[biomart-users] Biomart server almost continuously down?

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[biomart-users] Biomart server almost continuously down?

Francesco Mazzarotto

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Re: [biomart-users] Biomart server almost continuously down?

Rhoda Kinsella
Hi Francesco
As a work around, set your host to use the BioMart databases at www.ensembl.org and you can access the same data. 

library(biomaRt)
ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
etc...


Hope that helps
Cheers
Rhoda


On 25 Nov 2013, at 16:05, Francesco Mazzarotto <[hidden email]> wrote:


Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton,
Cambridge
CB10 1SD




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Re: [biomart-users] Biomart server almost continuously down?

Arek Kasprzyk
In reply to this post by Francesco Mazzarotto
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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That means you've stood up for something, sometime in your life.”

― Winston Churchill


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Re: [biomart-users] Biomart server almost continuously down?

Alejandra Eugenia Medina Rivera
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="UmxOjbt0-cEJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">fra.enjoy...@...> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Re: [biomart-users] Biomart server almost continuously down?

Arek Kasprzyk
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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That means you've stood up for something, sometime in your life.”

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Re: [biomart-users] Biomart server almost continuously down?

JL LT
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="r9NNY2aYhUQJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">medina....@...> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Re: [biomart-users] Biomart server almost continuously down?

Arek Kasprzyk
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

--
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That means you've stood up for something, sometime in your life.”

― Winston Churchill


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Re: [biomart-users] Biomart server almost continuously down?

Katrin Hörmann
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="0zNMLwKbUqkJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">jol...@...> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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That means you've stood up for something, sometime in your life.”

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Re: [biomart-users] Biomart server almost continuously down?

Arek Kasprzyk
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Re: [biomart-users] Biomart server almost continuously down?

Kevin Ttk
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="267HN7PaAH0J" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">katrin.e...@...> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Re: [biomart-users] Biomart server almost continuously down?

Katrin Hörmann
In reply to this post by Arek Kasprzyk
Dear Arek, 

I tried again today several times and always failed.

I'm also working in R with the datasets/hosts/etc: 
library(biomaRt)
unimart <- useMart("unimart",dataset="uniprot",
                   host="www.ebi.ac.uk",path="/uniprot/biomart/martservice")

Whenever I start a query, it takes ages and at some points gets aborted with the error message mentioned before. 

Am Donnerstag, 17. April 2014 11:17:34 UTC+2 schrieb Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="267HN7PaAH0J" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">katrin.e...@...> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Re: [biomart-users] Biomart server almost continuously down?

Arek Kasprzyk
In reply to this post by Kevin Ttk
Hi guys,
there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a


On 22 April 2014 14:44, Kevin Ttk <[hidden email]> wrote:
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
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20132 Milano
Italy

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Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Re: [biomart-users] Biomart server almost continuously down?

Katrin Hörmann
Hi Arek, 

thanks for taking care. 
Unfortunately, the service is still not working for me. Just tried it and still stuck with the following error message:
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.



Am Dienstag, 22. April 2014 18:48:57 UTC+2 schrieb Arek Kasprzyk:
Hi guys,
there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a


On 22 April 2014 14:44, Kevin Ttk <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="8vEde2Kt2gUJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">kevin....@...> wrote:
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Re: [biomart-users] Biomart server almost continuously down?

Arek Kasprzyk
guys:

the service is working fine here:

just tried:


is it possible that you have some connectivity problems on your side?

a








On 23 April 2014 09:47, Katrin Hörmann <[hidden email]> wrote:
Hi Arek, 

thanks for taking care. 
Unfortunately, the service is still not working for me. Just tried it and still stuck with the following error message:
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.



Am Dienstag, 22. April 2014 18:48:57 UTC+2 schrieb Arek Kasprzyk:
Hi guys,
there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a


On 22 April 2014 14:44, Kevin Ttk <[hidden email]> wrote:
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

--
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That means you've stood up for something, sometime in your life.”

