[biomart-users] getBM() not working

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[biomart-users] getBM() not working

Franco Caramia-2
Hi there,

I've been struggling for a while to do a simple biomaRt query:

> library(biomaRt)
> listMarts(host = "asia.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 85
2     ENSEMBL_MART_SNP  Ensembl Variation 85
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 85
4    ENSEMBL_MART_VEGA               Vega 65

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )

> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
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.


a quick check internet is working properly:

> if (is.character(RCurl::getURL("www.google.com"))) {
  out <- TRUE
  } else {
  out <- FALSE
  }

> out
[1] TRUE


Any ideas? It might be something trivial

Thanks,

Franco

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Re: [biomart-users] getBM() not working

Thomas Maurel
Dear Franco,

Your query is working fine for me:

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )
> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
#################
Results from server:
[1] "ENSG00000141510\tTP53\t7157\n"
attr(,"Content-Type")
                  charset 
"text/plain"      "utf-8" 
#################
Parsed results:
               V1   V2   V3
1 ENSG00000141510 TP53 7157
  ensembl_gene_id hgnc_symbol entrezgene
1 ENSG00000141510        TP53       7157

Could you please try again?
Thank you,
Regards,
Thomas

On 31 Aug 2016, at 13:40, Franco Caramia <[hidden email]> wrote:

Hi there,

I've been struggling for a while to do a simple biomaRt query:

> library(biomaRt)
> listMarts(host = "asia.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 85
2     ENSEMBL_MART_SNP  Ensembl Variation 85
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 85
4    ENSEMBL_MART_VEGA               Vega 65

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )

> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
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.


a quick check internet is working properly:

> if (is.character(RCurl::getURL("www.google.com"))) {
  out <- TRUE
  } else {
  out <- FALSE
  }

> out
[1] TRUE


Any ideas? It might be something trivial

Thanks,

Franco

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

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Re: [biomart-users] getBM() not working

Franco Caramia-2
Hi Thomas,

Thanks for your help.

The problem seems to only occur when I'm  behind a proxy. Which is a bit odd since the getMart() function is working fine:


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



I already tried a couple of suggestion from forums:

Sys.setenv("https_proxy" = "http://localhost:3128")

also:

> curl <- getCurlHandle() > curlSetOpt(.opts = > list(proxy="localhost:3128"),curl = curl)

Do you have any other suggestions? 

Thanks a lot,

Franco

On Wed, Aug 31, 2016 at 10:51 PM, Thomas Maurel <[hidden email]> wrote:
Dear Franco,

Your query is working fine for me:

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )
> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
#################
Results from server:
[1] "ENSG00000141510\tTP53\t7157\n"
attr(,"Content-Type")
                  charset 
"text/plain"      "utf-8" 
#################
Parsed results:
               V1   V2   V3
1 ENSG00000141510 TP53 7157
  ensembl_gene_id hgnc_symbol entrezgene
1 ENSG00000141510        TP53       7157

Could you please try again?
Thank you,
Regards,
Thomas

On 31 Aug 2016, at 13:40, Franco Caramia <[hidden email]> wrote:

Hi there,

I've been struggling for a while to do a simple biomaRt query:

> library(biomaRt)
> listMarts(host = "asia.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 85
2     ENSEMBL_MART_SNP  Ensembl Variation 85
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 85
4    ENSEMBL_MART_VEGA               Vega 65

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )

> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
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.


a quick check internet is working properly:

> if (is.character(RCurl::getURL("www.google.com"))) {
  out <- TRUE
  } else {
  out <- FALSE
  }

> out
[1] TRUE


Any ideas? It might be something trivial

Thanks,

Franco

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

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




--

Franco Caramia

Bioinformatics, Cancer Research

Tumour Suppression Laboratory 

Peter MacCallum Cancer Centre

Ph: <a href="tel:03%2096565157" target="_blank">03 96565157 M: <a href="tel:0406131422" target="_blank">0406131422


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Re: [biomart-users] getBM() not working

Steffen Durinck-2
Hi Franco,

In the biomaRt vignette we also suggest the following (not sure how different it is from what you already tried):

You can do this using the Sys.putenv command: 

Sys.putenv("http\_proxy" = "http://my.proxy.org:9999") 

Some users have reported that the workaround above does not work, in this case an alternative proxy solution below can be tried: 

options(RCurlOptions = list(proxy="uscache.kcc.com:80",proxyuserpwd="------:-------")


Best,
Steffen


On Wed, Aug 31, 2016 at 3:07 PM, Franco Caramia <[hidden email]> wrote:
Hi Thomas,

Thanks for your help.

