Hi, 

I have run the DESeq2 package for differential mRNA expression analysis and want to annotate the results table using the biomaRt package (as described in the Beginner's guide to using the DESeq2 package, https://bioc.ism.ac.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf). 

It has worked for me yesterday (Monday, 23rd of July), with the exact same code as follows (I removed the proxy info):  

library("biomaRt")
options(RCurlOptions = list(proxy="xxx.xxx.xx.xxx:xxx"))
​ensembl = useMart( "ensembl", dataset = "hsapiens_gene_ensembl" )

Now I get the following error message: 

Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  :
  Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

When checking the provided URL manually, I get the return with <MartRegistry> as a header, so according to ?listMarts the listing is correct and the issue should be reported to Bionconductor support.

I hope this is the right way to report issues, it is the first time I am using this resource; if I should use a different way to communicate this issue, please let me know so I can be compliant next time. 

Cheers,
Inken 

Here is my sessionInfo: 

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252    LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C                   
[5] LC_TIME=Swedish_Sweden.1252    

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

other attached packages:
[1] biomaRt_2.37.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17         AnnotationDbi_1.43.1 rstudioapi_0.7       magrittr_1.5         BiocGenerics_0.27.1  hms_0.4.2           
 [7] progress_1.2.0       IRanges_2.15.14      bit_1.1-14           R6_2.2.2             rlang_0.2.1          httr_1.3.1          
[13] stringr_1.3.1        blob_1.1.1           tools_3.5.0          parallel_3.5.0       Biobase_2.41.1       DBI_1.0.0           
[19] assertthat_0.2.0     yaml_2.1.19          bit64_0.9-7          digest_0.6.15        crayon_1.3.4         S4Vectors_0.19.16   
[25] bitops_1.0-6         RCurl_1.95-4.10      memoise_1.1.0        RSQLite_2.1.1        stringi_1.1.7        compiler_3.5.0      
[31] prettyunits_1.0.2    stats4_3.5.0         XML_3.98-1.11        pkgconfig_2.0.1