― Winston Churchill


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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Re: [biomart-users] Biomart server almost continuously down?

Katrin Hörmann
Don't think it's connectivity problems from our side, as I'm able to access anything else and also able to establish a connection to biomart. 
Problems only start with queries, even such that ran successfully last week.

Am Mittwoch, 23. April 2014 10:00:38 UTC+2 schrieb Arek Kasprzyk:
guys:

the service is working fine here:

just tried:

<a href="http://www.biomart.org/biomart/martservice?type=registry" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\46sa\75D\46sntz\0751\46usg\75AFQjCNH5Tff6c6fTrLYNWObeZJjZ_9GYzw';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\46sa\75D\46sntz\0751\46usg\75AFQjCNH5Tff6c6fTrLYNWObeZJjZ_9GYzw';return true;">http://www.biomart.org/biomart/martservice?type=registry

is it possible that you have some connectivity problems on your side?

a








On 23 April 2014 09:47, Katrin Hörmann <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="Fze3fKYRjGkJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">katrin.e...@...> wrote:
Hi Arek, 

thanks for taking care. 
Unfortunately, the service is still not working for me. Just tried it and still stuck with the following error message:
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.



Am Dienstag, 22. April 2014 18:48:57 UTC+2 schrieb Arek Kasprzyk:
Hi guys,
there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a


On 22 April 2014 14:44, Kevin Ttk <[hidden email]> wrote:
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Re: [biomart-users] Biomart server almost continuously down?

Arek Kasprzyk
Hi Katrin,
please send me the exact query that fails and i'll try to reproduce the problem here


On 23 April 2014 11:01, Katrin Hörmann <[hidden email]> wrote:
Don't think it's connectivity problems from our side, as I'm able to access anything else and also able to establish a connection to biomart. 
Problems only start with queries, even such that ran successfully last week.

Am Mittwoch, 23. April 2014 10:00:38 UTC+2 schrieb Arek Kasprzyk:
guys:

the service is working fine here:

just tried:


is it possible that you have some connectivity problems on your side?

a








On 23 April 2014 09:47, Katrin Hörmann <[hidden email]> wrote:
Hi Arek, 

thanks for taking care. 
Unfortunately, the service is still not working for me. Just tried it and still stuck with the following error message:
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.



Am Dienstag, 22. April 2014 18:48:57 UTC+2 schrieb Arek Kasprzyk:
Hi guys,
there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a


On 22 April 2014 14:44, Kevin Ttk <[hidden email]> wrote:
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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― Winston Churchill


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Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Re: [biomart-users] Biomart server almost continuously down?

Katrin Hörmann
ctrl.df <- read.csv2('20140325_Isobar_P5838.P5839.csv', header=TRUE, stringsAsFactors=F)
ctrl.df$protein.acs <- gsub("[,-].*",'',ctrl.df$protein.acs)

library(biomaRt)
unimart <- useMart("unimart",dataset="uniprot",
                   host="www.ebi.ac.uk",path="/uniprot/biomart/martservice")

go.terms=getBM(attributes=c("accession", "db2go_c__dm_description"), filters="accession",
               values=ctrl.df$protein.acs, mart=unimart)

The .csv file is in the attachment. For me, everything works fine until the function getBM is called.

Thanks for putting so much effort.

Best, Katrin
Am Mittwoch, 23. April 2014 11:10:54 UTC+2 schrieb Arek Kasprzyk:
Hi Katrin,
please send me the exact query that fails and i'll try to reproduce the problem here


On 23 April 2014 11:01, Katrin Hörmann <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="UFPg_GGvK7wJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">katrin.e...@...> wrote:
Don't think it's connectivity problems from our side, as I'm able to access anything else and also able to establish a connection to biomart. 
Problems only start with queries, even such that ran successfully last week.

