[BioMart Users] biomaRt: connection error - flush-hosts needed ?

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

[BioMart Users] biomaRt: connection error - flush-hosts needed ?

Oliver Burren
Hi,

Not sure that this is the correct place to post but getting the
following error using biomaRt with following code. I notice that the
host being returned is for the BioMart portal hence why I'm posting here
and not directly to Steffen.

Thanks for any help you can provide.

Olly Burren

#connect to BioMart
library(biomaRt)
ensembl <- useMart('ensembl')
ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
gene.details<-getGene(id='ENSG00000163599',
type="ensembl_gene_id",mart=ensembl)
Error in getBM(attributes = attrib, filters = type, values = id, mart =
mart) :
   Query ERROR: caught BioMart::Exception::Database: Could not connect
to mysql database ensembl_mart_71: DBI
connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...)
failed: Host '54.225.80.241' is blocked because of many connection
errors; unblock with 'mysqladmin flush-hosts' at
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm
line 98


sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] biomaRt_2.16.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.96-1.1




_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] biomaRt: connection error - flush-hosts needed ?

Rhoda Kinsella
HI Oliver
Until this issue is resolved at www.biomart.org, you can point your host to www.ensembl.org/biomart/martservice/ to get your data.
Hope that helps
Regards
Rhoda


On 29 May 2013, at 08:39, Oliver Burren <[hidden email]> wrote:

> Hi,
>
> Not sure that this is the correct place to post but getting the following error using biomaRt with following code. I notice that the host being returned is for the BioMart portal hence why I'm posting here and not directly to Steffen.
>
> Thanks for any help you can provide.
>
> Olly Burren
>
> #connect to BioMart
> library(biomaRt)
> ensembl <- useMart('ensembl')
> ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
> gene.details<-getGene(id='ENSG00000163599', type="ensembl_gene_id",mart=ensembl)
> Error in getBM(attributes = attrib, filters = type, values = id, mart = mart) :
>  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_71: DBI connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...) failed: Host '54.225.80.241' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts' at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98
>
>
> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods base
>
> other attached packages:
> [1] biomaRt_2.16.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.95-4.1 XML_3.96-1.1
>
>
>
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users

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



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] biomaRt: connection error - flush-hosts needed ?

Oliver Burren
Hi Rhoda,

Yup I saw in a previous post that you had said that was a potential
workaround  and tried that.

 > ensembl <- useMart('ENSEMBL_MART_ENSEMBL',host="www.ensembl.org")
 > ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
 > gene.details<-getGene(id='ENSG00000163599',
type="ensembl_gene_id",mart=ensembl)
Error in martCheck(mart, "ensembl") :
   This function only works when used with the ensembl BioMart.

So rather than rewrite a complicated function to use getBM I was going
to be patient... although it leads to the question as to why getGene()
function isn't supported on www.ensembl.org or is this just a feature of
biomaRt ?

Thanks for you help though.

O

On 29/05/13 08:59, Rhoda Kinsella wrote:

> HI Oliver
> Until this issue is resolved at www.biomart.org, you can point your host to www.ensembl.org/biomart/martservice/ to get your data.
> Hope that helps
> Regards
> Rhoda
>
>
> On 29 May 2013, at 08:39, Oliver Burren <[hidden email]> wrote:
>
>> Hi,
>>
>> Not sure that this is the correct place to post but getting the following error using biomaRt with following code. I notice that the host being returned is for the BioMart portal hence why I'm posting here and not directly to Steffen.
>>
>> Thanks for any help you can provide.
>>
>> Olly Burren
>>
>> #connect to BioMart
>> library(biomaRt)
>> ensembl <- useMart('ensembl')
>> ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
>> gene.details<-getGene(id='ENSG00000163599', type="ensembl_gene_id",mart=ensembl)
>> Error in getBM(attributes = attrib, filters = type, values = id, mart = mart) :
>>   Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_71: DBI connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...) failed: Host '54.225.80.241' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts' at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98
>>
>>
>> sessionInfo()
>> R version 3.0.1 (2013-05-16)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>> [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>> [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>> [7] LC_PAPER=C                 LC_NAME=C
>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods base
>>
>> other attached packages:
>> [1] biomaRt_2.16.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_1.95-4.1 XML_3.96-1.1
>>
>>
>>
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge,
> CB10 1SD
>
>
>

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] biomaRt: connection error - flush-hosts needed ?

Arek Kasprzyk
In reply to this post by Oliver Burren
Hi Oliver,
the issue should be resolved now.

a


On 29 May 2013 08:39, Oliver Burren <[hidden email]> wrote:
Hi,

Not sure that this is the correct place to post but getting the following error using biomaRt with following code. I notice that the host being returned is for the BioMart portal hence why I'm posting here and not directly to Steffen.

Thanks for any help you can provide.

Olly Burren

#connect to BioMart
library(biomaRt)
ensembl <- useMart('ensembl')
ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
gene.details<-getGene(id='ENSG00000163599', type="ensembl_gene_id",mart=ensembl)
Error in getBM(attributes = attrib, filters = type, values = id, mart = mart) :
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_71: DBI connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...) failed: Host '54.225.80.241' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts' at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98


sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] biomaRt_2.16.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.96-1.1




_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] biomaRt: connection error - flush-hosts needed ?

Oliver Burren
It's fixed. Thanks a lot  for the speedy resolution.

O

On 29/05/13 09:28, Arek Kasprzyk wrote:
Hi Oliver,
the issue should be resolved now.

a


On 29 May 2013 08:39, Oliver Burren <[hidden email]> wrote:
Hi,

Not sure that this is the correct place to post but getting the following error using biomaRt with following code. I notice that the host being returned is for the BioMart portal hence why I'm posting here and not directly to Steffen.

Thanks for any help you can provide.

Olly Burren

#connect to BioMart
library(biomaRt)
ensembl <- useMart('ensembl')
ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
gene.details<-getGene(id='ENSG00000163599', type="ensembl_gene_id",mart=ensembl)
Error in getBM(attributes = attrib, filters = type, values = id, mart = mart) :
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_71: DBI connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...) failed: Host '54.225.80.241' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts' at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98


sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] biomaRt_2.16.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.96-1.1




_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users