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Question: ABPkgBuilder error: unable to find an inherited method for function "baseFile<-"
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gravatar for Martin Kircher
10.9 years ago by
Martin Kircher20 wrote:
Hi! I try to use the ABPkgBuilder method in the AnnBuilder library. After trying it with my one data without success, I used the example given in the vignette (http://bioconductor.org/packages/1.9/bioc/vignettes/AnnBuilder/inst/d oc/ABPrimer.pdf) and in the help for ABPkgBuilder with the same result. library(AnnBuilder) library(GO) myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") myBaseType <- "gb" mySrcUrls <- c(LL = "http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz", UG = "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz", GO = "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml") myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data", "srcb")) myDir <- tempdir() ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "myname", maintainer = "myname at myemail.com"), fromWeb = TRUE) I result with the following error, which I do not understand: # # # # # # # # # # # # # Error in function (classes, fdef, mtable) : unable to find an inherited method for function "baseFile<-", for signature "NULL" # # # # # # # # # # # # # I am using R version 2.4.1 (2006-12-18) and Bioconductor 0.9... The libraries mentioned in the vignette, I have installed in the following versions: "AnnBuilder" "1.12.0", "RSQLite" "0.4-18", "DBI" "0.1-12", "annotate" "1.12.1", "XML" "1.4-1", "Biobase" "1.12.2" I also got an error testing this with R 2.2.0 and Bioconductor 0.8 on a different machine and platform... Both systems came up with a message containing "baseFile<-"... It would be great, if someone could help me! Thanks in advance! Martin Kircher
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