Hi,
I am getting an error for a biomaRt getBM() call which used to work
before. Has something changed in getBM() or the corresponding web
services - or might there be firewall problems? I have the environment
variable http_proxy set and other commands through the firewall, e.g.
package installations work. Also getting the same information from
biomart via wget and a xml query works through http_proxy. Here is the
output:
> library("biomaRt")
> mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
> o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
"illumina_humanwg_6_v2"), mart=mart)
V1
1 <html><head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<title>FEHLER: Die angeforderte URL konnte nicht gefunden
werden</title>
<style type="text/css">
Hi Wasco,
This works for me, maybe the server was temporarily down, any chance
you can
try again?
Steffen
On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck <wasco.wruck@charite.de>
wrote:
> Hi,
>
> I am getting an error for a biomaRt getBM() call which used to work
before.
> Has something changed in getBM() or the corresponding web services -
or
> might there be firewall problems? I have the environment variable
http_proxy
> set and other commands through the firewall, e.g. package
installations
> work. Also getting the same information from biomart via wget and a
xml
> query works through http_proxy. Here is the output:
>
> > library("biomaRt")
> > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> Checking attributes ... ok
> Checking filters ... ok
> > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
> "illumina_humanwg_6_v2"), mart=mart)
>
>
>
> V1
> 1 http://www.w3.org/TR/html4/**strict.dtd<http: www.w3.org="" tr="" html4="" s="" trict.dtd="">">
> <html><head> <meta http-equiv="Content-Type" content="text/html;
> charset=utf-8"> FEHLER: Die angeforderte URL konnte nicht
gefunden
> werden <style type="text/css">
Hi Steffen , hi Johannes,
I consistently get the same error. Something must have changed because
before some days it worked fine. Maybe I have to update.
Wasco
Am 8/10/2011 5:17 PM, schrieb Steffen Durinck:
> Hi Wasco,
>
> This works for me, maybe the server was temporarily down, any chance
> you can try again?
>
> Steffen
>
> On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck <wasco.wruck@charite.de> <mailto:wasco.wruck@charite.de>> wrote:
>
> Hi,
>
> I am getting an error for a biomaRt getBM() call which used to
> work before. Has something changed in getBM() or the
corresponding
> web services - or might there be firewall problems? I have the
> environment variable http_proxy set and other commands through
the
> firewall, e.g. package installations work. Also getting the same
> information from biomart via wget and a xml query works through
> http_proxy. Here is the output:
>
> > library("biomaRt")
> > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> Checking attributes ... ok
> Checking filters ... ok
> > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
> "illumina_humanwg_6_v2"), mart=mart)
>
>
>
>
> V1
> 1 "http://www.w3.org/TR/html4/strict.dtd"> <html><head> <meta> http-equiv="Content-Type" content="text/html; FEHLER: Die
> angeforderte URL konnte nicht gefunden werden <style> type="text/css">
Hi Wasco
well, it works for me as well (using R 2.13.1 and biomaRt_2.8.1), see
below.
I suggest to upgrade, most likely your R 2.11.0 and biomaRt_2.4.0
doesn't work with the Biomart database from ensembl 63 (which was
released a few weeks ago)....on the other hand the error message you
provide: "Die angeforderte URL konnte nicht gefunden werden" does
sound
like a firewall problem on your side......
Regards, Hans
> library("biomaRt")
> mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
+ "illumina_humanwg_6_v2"), mart=mart)
> head(o)
ensembl_gene_id ensembl_transcript_id illumina_humanwg_6_v2
1 ENSG00000203347 ENST00000366172
2 ENSG00000256017 ENST00000379355 ILMN_1676712
3 ENSG00000236057 ENST00000537266
4 ENSG00000236057 ENST00000446137
5 ENSG00000245602 ENST00000500835
6 ENSG00000247217 ENST00000499475
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.8.1
loaded via a namespace (and not attached):
[1] RCurl_1.6-6 XML_3.4-0
>
On 08/10/2011 06:00 PM, Wasco Wruck wrote:
> Hi Steffen , hi Johannes,
>
> I consistently get the same error. Something must have changed
because
> before some days it worked fine. Maybe I have to update.
>
> Wasco
>
> Am 8/10/2011 5:17 PM, schrieb Steffen Durinck:
>> Hi Wasco,
>>
>> This works for me, maybe the server was temporarily down, any
chance
>> you can try again?
>>
>> Steffen
>>
>> On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck<wasco.wruck at="" charite.de="">> <mailto:wasco.wruck at="" charite.de="">> wrote:
>>
>> Hi,
>>
>> I am getting an error for a biomaRt getBM() call which used to
>> work before. Has something changed in getBM() or the
corresponding
>> web services - or might there be firewall problems? I have the
>> environment variable http_proxy set and other commands through
the
>> firewall, e.g. package installations work. Also getting the
same
>> information from biomart via wget and a xml query works
through
>> http_proxy. Here is the output:
>>
>> > library("biomaRt")
>> > mart = useMart("ensembl", dataset =
"hsapiens_gene_ensembl")
>> Checking attributes ... ok
>> Checking filters ... ok
>> > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
>> "illumina_humanwg_6_v2"), mart=mart)
>>
>>
>>
>>
>> V1
>> 1> "http://www.w3.org/TR/html4/strict.dtd"> <html><head> <meta>> http-equiv="Content-Type" content="text/html;FEHLER:
Die
>> angeforderte URL konnte nicht gefunden werden <style>> type="text/css">
Hi Hans-Rudolf, Steffen, Johannes,
thank you for your answers and testing! I upgraded to the newest
versions but still got the same error. Using only one attribute to
useMart() I got a html error page which our network admin could
interpret - it was a not-easy-to-detect firewall problem concerning
HTTP1.1 expect!
