[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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[biomart-users] Re: Problem with using biomart

Anne Deslattes Mays
In reply to this post by gabrielle.perron00
Hello,

There seems to be a problem -- none of the commands within R are working at all within biomaRt.  This is the example from within the package.

> library(biomaRt)

>  getBM(attributes= "hgnc_symbol",

+         filters=c("go","chromosome_name"),

+         values=list(go, chrom), mart=ensembl)

Error in getBM(attributes = "hgnc_symbol", filters = c("go", "chromosome_name"),  : 

  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.


But none of them work -- 100% failure rate

> ?getBM

> affyids=c("202763_at","209310_s_at","207500_at")

> getBM(attributes = c('affy_hg_u133_plus_2', 'hgnc_symbol', 'chromosome_name',

+                    'start_position', 'end_position', 'band'),

+       filters = 'affy_hg_u133_plus_2', 

+       values = affyids, 

+       mart = ensembl)

Error in getBM(attributes = c("affy_hg_u133_plus_2", "hgnc_symbol", "chromosome_name",  : 

  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.


>    mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")

>      getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", "chromosome_name", "band"),

+            filters    = "affy_hg_u95av2",

+            values     = c("1939_at","1503_at","1454_at"), 

+            mart       = mart)

Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", "chromosome_name",  : 

  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

On Wednesday, December 20, 2017 at 9:48:47 AM UTC-5, [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.
<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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[biomart-users] Re: Problem with using biomart

Anne Deslattes Mays
Dear Thomas,

I am able to connect to the version mentioned in the top of this stream.

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

And now the queries work. It appears there remains a problem.

Best regards,
Anne

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Re: [biomart-users] Re: Problem with using biomart

Thomas Maurel
Dear Anne and Gabrielle,

The issue was fixed in the BiomaRt package but you need to update it: 

    source("https://bioconductor.org/biocLite.R")
    biocLite("BiocUpgrade")
I can run your query fine with the following biomaRt version using Ensembl Release 91 from December 2017:

> mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
>       getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", "chromosome_name", "band"),
+                          filters    = "affy_hg_u95av2",
+                          values     = c("1939_at","1503_at","1454_at"), 
+                          mart       = mart)
  affy_hg_u95av2 hgnc_symbol chromosome_name   band
1        1503_at       BRCA2              13  q13.1
2        1454_at       SMAD3              15 q22.33
3        1939_at        TP53              17  p13.1

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] biomaRt_2.34.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14         AnnotationDbi_1.40.0 magrittr_1.5         BiocGenerics_0.24.0 
 [5] progress_1.1.2       IRanges_2.12.0       bit_1.1-12           R6_2.2.2            
 [9] rlang_0.1.6          httr_1.3.1           stringr_1.2.0        blob_1.1.0          
[13] tools_3.4.3          parallel_3.4.3       Biobase_2.38.0       DBI_0.7             
[17] bit64_0.9-7          digest_0.6.14        assertthat_0.2.0     tibble_1.4.1        
[21] S4Vectors_0.16.0     bitops_1.0-6         curl_3.1             RCurl_1.95-4.10     
[25] memoise_1.1.0        RSQLite_2.0          stringi_1.1.6        compiler_3.4.3      
[29] pillar_1.1.0         prettyunits_1.0.2    stats4_3.4.3         XML_3.98-1.9   

Hope this helps,
Kind Regards,
Thomas

On 24 Jan 2018, at 15:04, Anne Deslattes Mays <[hidden email]> wrote:

Dear Thomas,

I am able to connect to the version mentioned in the top of this stream.

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

And now the queries work. It appears there remains a problem.

Best regards,
Anne


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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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