Am Mittwoch, 23. April 2014 10:00:38 UTC+2 schrieb Arek Kasprzyk:
guys:

the service is working fine here:

just tried:

<a href="http://www.biomart.org/biomart/martservice?type=registry" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\46sa\75D\46sntz\0751\46usg\75AFQjCNH5Tff6c6fTrLYNWObeZJjZ_9GYzw';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\46sa\75D\46sntz\0751\46usg\75AFQjCNH5Tff6c6fTrLYNWObeZJjZ_9GYzw';return true;">http://www.biomart.org/biomart/martservice?type=registry

is it possible that you have some connectivity problems on your side?

a








On 23 April 2014 09:47, Katrin Hörmann <[hidden email]> wrote:
Hi Arek, 

thanks for taking care. 
Unfortunately, the service is still not working for me. Just tried it and still stuck with the following error message:
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.



Am Dienstag, 22. April 2014 18:48:57 UTC+2 schrieb Arek Kasprzyk:
Hi guys,
there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a


On 22 April 2014 14:44, Kevin Ttk <[hidden email]> wrote:
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check <a href="http://www.biomart.org" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
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San Raffaele Scientific Institute
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20140325_Isobar_P5838.P5839.csv (378K) Download Attachment
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Re: [biomart-users] Biomart server almost continuously down?

Arek Kasprzyk
HI Katrin,
this actually looks like a different problem (a problem with UniProt instance). Please see my reply earlier on today to Dana


(I am cc'ing Steven who runs this instance. Perhaps he can have some input to this problem)

a



On 23 April 2014 11:35, Katrin Hörmann <[hidden email]> wrote:
ctrl.df <- read.csv2('20140325_Isobar_P5838.P5839.csv', header=TRUE, stringsAsFactors=F)
ctrl.df$protein.acs <- gsub("[,-].*",'',ctrl.df$protein.acs)

library(biomaRt)
unimart <- useMart("unimart",dataset="uniprot",
                   host="www.ebi.ac.uk",path="/uniprot/biomart/martservice")

go.terms=getBM(attributes=c("accession", "db2go_c__dm_description"), filters="accession",
               values=ctrl.df$protein.acs, mart=unimart)

The .csv file is in the attachment. For me, everything works fine until the function getBM is called.

Thanks for putting so much effort.

Best, Katrin
Am Mittwoch, 23. April 2014 11:10:54 UTC+2 schrieb Arek Kasprzyk:
Hi Katrin,
please send me the exact query that fails and i'll try to reproduce the problem here


On 23 April 2014 11:01, Katrin Hörmann <[hidden email]> wrote:
Don't think it's connectivity problems from our side, as I'm able to access anything else and also able to establish a connection to biomart. 
Problems only start with queries, even such that ran successfully last week.

Am Mittwoch, 23. April 2014 10:00:38 UTC+2 schrieb Arek Kasprzyk:
guys:

the service is working fine here:

just tried:


is it possible that you have some connectivity problems on your side?

a








On 23 April 2014 09:47, Katrin Hörmann <[hidden email]> wrote:
Hi Arek, 

thanks for taking care. 
Unfortunately, the service is still not working for me. Just tried it and still stuck with the following error message:
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.



Am Dienstag, 22. April 2014 18:48:57 UTC+2 schrieb Arek Kasprzyk:
Hi guys,
there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a


On 22 April 2014 14:44, Kevin Ttk <[hidden email]> wrote:
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

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That means you've stood up for something, sometime in your life.”

― Winston Churchill


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― Oscar Wilde

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― Oscar Wilde

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

--
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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Re: [biomart-users] Biomart server almost continuously down?

Steven Rosanoff
Thank you for your input. We are aware of the issue and trying to correct it. It looks like the source is our tomcat web service consistantly timing out. I will let you know as soon as it is resolved.

