Hi,

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 = "www.ensembl.org" )
ensembl = useMart( "ensembl", dataset = "scerevisiae_gene_ensembl", host = "www.uswest.ensembl.org" )

Does anyone has an explanation?

thanks

Assa

> sessionInfo()

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

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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            

Ensembl webservice is currently down for maintenance.  If you go to www.ensembl.org 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 = "uswest.ensembl.org", 
                   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.