biomaRt error when connecting to host
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Entering edit mode
Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 19 days ago
Munich, Germany

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            
biomart host connection • 2.6k views
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0
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Hi! Having the same problem! I guess it must be something with biomaRt and we will have to wait for them to solve it. 

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3
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Mike Smith ★ 5.2k
@mike-smith
Last seen 14 hours ago
EMBL Heidelberg / de.NBI

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.

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0
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thanks, this works

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1
Entering edit mode

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.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
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0
Entering edit mode

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

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1
Entering edit mode

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.

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1
Entering edit mode

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,

Thomas

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1
Entering edit mode

Dear All,

Everything should be back to normal now. 

Thanks a lot for your patience.

Kind Regards,

Thomas

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0
Entering edit mode

Looks like it works, indeed. Thanks!

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