I found out that is Windows specific, all the functions work fine in Mac I
just found out.
I also try different version of R on Win and none worked with biomaRt.
Any clue from this facts?
TNX,


Juan

On Wed, Mar 17, 2010 at 3:29 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 03/17/2010 06:54 AM, Juan Pablo Fededa wrote:
> > Thanks Martin,
> >
> > I get the next answer performing debug on useMart:
> >
> >
> >> library("biomaRt")
> >> debug(useMart)
> >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> > debugging in: useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> > debug: {
> >     if (local || mysql || !missing(user) || !missing(password)) {
> >         .Defunct(msg = "mysql access to Ensembl is no longer available
> > through this package the web service mode supports all queries.  If mysql
> is
> > needed a separate package will become available with limited mysql query
> > support.")
> >     }
> >     if (missing(biomart))
> >         stop("No biomart databases specified. Specify a biomart database
> to
> > use using the biomart argument")
> >     if (!(is.character(biomart)))
> >         stop("biomart argument is no string.  The biomart argument should
> be
> > a single character string")
> >     marts = NULL
> >     marts = listMarts(host = host, path = path, port = port,
> >         includeHosts = TRUE, archive = archive)
> >     mindex = match(biomart, marts$biomart)
> >     if (is.na(mindex) || archive) {
> >         mindex = match(biomart, marts$database)
> >     }
> >     if (is.na(mindex))
> >         stop("Incorrect BioMart name, use the listMarts function to see
> > which BioMart databases are available")
> >     if (is.na(marts$path[mindex]) || is.na(marts$vschema[mindex]) ||
> >         is.na(marts$host[mindex]) || is.na(marts$port[mindex]) ||
> >         is.na(marts$path[mindex]))
> >         stop("The selected biomart databases is not available due to
> error
> > in the BioMart central registry, please report so the BioMart registry
> file
> > can be fixed.")
> >     if (marts$path[mindex] == "")
> >         marts$path[mindex] = "/biomart/martservice"
> >     if (archive)
> >         biomart = marts$biomart[mindex]
> >     biomart = sub(" ", "%20", biomart)
> >     mart <- new("Mart", biomart = biomart, vschema =
> marts$vschema[mindex],
> >         host = paste("http://", marts$host[mindex], ":",
> marts$port[mindex],
> >
> >             marts$path[mindex], sep = ""), archive = archive)
> >     if (!missing(dataset)) {
> >         mart = useDataset(mart = mart, dataset = dataset)
> >     }
> >     return(mart)
> > }
> > Browse[2]>
> >
> >
> > In the step-by-step execution of the above function, R GUI starts not
> > responding after:
> >
> > mart = useDataset(mart = mart, dataset = dataset)
> >
> > Any clue about what is going on?
>
> now try debug(useDataset), and so on. Some functions might not be
> exported from biomaRt's name space, and then you will need to
> debug(biomaRt:::bmAttrFilter), for instance. When you do get to the
> 'bottom' of the problem, it would be good to know what the variable
> values are, e.g., some biomaRt functions seem to compose a variable
> named 'request' that contains the string to be sent to biomaRt.
>
> From Jenny's post, I'm not sure how successful this will be in the long
> run, but it would be helpful to have a precise location of the problem.
>
> Martin
>
> > Thanks again,
> >
> >
> > Juan
> >
> >
> >
> >
> >
> > On Wed, Mar 17, 2010 at 2:39 PM, Martin Morgan <mtmorgan@fhcrc.org>
> wrote:
> >
> >> On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote:
> >>> Dear bioconductor-help contributors,
> >>>
> >>>
> >>> I'm trying to use biomaRt package in R, and when I run the next line,
> the
> >> R
> >>> GUI crashes:
> >>>
> >>> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> >>>
> >>> Theres is no error message at all, simply R is not responding anymore.
> >>> when loading library(biomaRt) the prompt sign appears again, and you
> can
> >>> already run basic things like:
> >>> listMarts()
> >>
> >> This is unusual, because the only part of useMart that might end up with
> >> real trouble is a call to listMarts() ! Start R with the --vanilla
> >> argument, e.g., from the DOS shell
> >>
> >>  Rgui --vanilla
> >>
> >> try to place a debugger on useMart, and step through until R stops
> >> responding. Restart R, get to a similar place, and look at the arguments
> >> to the function that causes problems. Any hints?
> >>
> >>  > debug(useMart)
> >>   > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> >>   Browser[2]> n
> >>
> >> ('n' is for 'next', see ?browser)
> >>
> >> Martin
> >>
> >>>
> >>> When I run sessionInfo() I get this:
> >>>
> >>> R version 2.10.1 (2009-12-14)
> >>> i386-pc-mingw32
> >>>
> >>> locale:
> >>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> >>> States.1252
> >>> [3] LC_MONETARY=English_United States.1252
> >>> LC_NUMERIC=C
> >>> [5] LC_TIME=English_United States.1252
> >>>
> >>> attached base packages:
> >>> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>>
> >>> other attached packages:
> >>> [1] biomaRt_2.2.0
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] RCurl_1.3-1 XML_2.6-0
> >>>
> >>> Do you have any idea of what can I change to make it work?
> >>> Thanks in advance,
> >>>
> >>>       [[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
> >> Computational Biology / Fred Hutchinson Cancer Research Center
> >> 1100 Fairview Ave. N.
> >> PO Box 19024 Seattle, WA 98109
> >>
> >> Location: Arnold Building M1 B861
> >> Phone: (206) 667-2793
> >>
> >
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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