Question

Biomart: listMarts, listFilters and listAttributes work, but getBM doesn't

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invlasov • 0

@invlasov-10746

Last seen 7.9 years ago

Dear All,

I am a new biomart user, but I can't seem to get it running.
I am using following R code:

library(biomaRt)

# Here are the proxy settings, presumably they are correct, because without them listMarts and othe following functions don't work.

Sys.setenv("http_proxy" = "http://my.proxy.de:8080")

# Checking if it works.

a<-listMarts()

ensembl=useMart("ENSEMBL_MART_ENSEMBL")
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)

# these to seem to work also
b<-listAttributes(ensembl)
c<-listFilters(ensembl)

# This is processed for a very long time, and then gives an error message
d<-getBM(attributes=c('ensembl_gene_id'), filters ='affy_hg_u133_plus_2', values = "1552278_a_at", mart = ensembl)

Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

sessioninfo() output:

R version 3.2.4 (2016-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C                    LC_TIME=English_Canada.1252    

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

other attached packages:
[1] biomaRt_2.26.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.8        parallel_3.2.4       DBI_0.3.1            tools_3.2.4         
 [5] RCurl_1.95-4.8       Biobase_2.30.0       AnnotationDbi_1.32.3 RSQLite_1.0.0       
 [9] S4Vectors_0.8.11     BiocGenerics_0.16.1  stats4_3.2.4         bitops_1.0-6        
[13] XML_3.98-1.4

Thank you in advance for your help.

biomart • 1.4k views

ADD COMMENT • link updated 7.9 years ago by James W. MacDonald 65k • written 7.9 years ago by invlasov • 0

score 0 · Answer 1 · 2016-05-25

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

With any web-based query there is always the chance that there is a problem with the connection that will be resolved soon. As the error states, you had a (possibly) temporary problem connecting. What is implied is that you should wait for a while and try again.

ADD COMMENT • link 7.9 years ago James W. MacDonald 65k

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I am afraid this problem was reproducible for the whole last week. I tried again just now, and still no luck.

ADD REPLY • link 7.9 years ago invlasov • 0

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The useast ensembl mart is up at least:

> library(biomaRt)
> mart <- useMart("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl")
> getBM(attributes=c('ensembl_gene_id'), filters ='affy_hg_u133_plus_2', values = "1552278_a_at", mart = mart)
  ensembl_gene_id
1 ENSG00000076351
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 10586)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] biomaRt_2.28.0

loaded via a namespace (and not attached):
 [1] compiler_3.3.0       IRanges_2.6.0        parallel_3.3.0      
 [4] DBI_0.4-1            tools_3.3.0          RCurl_1.95-4.8      
 [7] Biobase_2.32.0       AnnotationDbi_1.34.3 RSQLite_1.0.0       
[10] S4Vectors_0.10.1     BiocGenerics_0.18.0  stats4_3.3.0        
[13] bitops_1.0-6         XML_3.98-1.4

But I don't have to go through a proxy, so maybe that has something to do with it. Unfortunately that's all the (lack of) help I can offer.

ADD REPLY • link 7.9 years ago James W. MacDonald 65k

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Thank you anyway.

I was just hoping to find out what do I need to tell our tech-support about setting up our internet access to solve this problem.

ADD REPLY • link 7.9 years ago invlasov • 0

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Hello,

I can confirm that the ensembl.org and archive websites are all up and working. I also suspect this has something to do with your proxy.

Could you please try the following syntax and see if this can help:

Sys.setenv(http_proxy="http://my.proxy.de:8080")

Best Regards,

Thomas

ADD REPLY • link 7.9 years ago Thomas Maurel ▴ 800

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Hi.

> Sys.setenv(http_proxy = "http://my.proxy.de:8080")
> 
> library(biomaRt)
> 
> a<-listMarts()
> ensembl=useMart("ENSEMBL_MART_ENSEMBL")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
> b<-listAttributes(ensembl)
> c<-listFilters(ensembl)
> d<-getBM(attributes=c('ensembl_gene_id'), filters ='affy_hg_u133_plus_2', values = "1552278_a_at", mart = ensembl)
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

Unfortunately, this gives exactly the same result.

ADD REPLY • link 7.9 years ago invlasov • 0

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Hello,

Could you please try our asian mirror and see if it make a difference:

> ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="asia.ensembl.org")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
> b<-listAttributes(ensembl)
> c<-listFilters(ensembl)
> d<-getBM(attributes=c('ensembl_gene_id'), filters ='affy_hg_u133_plus_2', values = "1552278_a_at", mart = ensembl)

> d
  ensembl_gene_id
1 ENSG00000076351

If this doesn't work, I am afraid you might have to contact your tech-support regarding your proxy. Everything seems to be working fine from our side.

Kind Regards,

Thomas

ADD REPLY • link 7.9 years ago Thomas Maurel ▴ 800