"Incorrect BioMart name" when trying to connect to current Ensembl

[Gil Hornung]

Hi,

I am trying to connect to biomart. When I'm trying the current Ensembl release, I get errors, but when I'm trying the archive then it works. This type of behavior happened in 2 out of two tries within a week.

Here is the what I get:

> ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice" ,dataset="drerio_gene_ensembl")
Error in useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org",  : 
  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
> ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="asia.ensembl.org", path="/biomart/martservice" ,dataset="drerio_gene_ensembl")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
> ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="dec2015.archive.ensembl.org", path="/biomart/martservice" ,dataset="drerio_gene_ensembl")

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] magrittr_1.5            DT_0.1                  reshape2_1.4.1          snowfall_1.84-6.1       snow_0.4-1              matrixStats_0.50.2     
 [7] piano_1.6.2             dplyr_0.4.1             biomaRt_2.22.0          DESeq2_1.6.3            RcppArmadillo_0.5.000.0 Rcpp_0.12.5            
[13] GenomicRanges_1.18.4    GenomeInfoDb_1.2.5      IRanges_2.0.1           S4Vectors_0.4.0         BiocGenerics_0.12.1     ggplot2_2.1.0          
[19] gplots_3.0.1            RColorBrewer_1.1-2     

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      annotate_1.44.0      AnnotationDbi_1.28.2 assertthat_0.1       backports_1.0.2      base64enc_0.1-3      BatchJobs_1.6       
 [8] BBmisc_1.9           Biobase_2.26.0       BiocParallel_1.0.3   bitops_1.0-6         brew_1.0-6           caTools_1.17.1       checkmate_1.7.4     
[15] chron_2.3-47         cluster_2.0.4        codetools_0.2-14     colorspace_1.2-6     data.table_1.9.6     DBI_0.4-1            digest_0.6.9        
[22] fail_1.3             foreach_1.4.3        foreign_0.8-66       Formula_1.2-1        gdata_2.17.0         genefilter_1.48.1    geneplotter_1.44.0  
[29] grid_3.1.1           gridExtra_2.2.1      gtable_0.2.0         gtools_3.5.0         Hmisc_3.17-4         htmltools_0.3.5      htmlwidgets_0.6     
[36] igraph_1.0.1         iterators_1.0.8      KernSmooth_2.23-15   lattice_0.20-33      latticeExtra_0.6-28  limma_3.22.7         locfit_1.5-9.1      
[43] marray_1.44.0        Matrix_1.2-6         munsell_0.4.3        nnet_7.3-12          plyr_1.8.3           RCurl_1.95-4.8       relations_0.6-6     
[50] rpart_4.1-10         RSQLite_1.0.0        scales_0.4.0         sendmailR_1.2-1      sets_1.0-16          slam_0.1-34          splines_3.1.1       
[57] stringi_1.1.1        stringr_1.0.0        survival_2.39-4      tools_3.1.1          XML_3.98-1.4         xtable_1.8-2         XVector_0.6.0

[Arek Kasprzyk]

Hi Gil,

do you mean that this is intermittent behaviour i. e sometimes it works sometimes it does not?

a.

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[Gil Hornung]

Thanks Arek.

It never works. I suspect it has to do with the biomaRt version (2.22.0).

When I tried working from a different machine with an updated R version and biomaRt, then I was able to log in.

I think Ensembl moved from biomARt 0.6 to 0.7 which caused incompatibility.

Gil

[Steffen Durinck]

Hi Gill,

I can not repeat the issues you report.  Everything works for me:

> library(biomaRt)

> ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice" ,dataset="drerio_gene_ensembl")

> ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="asia.ensembl.org", path="/biomart/martservice" ,dataset="drerio_gene_ensembl")

> ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="dec2015.archive.ensembl.org", path="/biomart/martservice" ,dataset="drerio_gene_ensembl")

Any chance you are behind a firewall? Try it from another location (e.g. your home network)

Cheers,

Steffen

[Gil Hornung]

Hi Steffen,

It worked when I used a different computer with an updated R and biomaRt.

Gil