[BioC] ABPkgBuilder error: unable to find an inherited method for function "baseFile<-"

[John Zhang]

I just fixed the problem in AnnBuilder (1.1.3.12). If you can not access the new 
version here is the solution for now.

mySrcUrls <- AnnBuilder:::getSrcUrl("all", "Homo sapiens")

then the code should run.

The short versions of source files do not work any more due to a switch from 
LocusLink to Entrez Gene.

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>From: Martin Kircher <kirmar at mpi-inf.mpg.de>
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>Subject: [BioC] ABPkgBuilder error: unable to find an inherited method for 
function "baseFile<-"
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>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/doc/ABPrim
er.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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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084