), header = FALSE, sep = "\t", stringsAsFactors =
FALSE)

5: .getBlast2GOData(tax_id, con)

4: .createTEMPNCBIBaseTable(con, files[i], tax_id)

3: .makeBaseDBFromDLs(files, tax_id, con)

2: makeOrgDbFromNCBI(tax_id = tax_id, genus = genus, species = species)

1: makeOrgPackageFromNCBI(version = "0.1", author = "Steven Osselaer
<sosselae@its.jnj.com>",

       maintainer = "Steven Osselaer <sosselae@its.jnj.com>", outputDir
= "/dvl/bix/current/chip/docs/R_repository/src/contrib",

       tax_id = "9986", genus = "Oryctolagus", species = "cuniculus")

> 

 


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