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Hi,
I am having problems displaying the BioMart databese:
listMarts()
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { :
argument is of length zero
I can resolve the URL from the browser (as suggested in the error message) and also, the R connection to the Internet is fine since I installed several packages from Bioconductor a few moments before.
I saw a few posts regarding similar issues from some years before (on Biostars), some of which answered by Mike. I tried to force useMart to use the central version:
> useMart(biomart = "ensembl",
+ host = "www.ensembl.org",
+ ensemblRedirect = FALSE)
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { :
argument is of length zero
In addition: Warning message:
In useMart(biomart = "ensembl", host = "www.ensembl.org", ensemblRedirect = FALSE) :
The argument "ensemblRedirect" has been deprecated and will be removed in the next biomaRt release.
But also this didn't work.
If anybody experienced something similar or have some fix to the problem, that would be really helpful.
Massimo
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.38.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 AnnotationDbi_1.44.0 rstudioapi_0.10 magrittr_1.5 BiocGenerics_0.28.0 hms_0.4.2
[7] progress_1.2.0 IRanges_2.16.0 bit_1.1-14 R6_2.4.0 rlang_0.3.4 httr_1.4.0
[13] stringr_1.4.0 blob_1.1.1 tools_3.5.3 parallel_3.5.3 Biobase_2.42.0 DBI_1.0.0
[19] assertthat_0.2.1 bit64_0.9-7 digest_0.6.18 crayon_1.3.4 S4Vectors_0.20.1 bitops_1.0-6
[25] RCurl_1.95-4.12 memoise_1.1.0 RSQLite_2.1.1 stringi_1.4.3 compiler_3.5.3 prettyunits_1.0.2
[31] stats4_3.5.3 XML_3.98-1.19 pkgconfig_2.0.2
Does it work any better if you are explicit about using https and the port e.g?