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Question: biomaRt error when connecting to host
1
gravatar for Assa Yeroslaviz
7 months ago by
Assa Yeroslaviz1.3k
Munich, Germany
Assa Yeroslaviz1.3k wrote:

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            
ADD COMMENTlink modified 7 months ago by Mike Smith2.1k • written 7 months ago by Assa Yeroslaviz1.3k

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 7 months ago by anajacintafernandes0
2
gravatar for Mike Smith
7 months ago by
Mike Smith2.1k
EMBL Heidelberg / de.NBI
Mike Smith2.1k wrote:

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.

ADD COMMENTlink modified 7 months ago • written 7 months ago by Mike Smith2.1k

thanks, this works

ADD REPLYlink written 7 months ago by Assa Yeroslaviz1.3k
1

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
ADD REPLYlink modified 7 months ago • written 7 months ago by Mike Smith2.1k

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

ADD REPLYlink written 7 months ago by Vladimir Kiselev120
1

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 7 months ago by Mike Smith2.1k
1

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

ADD REPLYlink written 7 months ago by Thomas Maurel700
1

Dear All,

Everything should be back to normal now. 

Thanks a lot for your patience.

Kind Regards,

Thomas

ADD REPLYlink written 7 months ago by Thomas Maurel700

Looks like it works, indeed. Thanks!

ADD REPLYlink written 7 months ago by Vladimir Kiselev120
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