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

[Martin Morgan]

Hi Alex -- from the help page for ABPkgBuilder:

 srcUrls: 'srcUrls' a vector of named character strings for the urls
          where source data files will be retrieved. Valid sources are
          LocusLink, UniGene, Golden Path, Gene Ontology, and KEGG. The
          names for the character strings should be LL, UG, GP, GO, and
          KEGG, respectively. LL and UG are required

Your srcUrls do not contain UG.

I'm not sure whether your gzip file problem has been solved? If it is
present, and the error is that R cannot find it; almost certainly it
is not on the PATH seen by R. Does going to the Start -> Run menu of
Windows, typing cmd and then in the resulting window gzip --version
find gzip? If not, then use the 'System' control panel, 'Advanced'
tab, 'Environment Variables' button to set PATH to include the
directory path to Rtools. If gzip is on your search path, then is the
path resulting from the R command Sys.getenv("PATH") correct? If not,
then a file (perhaps .Rhistory or .RData ??) or a script of your own
is messsing with the PATH.

Martin

"Alex Tsoi" <tsoi.teen at gmail.com> writes:

> 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 at fhcrc.org> wrote:
>
>           "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]] > > _______________________________________________ >
>      Bioconductor mailing list > Bioconductor at 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     

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org