[biomart-users] Is the BioMart webservice currently down?

classic Classic list List threaded Threaded
13 messages Options
Reply | Threaded
Open this post in threaded view
|

[biomart-users] Is the BioMart webservice currently down?

justin
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

[biomart-users] Re: Is the BioMart webservice currently down?

justin
Ah, I see. Running the getBM function with the verbose flag, I see the following detailed error message:

<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_id'/><Filter name = 'ensembl_gene_id' value = 'ENSG00000187510' /></Dataset></Query>
#################
Results from server:
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">\n<title>503 Service Temporarily Unavailable</title>\n</head>\n
[2] <body>\n<h1>Service Temporarily Unavailable</h1>\n<p>The server is temporarily unable to service your\nrequest due to maintenance downtime or capacity\nproblems. Pl ...
Error in getBM(attributes = c("ensembl_gene_id", "hgnc_id"), filters = "ensembl_gene_id",  : 
  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 Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

[biomart-users] Re: Is the BioMart webservice currently down?

justin
Looks like the server is down for maintenance. Is there a way to receive notifications when this will happen?

On Tuesday, December 11, 2018 at 1:19:49 PM UTC-5, [hidden email] wrote:
Ah, I see. Running the getBM function with the verbose flag, I see the following detailed error message:

<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_id'/><Filter name = 'ensembl_gene_id' value = 'ENSG00000187510' /></Dataset></Query>
#################
Results from server:
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">\n<title>503 Service Temporarily Unavailable</title>\n</head>\n
[2] <body>\n<h1>Service Temporarily Unavailable</h1>\n<p>The server is temporarily unable to service your\nrequest due to maintenance downtime or capacity\nproblems. Pl ...
Error in getBM(attributes = c("ensembl_gene_id", "hgnc_id"), filters = "ensembl_gene_id",  : 
  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 Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

Syed Haider-5
In reply to this post by justin
Hi Justin,

The below works for me connecting against the default ensembl.org. I wonder if you are connecting against a different server or perhaps server issues?

library(biomaRt);
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl");
getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human);

  ensembl_gene_id    hgnc_id
1 ENSG00000187510 HGNC:27887
2 ENSG00000187510 HGNC:33829


On Tue, 11 Dec 2018 at 18:06, <[hidden email]> wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.


--
<font color="green">Please consider environment before you print this!</font>

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

justin
Hi, Syed. If I disable redirection to my local mirror, via

human <- useMart("ensembl", dataset="hsapiens_gene_ensembl", verbose=TRUE, ensemblRedirect=FALSE)

the query works. Here is the output from the above command:

Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: http://www.ensembl.org:80/biomart/martservice
Checking attributes ...Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
Checking filters ...Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=filters&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok

On Tuesday, December 11, 2018 at 1:23:19 PM UTC-5, Syed Haider wrote:
Hi Justin,

The below works for me connecting against the default <a href="http://ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG2qP1DqJvXF2_K0VNu4h78TvvFVA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG2qP1DqJvXF2_K0VNu4h78TvvFVA&#39;;return true;">ensembl.org. I wonder if you are connecting against a different server or perhaps server issues?

library(biomaRt);
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl");
getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human);

  ensembl_gene_id    hgnc_id
1 ENSG00000187510 HGNC:27887
2 ENSG00000187510 HGNC:33829


On Tue, 11 Dec 2018 at 18:06, <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="IfdqLmtBBwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">jus...@...> wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="IfdqLmtBBwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">biomart-user...@googlegroups.com.
Visit this group at <a href="https://groups.google.com/group/biomart-users" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/group/biomart-users&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/group/biomart-users&#39;;return true;">https://groups.google.com/group/biomart-users.
For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;">https://groups.google.com/d/optout.


--
<font color="green">Please consider environment before you print this!</font>

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

justin
Sorry, for clarity, what I posted is the output from useMart when redirection is enabled (i.e., the scenario in which the query, using this mart object, fails)

On Tuesday, December 11, 2018 at 1:36:54 PM UTC-5, [hidden email] wrote:
Hi, Syed. If I disable redirection to my local mirror, via

human <- useMart("ensembl", dataset="hsapiens_gene_ensembl", verbose=TRUE, ensemblRedirect=FALSE)

the query works. Here is the output from the above command:

Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=version&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: <a href="http://www.ensembl.org:80/biomart/martservice" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice
Checking attributes ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=attributes&amp;dataset=hsapiens_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEtwNks0lYT2v3Qu2Mw-Pq9ScwBtg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEtwNks0lYT2v3Qu2Mw-Pq9ScwBtg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
Checking filters ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=filters&amp;dataset=hsapiens_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFxYfZxx_krcpWU2b7JQyxMLb-2AQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFxYfZxx_krcpWU2b7JQyxMLb-2AQ&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=filters&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok

On Tuesday, December 11, 2018 at 1:23:19 PM UTC-5, Syed Haider wrote:
Hi Justin,

The below works for me connecting against the default <a href="http://ensembl.org" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG2qP1DqJvXF2_K0VNu4h78TvvFVA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG2qP1DqJvXF2_K0VNu4h78TvvFVA&#39;;return true;">ensembl.org. I wonder if you are connecting against a different server or perhaps server issues?

library(biomaRt);
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl");
getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human);

  ensembl_gene_id    hgnc_id
1 ENSG00000187510 HGNC:27887
2 ENSG00000187510 HGNC:33829


On Tue, 11 Dec 2018 at 18:06, <[hidden email]> wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to biomart-user...@googlegroups.com.
Visit this group at <a href="https://groups.google.com/group/biomart-users" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://groups.google.com/group/biomart-users&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/group/biomart-users&#39;;return true;">https://groups.google.com/group/biomart-users.
For more options, visit <a href="https://groups.google.com/d/optout" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;">https://groups.google.com/d/optout.


