Question: biomaRt error when connecting to host
gravatar for Assa Yeroslaviz
2.5 years ago by
Assa Yeroslaviz1.4k
Munich, Germany
Assa Yeroslaviz1.4k wrote:


I'm trying to connect to biomaRt, but keep getting an error message:

Entity 'copy' not defined
Error: 1: Entity 'copy' not defined

This happen with several different hosts, so I don't think it is a host problem, but who knows...

ensembl = useMart( "ensembl", dataset = "scerevisiae_gene_ensembl" )
ensembl = useMart( "ensembl", dataset = "scerevisiae_gene_ensembl", host = "" )
ensembl = useMart( "ensembl", dataset = "scerevisiae_gene_ensembl", host = "" )

Does anyone has an explanation?



> sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS


 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:

 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:

 [1] BiocInstaller_1.24.0       pheatmap_1.0.8            
 [3] ggrepel_0.6.5              BiocParallel_1.8.1        
 [5] hwriter_1.3.2              GOstats_2.40.0            
 [7] graph_1.52.0               Category_2.40.0           
 [9] Matrix_1.2-8               AnnotationDbi_1.36.2      
[11] ggplot2_2.2.1              gplots_3.0.1              
[13] biomaRt_2.30.0             ReportingTools_2.14.0     
[15] knitr_1.15.1               RColorBrewer_1.1-2        
[17] genefilter_1.56.0          DESeq2_1.14.1             
[19] SummarizedExperiment_1.4.0 Biobase_2.34.0            
[21] GenomicRanges_1.26.2       GenomeInfoDb_1.10.3       
[23] IRanges_2.8.1              S4Vectors_0.12.1          
[25] BiocGenerics_0.20.0        stringr_1.2.0             
[27] WriteXLS_4.0.0            

loaded via a namespace (and not attached):

 [1] bitops_1.0-6                  httr_1.2.1                   
 [3] tools_3.3.2                   backports_1.0.5              
 [5] R6_2.2.0                      KernSmooth_2.23-15           
 [7] rpart_4.1-10                  Hmisc_4.0-2                  
 [9] DBI_0.5-1                     lazyeval_0.2.0               
[11] colorspace_1.3-2              nnet_7.3-12                  
[13] gridExtra_2.2.1               GGally_1.3.0                 
[15] htmlTable_1.9                 rtracklayer_1.34.2           
[17] ggbio_1.22.3                  caTools_1.17.1               
[19] scales_0.4.1                  checkmate_1.8.2              
[21] RBGL_1.50.0                   digest_0.6.12                
[23] Rsamtools_1.26.1              foreign_0.8-67               
[25] R.utils_2.5.0                 AnnotationForge_1.16.1       
[27] XVector_0.14.0                base64enc_0.1-3              
[29] dichromat_2.0-0               htmltools_0.3.5              
[31] ensembldb_1.6.2               limma_3.30.11                
[33] BSgenome_1.42.0               htmlwidgets_0.8              
[35] PFAM.db_3.4.0                 RSQLite_1.1-2                
[37] shiny_1.0.0                   gtools_3.5.0                 
[39] R.oo_1.21.0                   acepack_1.4.1                
[41] VariantAnnotation_1.20.2      RCurl_1.95-4.8               
[43] magrittr_1.5                  GO.db_3.4.0                  
[45] Formula_1.2-1                 Rcpp_0.12.9                  
[47] munsell_0.4.3                 R.methodsS3_1.7.1            
[49] stringi_1.1.2                 yaml_2.1.14                  
[51] edgeR_3.16.5                  zlibbioc_1.20.0              
[53] plyr_1.8.4                    AnnotationHub_2.6.4          
[55] gdata_2.17.0                  lattice_0.20-34              
[57] Biostrings_2.42.1             splines_3.3.2                
[59] GenomicFeatures_1.26.2        annotate_1.52.1              
[61] locfit_1.5-9.1                geneplotter_1.52.0           
[63] reshape2_1.4.2                XML_3.98-1.5                 
[65] biovizBase_1.22.0             latticeExtra_0.6-28          
[67] data.table_1.10.4             httpuv_1.3.3                 
[69] gtable_0.2.0                  reshape_0.8.6                
[71] assertthat_0.1                mime_0.5                     
[73] xtable_1.8-2                  survival_2.40-1              
[75] tibble_1.2                    OrganismDbi_1.16.0           
[77] GenomicAlignments_1.10.0      memoise_1.0.0                
[79] cluster_2.0.5                 interactiveDisplayBase_1.12.0
[81] GSEABase_1.36.0            
biomart connection host • 2.0k views
ADD COMMENTlink modified 2.5 years ago by Mike Smith4.0k • written 2.5 years ago by Assa Yeroslaviz1.4k

Hi! Having the same problem! I guess it must be something with biomaRt and we will have to wait for them to solve it. 

ADD REPLYlink written 2.5 years ago by anajacintafernandes20
Answer: biomaRt error when connecting to host
gravatar for Mike Smith
2.5 years ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

Ensembl webservice is currently down for maintenance.  If you go to at the moment you get a message about this.  The ensembl mirror sites are still available, but to access them with biomaRt you will have to use the developmental version > 2.31.6 (available here).  I only recently discovered there was a problem accessing the mirror sites, and so the fix hasn't made it into the release version of biomaRt.  If you are happy to use the devel version, you can access a mirror using:

ensembl = useMart( "ensembl", 
                   dataset = "scerevisiae_gene_ensembl", 
                   host = "", 
                   ensemblRedirect = FALSE)

The error message you received is not at all helpful, so I will try to update the package to report something more helpful in the future.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Mike Smith4.0k

thanks, this works

ADD REPLYlink written 2.5 years ago by Assa Yeroslaviz1.4k

Good to know.  

I've updated the package so from v2.31.8 you get a message that hopefully makes a little more sense e.g.

> ensembl = useMart("ensembl", dataset = "scerevisiae_gene_ensembl")
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, :
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Mike Smith4.0k

Thanks Mike! So is it a temporary or permanent problem? Are you planning to update the release branch any time soon?

ADD REPLYlink written 2.5 years ago by Vladimir Kiselev150

The service downtime should be temporary, the message on the Ensembl site says 'We expect to restore the service by 1200 GMT (UTC)', although I think it said that yesterday too.  I don't know any more than that.

The next release of Bioconductor is scheduled for two weeks time (April 25th).  Changes to the existing release versions of the packages are now closed, and then on that date the current devel version will become a new release (which should be biomaRt v2.32.0).  All the changes I've made will be present in that version.

ADD REPLYlink written 2.5 years ago by Mike Smith4.0k

Dear all,

I am afraid that we are experiencing some issues with our marts since yesterday's maintenance.  We are aiming to fix the issue as soon as possible.

Apologies for any inconvenience caused,

Kind Regards,


ADD REPLYlink written 2.5 years ago by Thomas Maurel770

Dear All,

Everything should be back to normal now. 

Thanks a lot for your patience.

Kind Regards,


ADD REPLYlink written 2.5 years ago by Thomas Maurel770

Looks like it works, indeed. Thanks!

ADD REPLYlink written 2.5 years ago by Vladimir Kiselev150
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