[BioC] Error in BioMart and wormbase

[Christof Winter]

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
>>
>> _______________________________________________
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>>
> 
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