--
<font color="green">Please consider environment before you print this!</font>

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

[biomart-users] Re: Is the BioMart webservice currently down?

justin
In reply to this post by justin
Is there a way to identify my local mirror and send a request to have the server brought back online?

On Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

Syed Haider-5
Ensembl helpdesk is the team to contact for this. Its very likely they would pick up this thread from here anyway and do what is necessary.

Best wishes,
Syed


On Tuesday, 11 December 2018, <[hidden email]> wrote:
Is there a way to identify my local mirror and send a request to have the server brought back online?

On Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.


--
<font color="green">Please consider environment before you print this!</font>

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

Thomas Maurel
Dear Justin,

Could you please let me know what is your local mirror so that I can check the server status.

Thanks a lot,
Kind Regards,
Thomas

On 11 Dec 2018, at 19:00, Syed Haider <[hidden email]> wrote:

Ensembl helpdesk is the team to contact for this. Its very likely they would pick up this thread from here anyway and do what is necessary.

Best wishes,
Syed


On Tuesday, 11 December 2018, <[hidden email]> wrote:
Is there a way to identify my local mirror and send a request to have the server brought back online?

On Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.


--
<font color="green">Please consider environment before you print this!</font>

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

Thomas Maurel
Dear Justin,

We have 4 Ensembl sites, the site will automatically redirect depending on where you are living: http://www.ensembl.org/info/about/mirrors.html
If you can please go to http://www.ensembl.org and let me know where you get redirected to.

Thanks,
Kind Regards,
Thomas 

On 12 Dec 2018, at 13:18, Justin McManus <[hidden email]> wrote:

It would be my pleasure; how do I check?

Sent from my iPhone

On Dec 12, 2018, at 5:43 AM, Thomas Maurel <[hidden email]> wrote:

Dear Justin,

Could you please let me know what is your local mirror so that I can check the server status.

Thanks a lot,
Kind Regards,
Thomas

On 11 Dec 2018, at 19:00, Syed Haider <[hidden email]> wrote:

Ensembl helpdesk is the team to contact for this. Its very likely they would pick up this thread from here anyway and do what is necessary.

Best wishes,
Syed


On Tuesday, 11 December 2018, <[hidden email]> wrote:
Is there a way to identify my local mirror and send a request to have the server brought back online?

On Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.


--
<font color="green">Please consider environment before you print this!</font>

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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


--
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

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

Thomas Maurel
or alternatively, if you paste the output of your command with redirect=True:

human <- useMart("ensembl", dataset="hsapiens_gene_ensembl", verbose=TRUE, ensemblRedirect=TRUE)

Thank you,
Kind Regards,
Thomas
On 12 Dec 2018, at 13:23, Thomas Maurel <[hidden email]> wrote:

Dear Justin,

We have 4 Ensembl sites, the site will automatically redirect depending on where you are living: http://www.ensembl.org/info/about/mirrors.html
If you can please go to http://www.ensembl.org and let me know where you get redirected to.

Thanks,
Kind Regards,
Thomas 

On 12 Dec 2018, at 13:18, Justin McManus <[hidden email]> wrote:

It would be my pleasure; how do I check?

Sent from my iPhone

On Dec 12, 2018, at 5:43 AM, Thomas Maurel <[hidden email]> wrote:

Dear Justin,

Could you please let me know what is your local mirror so that I can check the server status.

Thanks a lot,
Kind Regards,
Thomas

On 11 Dec 2018, at 19:00, Syed Haider <[hidden email]> wrote:

Ensembl helpdesk is the team to contact for this. Its very likely they would pick up this thread from here anyway and do what is necessary.

Best wishes,
Syed


On Tuesday, 11 December 2018, <[hidden email]> wrote:
Is there a way to identify my local mirror and send a request to have the server brought back online?

On Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  :
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.


--
<font color="green">Please consider environment before you print this!</font>

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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


--
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


--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

Thomas Maurel
Dear Justin,

I am afraid that BioMart is down on the useast mirror at the moment. We will fix this as soon as possible. I will get back to you once this is fixed.

