[BioC] Error in BioMart and wormbase
steffen at stat.Berkeley.EDU
steffen at stat.Berkeley.EDU
Wed Feb 4 21:44:58 CET 2009
Hi Christof,
Either you are not online or Ensembl was temporary down when you did your
query. Can you check if you're online and try it again?
I get:
> listMarts()
biomart
version
1 ensembl ENSEMBL 52 GENES
(SANGER UK)
2 snp ENSEMBL 52 VARIATION
(SANGER UK)
3 vega VEGA 33
(SANGER UK)
4 msd MSD
PROTOTYPE (EBI UK)
5 htgt HIGH THROUGHPUT GENE TARGETING AND TRAPPING
(SANGER UK)
6 ENSEMBL_MART_ENSEMBL GRAMENE GENES
(CSHL US)
7 ENSEMBL_MART_SNP GRAMENE SNPS
(CSHL US)
8 REACTOME REACTOME
(CSHL US)
9 wormbase_current WORMBASE
(CSHL US)
10 dicty DICTYBASE
(NORTHWESTERN US)
11 rgd__mart RGD
GENES (MCW US)
12 ipi_rat__mart RGD IPI
MART (MCW US)
13 SSLP__mart RGD MICROSATELLITE
MARKERS (MCW US)
14 g4public
HGNC (EBI UK)
15 pride
PRIDE (EBI UK)
16 uniprot_mart
UNIPROT (EBI UK)
17 ensembl_expressionmart_48
EURATMART (EBI UK)
18 biomartDB PARAMECIUM GENOME
(CNRS FRANCE)
19 Eurexpress Biomart EUREXPRESS (MRC
EDINBURGH UK)
20 pepseekerGOLD_mart06 PEPSEEKER (UNIVERSITY OF
MANCHESTER UK)
21 Pancreatic_Expression PANCREATIC EXPRESSION DATABASE (INSTITUTE OF
CANCER UK)
> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_1.99.4
loaded via a namespace (and not attached):
[1] RCurl_0.91-0 XML_1.98-1
Cheers,
Steffen
> Dear Steffen,
>
> I had the same problem as Ana. I did as you suggested and installed the
> dev
> version of biomaRt (downloading the .tar.gz and installing with R CMD
> INSTALL,
> running Debian Linux). Now I cannot even connect to BioMart anymore (I
> checked
> with another machine, there connecting still works, so it's not BioMart
> being down):
>
> > library(biomaRt)
> > listMarts()
> Error in value[[3]](cond) :
> Request to BioMart web service failed. Verify if you are still
> connected to
> the internet. Alternatively the BioMart web service is temporarily down.
> > sessionInfo()
> R version 2.7.1 (2008-06-23)
> i486-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_1.99.4
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-0 XML_1.99-0
>
> After getting this error, i also installed the dev versions of the
> packages XML
> and RCurl, but the error remains.
>
> Do you have any idea how to solve this? Could it be because of the base
> package
> "methods", which is not dev as well?
>
> Thanks,
> Christof
>
> steffen at stat.berkeley.edu wrote, On 28.01.2009
> 06:37:
>> Dear Ana,
>>
>> It looks like there is a problem with the XML configuration file for
>> that
>> dataset. If you upgrade to using the dev version of biomaRt
>> (http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html) you should
>> be fine for this dataset, as that version does not depend on this XML
>> file
>> anymore.
>>
>> worbase_gene works for me see below:
>>
>>> library(biomaRt)
>>>
>>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene")
>>
>> Checking attributes ... ok
>> Checking filters ... ok
>>> att = listAttributes(wormbase)
>>> att[1:10,]
>> name description
>> 1 species Species
>> 2 gene Gene WB ID
>> 3 sequence_name Sequence Name (Gene)
>> 4 public_name Gene Public Name
>> 5 cds Sequence Name (CDS)
>> 6 cgc_name Gene CGC Name
>> 7 transcript Sequence Name (Transcript)
>> 8 name_dmlist Gene Names (merged)
>> 9 cds_dmlist Sequence Names (CDS) (merged)
>> 10 transcript_dmlist Sequence Names (Transcript) (merged)
>>
>>> sessionInfo()
>> \R version 2.8.0 (2008-10-20)
>> powerpc-apple-darwin8.11.1
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] biomaRt_1.99.4
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.92-0 XML_1.98-1
>>
>>
>>
>>> Dear all,
>>>
>>> I've been experience a problem with BioMart when I tried to access
>>> wormbase. I am getting an error when I tried to use a specific dataset
>>> (wormbase_gene). This problem do not exist when I access any other
>>> dataset from wormbase. Besides, few months ago a used this code without
>>> problems.
>>>
>>>
>>>> library(biomaRt)
>>>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene")
>>> Checking attributes and filters ...Error in if (xmlGetAttr(xml,
>>> "displayType") == "list" && type != "boolean") options =
>>> parseOptions(xml) :
>>> missing value where TRUE/FALSE needed
>>>
>>>> listDatasets(wormbase)
>>> dataset description version
>>> 1 wormbase_paper Paper
>>> 2 wormbase_gene Gene
>>> 3 wormbase_anatomy_term Anatomy Term
>>> 4 wormbase_expr_pattern Expression Pattern
>>> 5 wormbase_go_term GO Term
>>> 6 wormbase_rnai RNAi
>>> 7 wormbase_phenotype Phenotype
>>> 8 wormbase_variation Variation
>>>
>>>> wormbase = useMart("wormbase_current", dataset = "wormbase_paper")
>>> Checking attributes and filters ... Ok
>>>
>>>
>>>
>>> I will appreciate any help.
>>>
>>> Ana.
>>>
>>>
>>> ##############################
>>>> sessionInfo()
>>> R version 2.8.0 (2008-10-20)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_MON
>>> ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.1252
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>>
>>> other attached packages:
>>> [1] biomaRt_1.16.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] RCurl_0.91-0 XML_1.94-0.1
>>>
>>> _______________________________________________
>>> 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
>>>
>>
>> _______________________________________________
>> 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
>>
>
> _______________________________________________
> 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
>
More information about the Bioconductor
mailing list