Question: makeOrgPackageFromNCBI another error - reversed commands
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7.8 years ago by
Guest User12k
Guest User12k wrote:
Hello, one more error. It seems there are the commands reversed: 1. seed <- new("AnnDbPkgSeed", Package = paste(dbName, ".db",... 2. dbName <- .generateOrgDbName(genus, species) As for question why not to use a standard org.Hs.eg.db - I want current GO. By the way is there some package, that allows to build/update GO.db? There are "Dropping GO IDs that are too new for the current GO.db" messages... sorry for not following thread - I am using the form for nonmembers... thank you + regards jiri The Error: Error in paste(dbName, ".db", sep = "") : object 'dbName' not found > traceback() 5: paste(dbName, ".db", sep = "") 4: initialize(value, ...) 3: initialize(value, ...) 2: new("AnnDbPkgSeed", Package = paste(dbName, ".db", sep = ""), Version = version, Author = author, Maintainer = maintainer, PkgTemplate = "ORGANISM.DB", AnnObjPrefix = dbName, organism = paste(genus, species), species = paste(genus, species), biocViews = "annotation", manufacturerUrl = "no manufacturer", manufacturer = "no manufacturer", chipName = "no manufacturer") 1: makeOrgPackageFromNCBI(version = "0.1", author = "JV <jv at="" gmail.com="">", maintainer = "JV <jv at="" gmail.com="">", outputDir = getwd(), tax_id = "9606", genus = "Homo", species = "sapiens") -- output of sessionInfo(): > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Czech_Czech Republic.1250 LC_CTYPE=Czech_Czech Republic.1250 LC_MONETARY=Czech_Czech Republic.1250 LC_NUMERIC=C LC_TIME=Czech_Czech Republic.1250 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RCurl_1.91-1.1 bitops_1.0-4.1 GO.db_2.6.1 GSEABase_1.16.1 graph_1.32.0 annotate_1.32.1 org.Hs.eg.db_2.6.4 RSQLite_0.11.1 DBI_0.2-5 [10] AnnotationDbi_1.16.18 Biobase_2.14.0 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] IRanges_1.12.6 tools_2.14.1 XML_3.9-4.1 xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.
biocviews go organism chipname • 497 views
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