Best wishes,
Wasco
Am 8/10/2011 6:48 PM, schrieb Hans-Rudolf Hotz:
> Hi Wasco
>
> well, it works for me as well (using R 2.13.1 and biomaRt_2.8.1),
see below.
>
> I suggest to upgrade, most likely your R 2.11.0 and biomaRt_2.4.0
> doesn't work with the Biomart database from ensembl 63 (which was
> released a few weeks ago)....on the other hand the error message you
> provide: "Die angeforderte URL konnte nicht gefunden werden" does
sound
> like a firewall problem on your side......
>
>
> Regards, Hans
>
>
> > library("biomaRt")
> > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
> + "illumina_humanwg_6_v2"), mart=mart)
> > head(o)
> ensembl_gene_id ensembl_transcript_id illumina_humanwg_6_v2
> 1 ENSG00000203347 ENST00000366172
> 2 ENSG00000256017 ENST00000379355 ILMN_1676712
> 3 ENSG00000236057 ENST00000537266
> 4 ENSG00000236057 ENST00000446137
> 5 ENSG00000245602 ENST00000500835
> 6 ENSG00000247217 ENST00000499475
> > sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_2.8.1
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.6-6 XML_3.4-0
> >
>
>
>
> On 08/10/2011 06:00 PM, Wasco Wruck wrote:
>> Hi Steffen , hi Johannes,
>>
>> I consistently get the same error. Something must have changed
because
>> before some days it worked fine. Maybe I have to update.
>>
>> Wasco
>>
>> Am 8/10/2011 5:17 PM, schrieb Steffen Durinck:
>>> Hi Wasco,
>>>
>>> This works for me, maybe the server was temporarily down, any
chance
>>> you can try again?
>>>
>>> Steffen
>>>
>>> On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck<wasco.wruck at="" charite.de="">>> <mailto:wasco.wruck at="" charite.de="">> wrote:
>>>
>>> Hi,
>>>
>>> I am getting an error for a biomaRt getBM() call which used
to
>>> work before. Has something changed in getBM() or the
corresponding
>>> web services - or might there be firewall problems? I have
the
>>> environment variable http_proxy set and other commands
through the
>>> firewall, e.g. package installations work. Also getting the
same
>>> information from biomart via wget and a xml query works
through
>>> http_proxy. Here is the output:
>>>
>>> > library("biomaRt")
>>> > mart = useMart("ensembl", dataset =
"hsapiens_gene_ensembl")
>>> Checking attributes ... ok
>>> Checking filters ... ok
>>> > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
>>> "illumina_humanwg_6_v2"), mart=mart)
>>>
>>>
>>>
>>>
>>> V1
>>> 1>> "http://www.w3.org/TR/html4/strict.dtd"> <html><head>
<meta>>> http-equiv="Content-Type" content="text/html;FEHLER:
Die
>>> angeforderte URL konnte nicht gefunden werden
<style>>> type="text/css">
Hi Wasco,
I have tried your example just now and it worked fine. But I'm
running more current versions of R and Bioconductor. Have you tried
updating R/Bioconductor?
> library("biomaRt")
> mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> mart
Object of class 'Mart':
Using the ensembl BioMart database
Using the hsapiens_gene_ensembl dataset
> o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
"illumina_humanwg_6_v2"), mart=mart)
> head(o)
ensembl_gene_id ensembl_transcript_id illumina_humanwg_6_v2
1 ENSG00000203347 ENST00000366172
2 ENSG00000256017 ENST00000379355 ILMN_1676712
3 ENSG00000236057 ENST00000537266
4 ENSG00000236057 ENST00000446137
5 ENSG00000245602 ENST00000500835
6 ENSG00000247217 ENST00000499475
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.8.1
loaded via a namespace (and not attached):
[1] RCurl_1.5-0 tools_2.13.0 XML_3.2-0
>
--Johannes
-----Original Message-----
From: Wasco Wruck [mailto:wasco.wruck@charite.de]
Sent: Wednesday, August 10, 2011 8:17 AM
To: bioconductor at r-project.org
Subject: [BioC] getBM returns error
Hi,
I am getting an error for a biomaRt getBM() call which used to work
before. Has something changed in getBM() or the corresponding web
services - or might there be firewall problems? I have the environment
variable http_proxy set and other commands through the firewall, e.g.
package installations work. Also getting the same information from
biomart via wget and a xml query works through http_proxy. Here is the
output:
> library("biomaRt")
> mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes ... ok Checking filters ... ok >
o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
"illumina_humanwg_6_v2"), mart=mart)
V1
1 <html><head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<title>FEHLER: Die angeforderte URL konnte nicht gefunden
werden</title>
<style type="text/css">
