accessing a local 0.8 mart instance with biomaRt
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1
Entering edit mode
cklopp66 ▴ 10
@cklopp66-7314
Last seen 9.1 years ago
France

Hi,

I try to extract data from a local biomart 0.8 instance using biomaRt but, when listing the marts, I get the following error :

> listMarts(host="ngspipelines.toulouse.inra.fr", port="9012", path="/martservice/marts", verbose = TRUE)
Attempting web service request:
http://ngspipelines.toulouse.inra.fr:9012/martservice/marts?type=registry&requestid=biomaRt
Erreur dans `colnames<-`(`*tmp*`, value = c("biomart", "version")) :
  attribut 'names' [2] doit être de même longueur que le vecteur [0]


I get the same error when using the official biomart.org website :

> listMarts(host="central.biomart.org", path="/martservice/marts", port=80, verbose = TRUE)
Attempting web service request:
http://central.biomart.org:80/martservice/marts?type=registry&requestid=biomaRt
Erreur dans `colnames<-`(`*tmp*`, value = c("biomart", "version")) :
  attribut 'names' [2] doit être de même longueur que le vecteur [0]

When I run the requests in a browser I get a correct XML file with the marts.

Is there a way to make this work?

Cheers,

Christophe

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8     LC_MONETARY=fr_FR.UTF-8   
 [6] LC_MESSAGES=fr_FR.UTF-8    LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.22.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1  bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.4   graph_1.44.1        
 [8] grid_3.1.2           IRanges_2.0.1        lattice_0.20-29      parallel_3.1.2       RCurl_1.95-4.5       RSQLite_1.0.0        S4Vectors_0.4.0     
[15] SparseM_1.6          stats4_3.1.2         tools_3.1.2          topGO_2.18.0         XML_3.98-1.1       


-- 
====================================================================
= Christophe KLOPP MIAT    INRA Toulouse                            =
= CS 52627       31326 Castanet-Tolosan                            =
= Tel: 33 5 61 28 50 36   Email: christophe.klopp@toulouse.inra.fr =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================

biomart rest • 1.2k views
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1
Entering edit mode
@steffen-durinck-4894
Last seen 9.5 years ago

Hi Christophe.

BioMart 0.8 is currently not supported by biomaRt, only BioMart 0.7 is.

We are actively working on making biomaRt compatible with BioMart 0.8 and hope to have something ready soon.

Best,

Steffen

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