The problem seems to only occur when I'm  behind a proxy. Which is a bit odd since the getMart() function is working fine:


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



I already tried a couple of suggestion from forums:

Sys.setenv("https_proxy" = "http://localhost:3128")

also:

> curl <- getCurlHandle() > curlSetOpt(.opts = > list(proxy="localhost:3128"),curl = curl)

Do you have any other suggestions? 

Thanks a lot,

Franco

On Wed, Aug 31, 2016 at 10:51 PM, Thomas Maurel <[hidden email]> wrote:
Dear Franco,

Your query is working fine for me:

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )
> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
#################
Results from server:
[1] "ENSG00000141510\tTP53\t7157\n"
attr(,"Content-Type")
                  charset 
"text/plain"      "utf-8" 
#################
Parsed results:
               V1   V2   V3
1 ENSG00000141510 TP53 7157
  ensembl_gene_id hgnc_symbol entrezgene
1 ENSG00000141510        TP53       7157

Could you please try again?
Thank you,
Regards,
Thomas

On 31 Aug 2016, at 13:40, Franco Caramia <[hidden email]> wrote:

Hi there,

I've been struggling for a while to do a simple biomaRt query:

> library(biomaRt)
> listMarts(host = "asia.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 85
2     ENSEMBL_MART_SNP  Ensembl Variation 85
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 85
4    ENSEMBL_MART_VEGA               Vega 65

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )

> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
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.


a quick check internet is working properly:

> if (is.character(RCurl::getURL("www.google.com"))) {
  out <- TRUE
  } else {
  out <- FALSE
  }

> out
[1] TRUE


Any ideas? It might be something trivial

Thanks,

Franco

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

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




--

Franco Caramia

Bioinformatics, Cancer Research

Tumour Suppression Laboratory 

Peter MacCallum Cancer Centre

Ph: <a href="tel:03%2096565157" target="_blank">03 96565157 M: <a href="tel:0406131422" target="_blank">0406131422


--
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To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

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Re: [biomart-users] getBM() not working

Franco Caramia-2
Hi Steffen,

Setting the proxy on RCurlOptions worked
options(RCurlOptions = list(proxy="uscache.kcc.com:80",proxyuserpwd="------:-------")


Many Thanks, 

Franco

On Thu, Sep 1, 2016 at 8:41 AM, Steffen Durinck <[hidden email]> wrote:
Hi Franco,

In the biomaRt vignette we also suggest the following (not sure how different it is from what you already tried):

You can do this using the Sys.putenv command: 

Sys.putenv("http\_proxy" = "http://my.proxy.org:9999") 

Some users have reported that the workaround above does not work, in this case an alternative proxy solution below can be tried: 

options(RCurlOptions = list(proxy="uscache.kcc.com:80",proxyuserpwd="------:-------")


Best,
Steffen


On Wed, Aug 31, 2016 at 3:07 PM, Franco Caramia <[hidden email]> wrote:
Hi Thomas,

Thanks for your help.

The problem seems to only occur when I'm  behind a proxy. Which is a bit odd since the getMart() function is working fine:


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



I already tried a couple of suggestion from forums:

Sys.setenv("https_proxy" = "http://localhost:3128")

also:

> curl <- getCurlHandle() > curlSetOpt(.opts = > list(proxy="localhost:3128"),curl = curl)

Do you have any other suggestions? 

