[BioC] AnnotationDbi : makeOrgPackageFromNCBI fails for 'Oryctolagus cuniculus' (Rabbit - tax id : 9986)

[Marc Carlson]

Hi Steven,

I am happy to hear you are using this tool.  The error indicates that 
for rabbits, NCBI does not have GO data, so the function then tries to 
get that data from blast2go, and the problem is that they have changed 
their web service so the URL that it generates no longer gets the data.  
I have worked out how to fix this, and so an updated package should be 
available in a day or so (once it is built by the build system).

   Marc


On 09/04/2012 04:18 AM, Osselaer, Steven [JRDBE Extern] wrote:
> 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 at its.jnj.com>",
>
> +    maintainer = "Steven Osselaer<sosselae at 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 at its.jnj.com>",
>
>         maintainer = "Steven Osselaer<sosselae at its.jnj.com>", outputDir
> = "/dvl/bix/current/chip/docs/R_repository/src/contrib",
>
>         tax_id = "9986", genus = "Oryctolagus", species = "cuniculus")
>
>
>
>
> 	[[alternative HTML version deleted]]
>
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