[BioC] AnnBuilder/ABPkgBuilder: lots of Errors

John Zhang jzhang at jimmy.harvard.edu
Tue Sep 7 15:42:15 CEST 2004


>If i install AnnBuilder 1.4.2 i get it installed but then the same  
>thing happens that was reported earlier, see mail below.
>
> > 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 = "testPkg", pkgPath =  
>myDir,  organism = "human", version = "1.1.0", makeXML = TRUE, author =  
>list(author = "kees", maintainer = "kees at myemail.com"), fromWeb = TRUE)
>[1] "It may take me a while to process the data. Be patient!"
>Error in url(sourceURLs[["GO"]], open = "r") :
>	Object "sourceURLs" not found


The bug has been fixed but not pushed to the release vresion yet. You may try 

> getSrcUrl("GO")

before running your code. Let me know if this does not work for you. Thanks.



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