Thanks a lot,

Franco

On Wed, Aug 31, 2016 at 10:51 PM, Thomas Maurel <[hidden email]> wrote:
Dear Franco,

Your query is working fine for me:

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )
> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
#################
Results from server:
[1] "ENSG00000141510\tTP53\t7157\n"
attr(,"Content-Type")
                  charset 
"text/plain"      "utf-8" 
#################
Parsed results:
               V1   V2   V3
1 ENSG00000141510 TP53 7157
  ensembl_gene_id hgnc_symbol entrezgene
1 ENSG00000141510        TP53       7157

Could you please try again?
Thank you,
Regards,
Thomas

On 31 Aug 2016, at 13:40, Franco Caramia <[hidden email]> wrote:

Hi there,

I've been struggling for a while to do a simple biomaRt query:

> library(biomaRt)
> listMarts(host = "asia.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 85
2     ENSEMBL_MART_SNP  Ensembl Variation 85
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 85
4    ENSEMBL_MART_VEGA               Vega 65

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )

> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
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.


a quick check internet is working properly:

> if (is.character(RCurl::getURL("www.google.com"))) {
  out <- TRUE
  } else {
  out <- FALSE
  }

> out
[1] TRUE


Any ideas? It might be something trivial

Thanks,

Franco

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

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




--

Franco Caramia

Bioinformatics, Cancer Research

Tumour Suppression Laboratory 

Peter MacCallum Cancer Centre

Ph: <a href="tel:03%2096565157" target="_blank">03 96565157 M: <a href="tel:0406131422" target="_blank">0406131422


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




--

Franco Caramia

Bioinformatics, Cancer Research

Tumour Suppression Laboratory 

Peter MacCallum Cancer Centre

Ph: <a href="tel:03%2096565157" target="_blank">03 96565157 M: <a href="tel:0406131422" target="_blank">0406131422


--
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Re: [biomart-users] getBM() not working

Thomas Maurel
In reply to this post by Franco Caramia-2
Dear Franco,

I remember that Sys.setenv(“https_proxy” = “http://localhost:3128”) worked fine for my proxy in the past. I also found the following suggestion on the Bioconductor support site:
Sys.putenv(“http_proxy" = "http://my.proxy.org:9999")

I am afraid that I don’t have any other suggestions.

Kind Regards,
Thomas
On 31 Aug 2016, at 23:07, Franco Caramia <[hidden email]> wrote:

Hi Thomas,

Thanks for your help.

The problem seems to only occur when I'm  behind a proxy. Which is a bit odd since the getMart() function is working fine:


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



I already tried a couple of suggestion from forums:

Sys.setenv("https_proxy" = "http://localhost:3128")

also:

> curl <- getCurlHandle() > curlSetOpt(.opts = > list(proxy="localhost:3128"),curl = curl)

Do you have any other suggestions? 

Thanks a lot,

Franco

On Wed, Aug 31, 2016 at 10:51 PM, Thomas Maurel <[hidden email]> wrote:
Dear Franco,

Your query is working fine for me:

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )
> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
#################
Results from server:
[1] "ENSG00000141510\tTP53\t7157\n"
attr(,"Content-Type")
                  charset 
"text/plain"      "utf-8" 
#################
Parsed results:
               V1   V2   V3
1 ENSG00000141510 TP53 7157
  ensembl_gene_id hgnc_symbol entrezgene
1 ENSG00000141510        TP53       7157

Could you please try again?
Thank you,
Regards,
Thomas

On 31 Aug 2016, at 13:40, Franco Caramia <[hidden email]> wrote:

Hi there,

I've been struggling for a while to do a simple biomaRt query:

> library(biomaRt)
> listMarts(host = "asia.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 85
2     ENSEMBL_MART_SNP  Ensembl Variation 85
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 85
4    ENSEMBL_MART_VEGA               Vega 65

> ensembl = useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host ="asia.ensembl.org" )

> getBM(attributes=c('ensembl_gene_id','hgnc_symbol','entrezgene'), filters = 'hgnc_symbol', values =c("TP53"), mart = ensembl, verbose = T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query>
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.


a quick check internet is working properly:

> if (is.character(RCurl::getURL("www.google.com"))) {
  out <- TRUE
  } else {
  out <- FALSE
  }

> out
[1] TRUE


Any ideas? It might be something trivial

Thanks,

Franco

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




-- 

Franco Caramia

Bioinformatics, Cancer Research

Tumour Suppression Laboratory 

Peter MacCallum Cancer Centre

Ph: <a href="tel:03%2096565157" target="_blank" class="">03 96565157 M: <a href="tel:0406131422" target="_blank" class="">0406131422


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

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