Question: BioMart web service you're accessing may be down
0
gravatar for massimo.x.petretich
7 days ago by
massimo.x.petretich0 wrote:

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   
annotation • 47 views
ADD COMMENTlink written 7 days ago by massimo.x.petretich0

Does it work any better if you are explicit about using https and the port e.g?

listMarts(host = "https://www.ensembl.org", port = 443)
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 96
2   ENSEMBL_MART_MOUSE      Mouse strains 96
3     ENSEMBL_MART_SNP  Ensembl Variation 96
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 96
ADD REPLYlink written 7 days ago by Mike Smith3.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 269 users visited in the last hour