[BioMart Users] R biomaRt 'Please report this to the mailing list'

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[BioMart Users] R biomaRt 'Please report this to the mailing list'

John Coulthard
Hi

When following the instructions in the biomaRt.pdf I get the error below which ends 'Please report this to the mailing list' (I hope it means the biomart mailing list rather than R or bioconductor lists).

Did I do something wrong or do I wait for something to be fixed?
I am behind a proxy server but I can download packages so I don't think that is the issue.

Many thanks
John

$ R

R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(biomaRt)
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> affyids = c("202763_at", "209310_s_at", "207500_at")
> getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2",values = affyids, mart = ensembl)
                                                                                      & nbsp;                                      V1
1                           <!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN http://www.w3.org/TR/html4/loose.dtd>
2                                             <HTML><HEAD><META HTTP-EQUIV=Content-Type CONTENT=text/html; charset=iso-8859-1>
3                     & nbsp;                                          <TITLE>ERROR: The requested URL could not be retrieved</TITLE>
4 <STYLE type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
5                                                                                      & nbsp;                          </HEAD><BODY>
6                                                                                                               <H1>ERROR</H1>
Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2",  :
  The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.





> sessionInfo()
R version 2.14.1 (2011-12-22)
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    &nb s p;          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_2.10.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1 XML_3.9-4  
>




> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> biocLite("org.Hs.eg.db")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'org.Hs.eg.db'
Installing package(s) into \u2018/usr/local/lib/R/site-library\u2019
(as \u2018lib\u2019 is unspecified)
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
  'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/2.14
to install packages into?  (y/n) y
trying URL 'http://www.bioconductor.org/packages/2.9/data/annotation/src/contrib/org.Hs.eg.db_2.6.4.tar.gz'
Content type 'application/x-gzip' length 46530609 bytes (44.4 Mb)
opened URL
==================================================
downloaded 44.4 Mb

* installing *source* package \u2018org.Hs.eg.db\u2019 ...
** R
** inst
etc, etc.


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Re: [BioMart Users] R biomaRt 'Please report this to the mailing list'

Sean Davis
Hi, John.

The email list to which the message refers is, indeed, the bioconductor email list, but a few of us read both.  

The first step is to upgrade your R version to the current version and then reinstall biomaRt.  If you still have problems, let us know on the bioconductor mailing list.  

Thanks,
Sean


On Thu, Aug 2, 2012 at 6:48 AM, John Coulthard <[hidden email]> wrote:
Hi

When following the instructions in the biomaRt.pdf I get the error below which ends 'Please report this to the mailing list' (I hope it means the biomart mailing list rather than R or bioconductor lists).

Did I do something wrong or do I wait for something to be fixed?
I am behind a proxy server but I can download packages so I don't think that is the issue.

Many thanks
John

$ R

R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(biomaRt)
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> affyids = c("202763_at", "209310_s_at", "207500_at")
> getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2",values = affyids, mart = ensembl)
                                                                                      & nbsp;                                      V1
1                           <!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN http://www.w3.org/TR/html4/loose.dtd>
2                                             <HTML><HEAD><META HTTP-EQUIV=Content-Type CONTENT=text/html; charset=iso-8859-1>
3                     & nbsp;                                          <TITLE>ERROR: The requested URL could not be retrieved</TITLE>
4 <STYLE type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
5                                                                                      & nbsp;                          </HEAD><BODY>
6                                                                                                               <H1>ERROR</H1>
Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2",  :
  The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.





> sessionInfo()
R version 2.14.1 (2011-12-22)
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    &nb s p;          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_2.10.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1 XML_3.9-4  
>




> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> biocLite("org.Hs.eg.db")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'org.Hs.eg.db'
Installing package(s) into \u2018/usr/local/lib/R/site-library\u2019
(as \u2018lib\u2019 is unspecified)
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
  'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/2.14
to install packages into?  (y/n) y
trying URL 'http://www.bioconductor.org/packages/2.9/data/annotation/src/contrib/org.Hs.eg.db_2.6.4.tar.gz'
Content type 'application/x-gzip' length 46530609 bytes (44.4 Mb)
opened URL
==================================================
downloaded 44.4 Mb

* installing *source* package \u2018org.Hs.eg.db\u2019 ...
** R
** inst
etc, etc.



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Users mailing list
[hidden email]
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Re: [BioMart Users] R biomaRt 'Please report this to the mailing list'

John Coulthard
In reply to this post by John Coulthard
I deciphered the column of html I was getting returned by getBM, it says...

ERROR
The requested URL could not be retrieved

While trying to process the request:

                                                                                          POST /biomart/martservice? HTTP/1.1
                                      &nbs p;                                                                 Host: www.biomart.org
                                                                                                & n bsp;                 Accept: */*
                                                                                                 Proxy-Connection: Keep-Alive
                                             & nbsp;                                                             Content-Length: 483
                                                                                                     & nbsp;    Expect: 100-continue
                                         Content-Type: multipart/form-data; boundary=----------------------------2224e5531f52
                                                                                                       & nbsp;               

The following error was encountered:

    Invalid Request

Some aspect of the HTTP Request is invalid. Possible problems:

    Missing or unknown request method
    Missing URL
    Missing HTTP Identifier (HTTP/1.0)
    Request is too large
    Content-Length missing for POST or PUT requests
    Illegal character in hostname; underscores are not allowed

Your cache administrator is [hidden email].
Generated Thu, 02 Aug 2012 11:12:23 GMT by south (squid/2.7.STABLE9)


From: [hidden email]
To: [hidden email]
Date: Thu, 2 Aug 2012 10:48:17 +0000
Subject: [BioMart Users] R biomaRt 'Please report this to the mailing list'

Hi

When following the instructions in the biomaRt.pdf I get the error below which ends 'Please report this to the mailing list' (I hope it means the biomart mailing list rather than R or bioconductor lists).

Did I do something wrong or do I wait for something to be fixed?
I am behind a proxy server but I can download packages so I don't think that is the issue.

Many thanks
John

$ R

R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(biomaRt)
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> affyids = c("202763_at", "209310_s_at", "207500_at")
> getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2",values = affyids, mart = ensembl)
                                                                                      & nbsp;                                      V1
1                           <!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN http://www.w3.org/TR/html4/loose.dtd>
2                                             <HTML><HEAD><META HTTP-EQUIV=Content-Type CONTENT=text/html; charset=iso-8859-1>
3                     & nbsp;                                          <TITLE>ERROR: The requested URL could not be retrieved</TITLE>
4 <STYLE type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
5                                                                                      & nbsp;                          </HEAD><BODY>
6                                                                                                               <H1>ERROR</H1>
Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2",  :
  The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.





> sessionInfo()
R version 2.14.1 (2011-12-22)
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    &am p;nb s p;          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_2.10.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1 XML_3.9-4  
>




> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> biocLite("org.Hs.eg.db")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'org.Hs.eg.db'
Installing package(s) into \u2018/usr/local/lib/R/site-library\u2019
(as \u2018lib\u2019 is unspecified)
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
  'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/2.14
to install packages into?  (y/n) y
trying URL 'http://www.bioconductor.org/packages/2.9/data/annotation/src/contrib/org.Hs.eg.db_2.6.4.tar.gz'
Content type 'application/x-gzip' length 46530609 bytes (44.4 Mb)
opened URL
==================================================
downloaded 44.4 Mb

* installing *source* package \u2018org.Hs.eg.db\u2019 ...
** R
** inst
etc, etc.


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

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