[BioC] problems when trying to use biomaRt
Jenny Drnevich
drnevich at illinois.edu
Wed Mar 17 16:13:56 CET 2010
Hi Martin,
>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.
Here are my variable values:
debug: tryCatchList(expr, classes, parentenv, handlers)
Browse[2]> expr
[1] "\n<MartRegistry>\n <MartURLLocation
database=\"ensembl_mart_57\" default=\"1\" displayName=\"ENSEMBL
GENES 57 (SANGER UK)\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"ensembl\" path=\"/biomart/martservice\"
port=\"80\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"snp_mart_57\" default=\"0\"
displayName=\"ENSEMBL VARIATION 57 (SANGER UK)\"
host=\"www.biomart.org\" includeDatasets=\"\" martUser=\"\"
name=\"snp\" path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"functional_genomics_mart_57\" default=\"0\"
displayName=\"ENSEMBL FUNCTIONAL GENOMICS 57 (SANGER UK)\"
host=\"www.biomart.org\" includeDatasets=\"\" martUser=\"\"
name=\"functional_genomics\" path=\"/biomart/martservice\"
port=\"80\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"vega_mart_57\" default=\"0\"
displayName=\"VEGA 37 (SANGER UK)\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"vega\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"genomic_features_mart_57\" default=\"0\"
displayName=\"ENSEMBL GENOMIC FEATURES 57 (SANGER UK)\"
host=\"www.biomart.org\" includeDatasets=\"\" martUser=\"\"
name=\"genomic_features\" path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"ontology_mart_57\" default=\"0\" displayName=\"ENSEMBL
ONTOLOGY 57 (SANGER UK)\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"ontology\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"sequence_mart_57\" default=\"0\" displayName=\"ENSEMBL
SEQUENCE 57 (SANGER UK)\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"sequence\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"bacterial_mart_4\" default=\"0\" displayName=\"ENSEMBL
BACTERIA 4 (EBI UK)\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"bacterial_mart_4\" path=\"/biomart/martservice\"
port=\"80\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"bacterial_sequence_mart_4\"
default=\"0\" displayName=\"\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"bacterial_sequence_mart_4\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"fungal_mart_4\" default=\"0\" displayName=\"ENSEMBL FUNGAL
4 (EBI UK)\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"fungal_mart_4\" path=\"/biomart/martservice\"
port=\"80\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"fungal_sequence_mart_4\"
default=\"0\" displayName=\"\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"fungal_sequence_mart_4\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"metazoa_genomic_features_mart_4\" default=\"0\"
displayName=\"\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"metazoa_genomic_features_mart_4\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"metazoa_mart_4\" default=\"1\" displayName=\"ENSEMBL
METAZOA 4 (EBI UK)\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"metazoa_mart_4\" path=\"/biomart/martservice\"
port=\"80\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"metazoa_sequence_mart_4\"
default=\"0\" displayName=\"\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"metazoa_sequence_mart_4\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"plant_mart_4\" default=\"0\" displayName=\"ENSEMBL PLANT 4
(EBI UK)\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"plant_mart_4\" path=\"/biomart/martservice\"
port=\"80\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"plant_sequence_mart_4\"
default=\"0\" displayName=\"\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"plant_sequence_mart_4\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"protist_mart_4\" default=\"1\" displayName=\"ENSEMBL
PROTISTS 4 (EBI UK)\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"protist_mart_4\" path=\"/biomart/martservice\"
port=\"80\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"protist_sequence_mart_4\"
default=\"0\" displayName=\"\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"protist_sequence_mart_4\"
