[biomart-users] Problem with using biomart

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[biomart-users] Problem with using biomart

gabrielle.perron00
Hi,

It seems that there is an issue with biomart as a script that I commonly use stopped working. Here is an example of command and the error produced:

> ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")
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

Are there problems with the server?

Thank you.

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Re: [biomart-users] Problem with using biomart

Steffen Durinck-2
Hi Gabrielle,

Thank you for reporting this.

The error is due to a quote in one of the dataset:  Ma's night monkey genes (Anan_2.0)
This quote is breaking the R code.

I would connect to the previous version of Ensembl to keep your queries going until the issue is fixed.

ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host="aug2017.archive.ensembl.org")

Cheers,
Steffen

On Wed, Dec 20, 2017 at 6:48 AM, <[hidden email]> wrote:
Hi,

It seems that there is an issue with biomart as a script that I commonly use stopped working. Here is an example of command and the error produced:

> ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")
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.

Are there problems with the server?

Thank you.

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Re: [biomart-users] Problem with using biomart

Gil Hornung
Dear Steffen,

Has this issue been fixed? I am unable to find the hsapiens_gene_ensembl dataset in the dec2017 release, but I do find it in aug017 release, so I think it is related to this issue:

> mart90 = biomaRt::useMart(biomart="ENSEMBL_MART_ENSEMBL",
+                         host="aug2017.archive.ensembl.org", # Release 90
+                         path="/biomart/martservice",
+                         dataset="hsapiens_gene_ensembl")
> mart91 = biomaRt::useMart(biomart="ENSEMBL_MART_ENSEMBL",
+                         host="dec2017.archive.ensembl.org", # Release 91
+                         path="/biomart/martservice",
+                         dataset="hsapiens_gene_ensembl")
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.8 (Santiago)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.26.1 readxl_1.0.0   knitr_1.15.1   ggplot2_2.2.1  dplyr_0.5.0    tibble_1.2     tidyr_0.6.0   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10         AnnotationDbi_1.32.3 magrittr_1.5         IRanges_2.4.8        BiocGenerics_0.16.1  hms_0.3              munsell_0.4.3        colorspace_1.3-2    
 [9] R6_2.2.0             plyr_1.8.4           tools_3.2.1          parallel_3.2.1       grid_3.2.1           Biobase_2.30.0       gtable_0.2.0         DBI_0.6             
[17] digest_0.6.12        yaml_2.1.14          lazyeval_0.2.0       assertthat_0.1       readr_1.1.1          S4Vectors_0.8.11     bitops_1.0-6         RCurl_1.95-4.8      
[25] memoise_1.0.0        RSQLite_1.1-2        cellranger_1.1.0     scales_0.4.1         stats4_3.2.1         XML_3.98-1.5   

 
Hi Gabrielle,

Thank you for reporting this.

The error is due to a quote in one of the dataset:  Ma's night monkey genes (Anan_2.0)
This quote is breaking the R code.

I would connect to the previous version of Ensembl to keep your queries going until the issue is fixed.

ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host="<a href="http://aug2017.archive.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Faug2017.archive.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH0kuzAIYhTN83kODzVYDNZZGfAMg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Faug2017.archive.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH0kuzAIYhTN83kODzVYDNZZGfAMg&#39;;return true;">aug2017.archive.ensembl.org")

Cheers,
Steffen

On Wed, Dec 20, 2017 at 6:48 AM, <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="8JgQzMBNCgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">gabrielle...@...> wrote:
Hi,

It seems that there is an issue with biomart as a script that I commonly use stopped working. Here is an example of command and the error produced:

> ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")
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.
<a href="http://www.ensembl.org:80/biomart/martservice?type=registry&amp;requestid=biomaRt" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dregistry%26requestid%3DbiomaRt\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG2qP9r3pP3MS4nosxww7R9o_sbKg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dregistry%26requestid%3DbiomaRt\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG2qP9r3pP3MS4nosxww7R9o_sbKg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

Are there problems with the server?

Thank you.

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