biomaRt no longer works with proxy after upgrade
2
1
Entering edit mode
enricoferrero ▴ 570
@enricoferrero-6037
Last seen 6 months ago
Switzerland

Hi,

I work behind a HTTP proxy that requires authentication and I used to be able to connect to biomaRt using these settings:

options(RCurlOptions = list(proxy="http://proxy.domain.com:800", proxyuserpwd="myuser:mypassword"))

as outlined in the biomaRt vignette.

 

Since I upgraded to Bioconductor 3.2, this no longer works and I get this error:

> library(biomaRt)
> listMarts()
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

 

So, how can I make biomaRt work (again) through a proxy that requires authentication?

Thank you.

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=C               LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=C              LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] RCurl_1.95-4.7       bitops_1.0-6         biomaRt_2.26.0       BiocInstaller_1.20.0 vimcom_1.2-6         colorout_1.0-2       setwidth_1.0-4

loaded via a namespace (and not attached):
 [1] IRanges_2.4.1        XML_3.98-1.3         DBI_0.3.1            stats4_3.2.2         RSQLite_1.0.0        S4Vectors_0.8.0      tools_3.2.2          Biobase_2.30.0       parallel_3.2.2       BiocGenerics_0.16.0  AnnotationDbi_1.32.0

Original discussion: biomaRt proxy issues

biomart proxy rcurl • 4.4k views
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13
Entering edit mode
hygine ▴ 140
@hygine-9143
Last seen 5.7 years ago
beijing

3 type have changed in use:

listMarts(host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="aplatyrhynchos_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="drerio_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="ggallus_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="oaries_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="rnorvegicus_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="sscrofa_gene_ensembl", host="www.ensembl.org")

 

listMarts(host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="bmori_eg_gene", host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="amellifera_eg_gene", host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="cgigas_eg_gene", host="metazoa.ensembl.org")

 

listMarts(host="plants.ensembl.org")

useMart("plants_mart",dataset="zmays_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="sbicolor_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="stuberosum_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="osativa_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="creinhardtii_eg_gene", host="plants.ensembl.org")

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0
Entering edit mode

Thanks for the list. Using "www.ensembl.org" only gives the latest alignment, but you can access older alignments using archived depositories (example for mm9):

mouse <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "may2012.archive.ensembl.org")

They have a special host for hg19:

human <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "grch37.ensembl.org")

See also http://useast.ensembl.org/info/website/archives/index.html

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5
Entering edit mode
Johannes Rainer ★ 1.9k
@johannes-rainer-6987
Last seen 8 weeks ago
Italy

Dear Enrico,

it's a problem with the main biomart site. Apparently they don't provide the biomart service at present (see also lots of related recent posts).

Check answer in Problem with biomart's listMarts function

Basically, you should switch to the ensembl biomart server.

e.g.

ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host="www.ensembl.org")

 

hope that helps

 

cheers, jo

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0
Entering edit mode

Hi!

I am facing a similar issue with biomaRt. I'm working behind a proxy and have modified the Renviron file to incorporate the proxy addresses and port. I have also used the RCurlOptions to feed in the proxy as suggested in the biomart vignette. I am using the useMart command as suggested by Johannes Rainer:

ensembl<-useMart("ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl",
+ host="www.ensembl.org")

which doesn't throw any error. listMarts and listAttributes, everything works fine but when I actually come to getBM the connection is refused. The command that I'm using is (I'm following DESeq2 beginner's guide)

> genemap<-getBM(attributes=c("entrezgene", "ensembl_gene_id",
+ "mgi_symbol"), filters="ensembl_gene_id",
+ values=res24$ensembl, 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.

I can connect to ensembl and access the data on its ftp servers through browser.

Any suggestions will be much appreciated. Thanks!

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN       
 [4] LC_COLLATE=en_IN     LC_MONETARY=en_IN    LC_MESSAGES=en_IN   
 [7] LC_PAPER=en_IN       LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] RCurl_1.95-4.8             bitops_1.0-6              
 [3] biomaRt_2.26.1             DESeq2_1.10.1             
 [5] RcppArmadillo_0.6.600.4.0  Rcpp_0.12.4               
 [7] SummarizedExperiment_1.0.2 Biobase_2.30.0            
 [9] GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
[11] IRanges_2.4.8              S4Vectors_0.8.11          
[13] BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2   futile.logger_1.4.1  plyr_1.8.3          
 [4] XVector_0.10.0       futile.options_1.0.0 zlibbioc_1.16.0     
 [7] rpart_4.1-10         RSQLite_1.0.0        annotate_1.48.0     
[10] gtable_0.2.0         lattice_0.20-33      DBI_0.3.1           
[13] gridExtra_2.2.1      genefilter_1.52.1    cluster_2.0.3       
[16] locfit_1.5-9.1       grid_3.2.3           nnet_7.3-12         
[19] AnnotationDbi_1.32.3 XML_3.98-1.4         survival_2.38-3     
[22] BiocParallel_1.4.3   foreign_0.8-66       latticeExtra_0.6-28
[25] Formula_1.2-1        geneplotter_1.48.0   ggplot2_2.1.0       
[28] lambda.r_1.1.7       Hmisc_3.17-2         scales_0.4.0        
[31] splines_3.2.3        colorspace_1.2-6     xtable_1.8-2        
[34] acepack_1.3-3.3      munsell_0.4.3

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