path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"0\" />\n <MartURLLocation
database=\"msd_mart_4\" default=\"0\" displayName=\"MSD PROTOTYPE
(EBI UK)\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"msd\" path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"utlp\" default=\"\" displayName=\"HIGH THROUGHPUT GENE
TARGETING AND TRAPPING (SANGER UK)\" host=\"www.sanger.ac.uk\"
includeDatasets=\"\" martUser=\"\" name=\"htgt\"
path=\"/htgt/biomart/martservice\" port=\"80\" redirect=\"1\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"test_reactome_mart\" default=\"1\" displayName=\"REACTOME
(CSHL US)\" host=\"banon.cshl.edu\"
includeDatasets=\"complex,pathway,reaction,interaction\"
martUser=\"\" name=\"REACTOME\" path=\"/biomart/martservice\"
port=\"5555\" redirect=\"1\" serverVirtualSchema=\"default\"
visible=\"1\" />\n <MartURLLocation database=\"wormmart\"
default=\"1\" displayName=\"WORMBASE (CSHL US)\"
host=\"www.wormbase.org\" includeDatasets=\"\" martUser=\"\"
name=\"wormbase_current\" path=\"/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation default=\"0\" displayName=\"DICTYBASE
(NORTHWESTERN US)\" host=\"www.dictybase.org\" includeDatasets=\"\"
martUser=\"\" name=\"dicty\" path=\"/biomart/martservice\"
port=\"80\" redirect=\"1\" serverVirtualSchema=\"dictyMart\"
visible=\"1\" />\n <MartURLLocation database=\"biomart\"
default=\"1\" displayName=\"MGI (JACKSON LABORATORY US)\"
host=\"biomart.informatics.jax.org\" includeDatasets=\"markers\"
name=\"biomart\" path=\"/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"rgd__mart\" default=\"\"
displayName=\"RGD GENES (MCW US)\" host=\"rote.hmgc.mcw.edu\"
includeDatasets=\"\" martUser=\"\" name=\"rgd__mart\"
path=\"/biomart/martservice\" port=\"9999\" redirect=\"1\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"ipi_rat__mart\" default=\"\" displayName=\"RGD IPI MART
(MCW US)\" host=\"rote.hmgc.mcw.edu\" includeDatasets=\"\"
martUser=\"\" name=\"ipi_rat__mart\" path=\"/biomart/martservice\"
port=\"9999\" redirect=\"1\" serverVirtualSchema=\"default\"
visible=\"1\" />\n <MartURLLocation database=\"SSLP__mart\"
default=\"\" displayName=\"RGD MICROSATELLITE MARKERS (MCW US)\"
host=\"rote.hmgc.mcw.edu\" includeDatasets=\"\" martUser=\"\"
name=\"SSLP__mart\" path=\"/biomart/martservice\" port=\"9999\"
redirect=\"1\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"g4public\" default=\"\"
displayName=\"HGNC (EBI UK)\" host=\"www.genenames.org\"
includeDatasets=\"\" name=\"g4public\" path=\"/biomart/martservice\"
port=\"80\" redirect=\"1\" serverVirtualSchema=\"default\"
visible=\"1\" />\n <MartURLLocation database=\"pride_mart_1\"
default=\"1\" displayName=\"PRIDE (EBI UK)\" host=\"www.ebi.ac.uk\"
includeDatasets=\"\" martUser=\"\" name=\"pride\"
path=\"/pride/biomart/martservice\" port=\"80\" redirect=\"1\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"intermart_2\" default=\"1\" displayName=\"INTERPRO (EBI
UK)\" host=\"www.biomart.org\" includeDatasets=\"\" martUser=\"\"
name=\"prod-intermart_2\" path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"SPMART\" default=\"\" displayName=\"UNIPROT (EBI UK)\"
host=\"www.ebi.ac.uk\" includeDatasets=\"\" martUser=\"\"
name=\"uniprot_mart\" path=\"/uniprot/biomart/martservice\"
port=\"80\" redirect=\"1\" serverVirtualSchema=\"default\"
visible=\"1\" />\n <MartURLLocation
database=\"ensembl_expressionmart_48\" default=\"1\"
displayName=\"EURATMART (EBI UK)\" host=\"www.ebi.ac.uk\"
includeDatasets=\"\" martUser=\"\" name=\"ensembl_expressionmart_48\"
path=\"/euratools/biomart/martservice\" port=\"80\" redirect=\"1\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"biomartDB\" default=\"\" displayName=\"PARAMECIUM GENOME
(CNRS FRANCE)\" host=\"paramecium.cgm.cnrs-gif.fr\"
includeDatasets=\"macronuclear\" martUser=\"\" name=\"biomartDB\"
path=\"/biomart/martservice\" port=\"80\" redirect=\"1\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"tdb_biomart_new\" default=\"\" displayName=\"EUREXPRESS
(MRC EDINBURGH UK)\" host=\"biomart.eurexpress.org\"
includeDatasets=\"template\" martUser=\"\" name=\"Eurexpress
