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?
> 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:  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  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  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):  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