[BioC] Problem with ABPkgBuilder function

[John Zhang]

>#As test I am using a two column file, "tmp.txt", containing  999 
>applera ids associated to LLIDs .
>#getting the URLs available for Mm
>mySrcUrls <- getSrcUrl("all", organism = "Mus musculus")
>#I select only the GP, KEGG
>mySrcUrls<-mySrcUrls[c(2,5)]
>#since I got errors for LL, UG, and I wanted a new GO dataset I 
>downloaded them locally
>mydir <- getwd()
>myll <- paste(mydir, "LL_tmpl.gz", sep="\/")
>names(myll) <- "LL"
>myug <- paste(mydir, "Mm.data.gz", sep="\/")
>names(myug) <- "UG"
>mygo <- paste(mydir, "go_200502-termdb.rdf-xml.gz", sep="\/")#I did not 
>find a go_200502-termdb.xml.gz !!
>names(mygo) <- "GO"
>mysrc <- c(myll, myug, mygo)
>mytest<- paste(mydir, "tmp.txt", sep="\/")
>
>ABPkgBuilder(baseName = mytest, srcUrls = mySrcUrls, baseMapType =
>             "ll", pkgName = "appleraPkg", otherSrc = mysrc,
>             pkgPath = "./tmp", organism = "Mouse musculus", version = 
>"1.0.0",
>             makeXML = TRUE, author = list(author = "raf", maintainer =
>                             "raffaele.calogero at unito.it"), fromWeb = TRUE)
> 

One thing I can tell is that you should set fromWeb = FALSE as you are accessing 
locally stored data as the sources.

>
>
>
>-- 
>
>----------------------------------------
>Prof. Raffaele A. Calogero
>Bioinformatics and Genomics Unit
>Dipartimento di Scienze Cliniche e Biologiche
>c/o Az. Ospedaliera S. Luigi
>Regione Gonzole 10, Orbassano
>10043 Torino
>tel.   ++39 0116705420
>Lab.   ++39 0116705408
>Fax    ++39 0119038639
>Mobile ++39 3333827080
>email: raffaele.calogero at unito.it
>www:   www.bioinformatica.unito.it
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084