Biomart\" path=\"/biomart/martservice\" port=\"80\" redirect=\"1\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"pepseekerGOLD_mart06\" default=\"0\"
displayName=\"PEPSEEKER (UNIVERSITY OF MANCHESTER UK)\"
host=\"www.ispider.manchester.ac.uk\" includeDatasets=\"peptide\"
martUser=\"\" name=\"pepseekerGOLD_mart06\"
path=\"/pepseeker/biomart/martservice\" port=\"80\" redirect=\"1\"
serverVirtualSchema=\"pepseekerGOLD\" visible=\"1\"
/>\n <MartURLLocation database=\"datacippotato_martpot_001\"
default=\"\" displayName=\"DB_POTATO (INTERNATIONAL POTATO
CENTER-CIP)\" host=\"germplasmdb.cip.cgiar.org\" includeDatasets=\"\"
martUser=\"\" name=\"Potato_01\" path=\"/biomart/martservice\"
port=\"80\" redirect=\"1\" serverVirtualSchema=\"default\"
visible=\"1\" />\n <MartURLLocation
database=\"datacipsweet_martsweet_001\" default=\"\"
displayName=\"DB_SWEETPOTATO (INTERNATIONAL POTATO CENTER-CIP)\"
host=\"germplasmdb.cip.cgiar.org\" includeDatasets=\"\" martUser=\"\"
name=\"Sweetpotato_01\" path=\"/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"phytozome_mart_v5\" default=\"\"
displayName=\"PHYTOZOME (JGI/CIG US)\" host=\"www.phytozome.net\"
includeDatasets=\"\" martUser=\"\" name=\"phytozome_mart\"
path=\"/biomart/martservice\" port=\"80\" redirect=\"1\"
serverVirtualSchema=\"zome_mart\" visible=\"1\"
/>\n <MartURLLocation database=\"sequence_mart_v5\" default=\"\"
displayName=\"Sequences\" host=\"www.phytozome.net\"
includeDatasets=\"sequence_phytozome\" martUser=\"\"
name=\"sequence_mart\" path=\"/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"zome_mart\" visible=\"0\"
/>\n <MartURLLocation database=\"mart_cyanobase_1\" default=\"1\"
displayName=\"CYANOBASE 1 (KAZUSA JAPAN)\" host=\"mart.kazusa.or.jp\"
includeDatasets=\"\" martUser=\"default\" name=\"cyanobase_1\"
path=\"/biomart/martservice\" port=\"80\" redirect=\"1\"
serverVirtualSchema=\"default\" visible=\"1\" />\n <MartURLLocation
database=\"hapmart_27_36\" default=\"1\" displayName=\"HAPMAP 27
(NCBI US)\" host=\"hapmap.ncbi.nlm.nih.gov\" includeDatasets=\"\"
name=\"HapMap_rel27\" path=\"/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"rel27_NCBI_Build36\"
visible=\"1\" />\n <MartURLLocation database=\"cosp\" default=\"1\"
displayName=\"COSMIC (SANGER UK)\" host=\"www.sanger.ac.uk\"
includeDatasets=\"\" martUser=\"\" name=\"CosmicMart\"
path=\"/genetics/CGP/cosmic/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"cosmic\" visible=\"1\"
/>\n <MartURLLocation database=\"ciliumDBall\" default=\"\"
displayName=\"CILDB INPARANOID AND FILTERED BEST HIT (CNRS FRANCE)\"
host=\"cildb.cgm.cnrs-gif.fr\" includeDatasets=\"\"
name=\"ciliumDBall\" path=\"/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"ciliumDBinp\" default=\"\"
displayName=\"CILDB INPARANOID (CNRS FRANCE)\"
host=\"cildb.cgm.cnrs-gif.fr\" includeDatasets=\"\"
name=\"ciliumDBinp\" path=\"/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"ciliumDBcutoff\" default=\"\"
displayName=\"CILDB FILTERED BLASTP (CNRS FRANCE)\"
host=\"cildb.cgm.cnrs-gif.fr\" includeDatasets=\"\"
name=\"ciliumDBcutoff\" path=\"/biomart/martservice\" port=\"80\"
redirect=\"1\" serverVirtualSchema=\"default\" visible=\"1\"
/>\n <MartURLLocation database=\"ensembl_latest\" default=\"\"
displayName=\"PANCREATIC EXPRESSION DATABASE (INSTITUTE OF CANCER
UK)\" host=\"www.pancreasexpression.org\" includeDatasets=\"\"
martUser=\"\" name=\"Ensembl56\" path=\"/biomart/martservice\"
port=\"80\" redirect=\"1\" serverVirtualSchema=\"default\"
visible=\"1\" />\n</MartRegistry>\n"
Browse[2]> classes
[1] "error"
Browse[2]> parentenv
<environment: 0x023bb8e8>
Browse[2]> handlers
$error
function (e)
{
stop("Request to BioMart web service failed. Verify if you are
still connected to the internet. Alternatively the BioMart web
service is temporarily down.")
}
<environment: 0x023bb8e8>
Browse[2]>
Thanks,
Jenny
>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
>
>_______________________________________________
>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
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
More information about the Bioconductor
mailing list