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") > [[alternative HTML version deleted]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives:http://news.gmane.org/gmane.science.biology.info rmatics.conductor