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Question: biomaRt no longer works with proxy after upgrade
1
gravatar for enricoferrero
2.0 years ago by
enricoferrero550
United Kingdom
enricoferrero550 wrote:

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

ADD COMMENTlink modified 2.0 years ago by hygine140 • written 2.0 years ago by enricoferrero550
13
gravatar for hygine
2.0 years ago by
hygine140
beijing
hygine140 wrote:

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")

ADD COMMENTlink written 2.0 years ago by hygine140

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

ADD REPLYlink modified 18 months ago • written 18 months ago by petervangalen0
5
gravatar for Johannes Rainer
2.0 years ago by
Johannes Rainer1.1k
Italy
Johannes Rainer1.1k wrote:

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

ADD COMMENTlink written 2.0 years ago by Johannes Rainer1.1k

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

ADD REPLYlink modified 20 months ago • written 20 months ago by aditi0
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