Apologies for any inconvenience caused.
Kind Regards,
Thomas

On 12 Dec 2018, at 14:09, Justin McManus <[hidden email]> wrote:

Looks like it's http://useast.ensembl.org/index.html, which makes sense because I'm in NYC

On Wed, Dec 12, 2018 at 8:27 AM Thomas Maurel <[hidden email]> wrote:
or alternatively, if you paste the output of your command with redirect=True:

human <- useMart("ensembl", dataset="hsapiens_gene_ensembl", verbose=TRUE, ensemblRedirect=TRUE)

Thank you,
Kind Regards,
Thomas
On 12 Dec 2018, at 13:23, Thomas Maurel <[hidden email]> wrote:

Dear Justin,

We have 4 Ensembl sites, the site will automatically redirect depending on where you are living: http://www.ensembl.org/info/about/mirrors.html
If you can please go to http://www.ensembl.org and let me know where you get redirected to.

Thanks,
Kind Regards,
Thomas 

On 12 Dec 2018, at 13:18, Justin McManus <[hidden email]> wrote:

It would be my pleasure; how do I check?

Sent from my iPhone

On Dec 12, 2018, at 5:43 AM, Thomas Maurel <[hidden email]> wrote:

Dear Justin,

Could you please let me know what is your local mirror so that I can check the server status.

Thanks a lot,
Kind Regards,
Thomas

On 11 Dec 2018, at 19:00, Syed Haider <[hidden email]> wrote:

Ensembl helpdesk is the team to contact for this. Its very likely they would pick up this thread from here anyway and do what is necessary.

Best wishes,
Syed


On Tuesday, 11 December 2018, <[hidden email]> wrote:
Is there a way to identify my local mirror and send a request to have the server brought back online?

On Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  : 
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

-- 
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.


-- 
<font color="green">Please consider environment before you print this!</font>

-- 
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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


--
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


-- 
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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



-- 
Justin McManus, Ph.D.
Senior Scientist
Lead Computational Biologist
Kallyope, Inc.
430 East 29th Street, Suite 1050
New York, NY 10016
(646) 596-3471

--
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

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Is the BioMart webservice currently down?

Thomas Maurel
Dear Justin,

The issue has now been resolved, thanks a lot for your patience and for reporting this.

Kind Regards,
Thomas

On 12 Dec 2018, at 15:07, Justin McManus <[hidden email]> wrote:

No problem, Thomas. Thanks for the update!

On Wed, Dec 12, 2018 at 9:42 AM Thomas Maurel <[hidden email]> wrote:
Dear Justin,

I am afraid that BioMart is down on the useast mirror at the moment. We will fix this as soon as possible. I will get back to you once this is fixed.

Apologies for any inconvenience caused.
Kind Regards,
Thomas

On 12 Dec 2018, at 14:09, Justin McManus <[hidden email]> wrote:

Looks like it's http://useast.ensembl.org/index.html, which makes sense because I'm in NYC

On Wed, Dec 12, 2018 at 8:27 AM Thomas Maurel <[hidden email]> wrote:
or alternatively, if you paste the output of your command with redirect=True:

human <- useMart("ensembl", dataset="hsapiens_gene_ensembl", verbose=TRUE, ensemblRedirect=TRUE)

Thank you,
Kind Regards,
Thomas
On 12 Dec 2018, at 13:23, Thomas Maurel <[hidden email]> wrote:

Dear Justin,

We have 4 Ensembl sites, the site will automatically redirect depending on where you are living: http://www.ensembl.org/info/about/mirrors.html
If you can please go to http://www.ensembl.org and let me know where you get redirected to.

Thanks,
Kind Regards,
Thomas 

On 12 Dec 2018, at 13:18, Justin McManus <[hidden email]> wrote:

It would be my pleasure; how do I check?

Sent from my iPhone

On Dec 12, 2018, at 5:43 AM, Thomas Maurel <[hidden email]> wrote:

Dear Justin,

Could you please let me know what is your local mirror so that I can check the server status.

Thanks a lot,
Kind Regards,
Thomas

On 11 Dec 2018, at 19:00, Syed Haider <[hidden email]> wrote:

Ensembl helpdesk is the team to contact for this. Its very likely they would pick up this thread from here anyway and do what is necessary.

Best wishes,
Syed


On Tuesday, 11 December 2018, <[hidden email]> wrote:
Is there a way to identify my local mirror and send a request to have the server brought back online?

On Tuesday, December 11, 2018 at 1:06:57 PM UTC-5, [hidden email] wrote:
The following simple query, which ordinarily works, is currently failing

getBM(attributes=c("ensembl_gene_id", "hgnc_id"), filters="ensembl_gene_id", values=c("ENSG00000187510"), mart=human)

with the error:

Error in getBM(attributes = c("hgnc_id"), filters = c("ensembl_gene_id"),  : 
  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.

The mart object 'human' is obtained with
human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

-- 
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.


-- 
<font color="green">Please consider environment before you print this!</font>

-- 
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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


--
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


-- 
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
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



-- 
Justin McManus, Ph.D.
Senior Scientist
Lead Computational Biologist
Kallyope, Inc.
430 East 29th Street, Suite 1050
New York, NY 10016
(646) 596-3471

--
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



--
Justin McManus, Ph.D.
Senior Scientist
Lead Computational Biologist
Kallyope, Inc.
430 East 29th Street, Suite 1050
New York, NY 10016
(646) 596-3471

--
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

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.