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

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")

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