Is biomaRt server down
1
0
Entering edit mode
ls760 • 0
@ls760-20976
Last seen 3.8 years ago

Hello,

Is the biomaRt server down? I can't make BiomaRt library working. I am interested in several features and genes of GRCh38

> library("biomaRt")
Warning messages:
1: package ‘ggplot2’ was built under R version 3.5.2 
2: package ‘tibble’ was built under R version 3.5.2 
3: package ‘tidyr’ was built under R version 3.5.2 
4: package ‘purrr’ was built under R version 3.5.2 
5: package ‘dplyr’ was built under R version 3.5.2 
6: package ‘stringr’ was built under R version 3.5.2 
7: package ‘forcats’ was built under R version 3.5.2 
> listMarts()
Error in listMarts() : 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
> mart <- useMart("ensembl","hsapiens_gene_ensembl", host = "useast.ensembl.org")
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://useast.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
> listMarts(host="www.ensembl.org")
Error in listMarts(host = "www.ensembl.org") : 
  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
> listEnsembl()
Error in listMarts(mart = mart, host = host, verbose = verbose) : 
  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

Any advice would be much appreciated, Thanks

software error • 499 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 4 minutes ago
United States
> library(biomaRt)
> listEnsembl()
             biomart               version
1            ensembl      Ensembl Genes 97
2 ENSEMBL_MART_MOUSE      Mouse strains 97
3                snp  Ensembl Variation 97
4         regulation Ensembl Regulation 97
> mart <- useEnsembl("ensembl", "hsapiens_gene_ensembl")
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] biomaRt_2.40.4

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2           AnnotationDbi_1.46.1 magrittr_1.5        
 [4] hms_0.5.1            progress_1.2.2       BiocGenerics_0.30.0 
 [7] IRanges_2.18.2       bit_1.1-14           R6_2.4.0            
[10] rlang_0.4.0          httr_1.4.1           stringr_1.4.0       
[13] blob_1.2.0           tools_3.6.1          parallel_3.6.1      
[16] Biobase_2.44.0       DBI_1.0.0            assertthat_0.2.1    
[19] bit64_0.9-7          digest_0.6.20        tibble_2.1.3        
[22] crayon_1.3.4         vctrs_0.2.0          S4Vectors_0.22.0    
[25] bitops_1.0-6         curl_4.0             RCurl_1.95-4.12     
[28] zeallot_0.1.0        memoise_1.1.0        RSQLite_2.1.2       
[31] stringi_1.4.3        compiler_3.6.1       pillar_1.4.2        
[34] prettyunits_1.0.2    backports_1.1.4      stats4_3.6.1        
[37] XML_3.98-1.20        pkgconfig_2.0.2     
ADD COMMENT
0
Entering edit mode

It's working now, I don't know what I did wrong. Thanks.

ADD REPLY

Login before adding your answer.

Traffic: 760 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6