Thanks Martin, I fixed the problems in Windows and Linux, and I used:
>  mysrcUrl <-  c(LL = "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz",
GO = "http://www.godatabase.org/dev/database/archive/latest")

however, now I received another problem:

(Windows)
Error in function (classes, fdef, mtable)  :
        unable to find an inherited method for function "baseFile<-", for
signature "NULL"

(Linux)
Error in "baseFile<-"(`*tmp*`, value = "/tmp/Rtmp6w4jG8/tempFile74b0dc51") :

        no direct or inherited method for function 'baseFile<-' for this
call


Appreciate for any suggestion

Thanks,
Alex






> Error in system(paste("gzip -d", fileName), intern = TRUE) :
>         gzip not found
> Error in unzipFile(fileName, destDir, TRUE) :
>         Gzip is either not installed or not in your path.
>  You may need to install the Rtools available at:
>   http://www.stats.ox.ac.uk/pub/Rtools/

I also checked my gzip --version, and it is supposed to be the version in
Rtools ....


On 5/12/07, Martin Morgan <mtmorgan@fhcrc.org> wrote:
>
> "Alex Tsoi" <tsoi.teen@gmail.com> writes:
>
> > Hi All,
> >
> > I am working to use AnnBuilder to build a package for a microarray.
> >
> > I am here just use the small data set from thgu95a in the AnnBuilder as
> > illustrations of the problems I am facing
> >
> >
> > When I use my R 2.4.1 in windows,
> >> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a")
> >> myBaseType <- "gb"
> >> mySrcUrls <- getOption("AnnBuilderSourceUrls")
> >> myDir <- tempdir()
> >> ABPkgBuilder(baseName = myBase, srcUrl = mySrcUrls, baseMapType =
> > myBaseType,
> > + pkgName = "myPkg", pkgPath = myDir, organism = "Homo sapens", version
> = "
> > 1.1.0", author = "alex", fromWeb = TRUE)
> >
> > and I receive the error:
> >
> > Error in system(paste("gzip -d", fileName), intern = TRUE) :
> >         gzip not found
> > Error in unzipFile(fileName, destDir, TRUE) :
> >         Gzip is either not installed or not in your path.
> >  You may need to install the Rtools available at:
> >   http://www.stats.ox.ac.uk/pub/Rtools/
> >
> >
> > but I already have the Gzip installed in my windows, and it is in the
> path
> > already.....
>
> Probably though your gzip is not the one R is expecting. R uses
> several non-standard versions of tools, and these have to be 'found'
> first. Likely you need to follow the directions in the 'R Installation
> and Administration' guide, appendix E (available at
> http://r-project.org, or 'HTML help' under the 'Help' menu).. The
> instructions are tedious, and you have to follow them exactly. When
> you think you've got things set up, open a 'cmd' window and type gzip
> --version and see that it is the right one, i.e., the one in Rtools;
> remember that the directory where Rtools is installed needs to be at
> the front of the 'PATH' environment variable.
>
> Sorry if this is all familiar to you, and not relevnt. I've just
> started to use AnnBuilder on windows myself, and would not be entirely
> surprised if there are other problems.
>
>
> > Then I tried to use LInux with R 2.3.1 installed, and I used the same
> code
> > as above and I get this error message:
> >
> > Error in validObject(.Object) : invalid class "GO" object: invalid
> object
> > for slot "srcUrl" in class "GO": got class "list", should be or extend
> class
> > "character"
> >
> > However, my object for srcUrl$GO is;
> >
> >> mySrcUrls$GO
> > [1] "http://www.godatabase.org/dev/database/archive/latest"
> >
>
> From ?ABPkgBuilder:
>
>    srcUrls: 'srcUrls' a vector of named character strings for the urls
>
> but
>
> > class(mySrcUrls)
> [1] "list"
>
> so either unlist(mySrcUrls) to get the list as a character vector or
> mySrcUrls[["GO"]] to get the GO url.
>
> Martin
>
> > I greatly appreciate if anyone could show me how to solve the problem.
> > Thanks,
> >
> > Alex-
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> Martin Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
>

	[[alternative HTML version deleted]]

