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/ =
====================================================================
