[BioC] ABPkgBuilder error: unable to find an inherited method for function "baseFile<-"
Martin Kircher
kirmar at mpi-inf.mpg.de
Thu Jan 11 11:43:47 CET 2007
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/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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