[BioC] Question on AnnBuilder (on Windows and Linux)

[Martin Morgan]

"Alex Tsoi" <tsoi.teen at 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]]
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org