Regards,
Steve

On 23/04/2014 10:47, Arek Kasprzyk wrote:
HI Katrin,
this actually looks like a different problem (a problem with UniProt instance). Please see my reply earlier on today to Dana


(I am cc'ing Steven who runs this instance. Perhaps he can have some input to this problem)

a



On 23 April 2014 11:35, Katrin Hörmann <[hidden email]> wrote:
ctrl.df <- read.csv2('20140325_Isobar_P5838.P5839.csv', header=TRUE, stringsAsFactors=F)
ctrl.df$protein.acs <- gsub("[,-].*",'',ctrl.df$protein.acs)

library(biomaRt)
unimart <- useMart("unimart",dataset="uniprot",
                   host="www.ebi.ac.uk",path="/uniprot/biomart/martservice")

go.terms=getBM(attributes=c("accession", "db2go_c__dm_description"), filters="accession",
               values=ctrl.df$protein.acs, mart=unimart)

The .csv file is in the attachment. For me, everything works fine until the function getBM is called.

Thanks for putting so much effort.

Best, Katrin
Am Mittwoch, 23. April 2014 11:10:54 UTC+2 schrieb Arek Kasprzyk:
Hi Katrin,
please send me the exact query that fails and i'll try to reproduce the problem here


On 23 April 2014 11:01, Katrin Hörmann <[hidden email]> wrote:
Don't think it's connectivity problems from our side, as I'm able to access anything else and also able to establish a connection to biomart. 
Problems only start with queries, even such that ran successfully last week.

Am Mittwoch, 23. April 2014 10:00:38 UTC+2 schrieb Arek Kasprzyk:
guys:

the service is working fine here:

just tried:


is it possible that you have some connectivity problems on your side?

a








On 23 April 2014 09:47, Katrin Hörmann <[hidden email]> wrote:
Hi Arek, 

thanks for taking care. 
Unfortunately, the service is still not working for me. Just tried it and still stuck with the following error message:
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.



Am Dienstag, 22. April 2014 18:48:57 UTC+2 schrieb Arek Kasprzyk:
Hi guys,
there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a


On 22 April 2014 14:44, Kevin Ttk <[hidden email]> wrote:
Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:
Hi Katrin,
could you try again please? I don't seem to be able to reproduce those errors

a


On 17 April 2014 11:05, Katrin Hörmann <[hidden email]> wrote:
Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?
I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

Am Donnerstag, 27. Februar 2014 15:14:34 UTC+1 schrieb Arek Kasprzyk:
Hi JL,
There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a


On 27 February 2014 14:54, JL LT <[hidden email]> wrote:
Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL







El lunes, 24 de febrero de 2014 22:46:15 UTC+1, Arek Kasprzyk escribió:
Hi Alejandra,
thank you for reporting this. The service should be restored now

a


On 24 February 2014 22:09, Alejandra Eugenia Medina Rivera <[hidden email]> wrote:
Hi

I'm having problems also loading on R
listMarts()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

El martes, 26 de noviembre de 2013 04:15:37 UTC-5, Arek Kasprzyk escribió:
Hi Francesco,
thank you for reporting this. There seems to be a problem with the database server.
Please bear with us while we fix the issue

a


On 25 November 2013 17:05, Francesco Mazzarotto <[hidden email]> wrote:

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco
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That means you've stood up for something, sometime in your life.”

― Winston Churchill


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"When the gods wish to punish us, they answer our prayers"
― Oscar Wilde

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"When the gods wish to punish us, they answer our prayers"
― Oscar Wilde

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

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Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy



-- 
Steven Rosanoff
Software Engineer
EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 494565
Email: [hidden email] 

Learn more about EBI at: http://www.ebi.ac.uk

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Re: [biomart-users] Biomart server almost continuously down?

Bernard Chang
Hello Steve, could you post an update when things may be working again.  I got the same error message as others have reported.

Cheers,
Bernard


On Wednesday, April 23, 2014 5:53:06 AM UTC-4, Steven Rosanoff wrote:
Thank you for your input. We are aware of the issue and trying to correct it. It looks like the source is our tomcat web service consistantly timing out. I will let you know as soon as it is resolved.

Regards,
Steve


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123