[BioC] problems when trying to use biomaRt
Jenny Drnevich
drnevich at illinois.edu
Wed Mar 17 23:05:38 CET 2010
Hi Juan,
Was your Mac on the same internet connection as your PC? I have
trouble with my PC in my office, but other PC's at the University
(but not our network) don't have this problem. I think one of my
co-workers has a Mac - if I have time tomorrow, I'll see if he'll let
me test it out on his machine through our network.
Jenny
At 09:47 AM 3/17/2010, Juan Pablo Fededa wrote:
>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 at 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 at 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 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
> > >> 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
> >
>
> [[alternative HTML version deleted]]
>
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Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu
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