[BioC] biomaRt - ensembl - proxy - NCBI36/hg18 - problems

Wolfgang Huber whuber at embl.de
Wed Mar 24 21:08:01 CET 2010


Dear Anthony

I just tried your code example (as requoted in cleaned up form below) 
from a computer 'directly on the internet', and got a result, so your 
problem appears to be related to your particular site (i.e. internet 
connection).

I am sorry that I cannot help further with that, as I have not recently 
had the need to use proxies. Maybe someone else has an idea...?

Wolfgang



library("biomaRt")

listMarts(host="may2009.archive.ensembl.org",
           path="/biomart/martservice",archive=FALSE)

ensembl = useMart("ENSEMBL_MART_ENSEMBL",
   dataset="hsapiens_gene_ensembl",
   host="may2009.archive.ensembl.org",
   path="/biomart/martservice",
   archive=FALSE)

chrom <- 5
chr.start <- 110000000
chr.stop  <- 113000000

r = getBM(attributes="hgnc_symbol",
       filters=c("chromosome_name","start","end"),
       values=list(chrom,chr.start,chr.stop),mart=ensembl)

 > r
    hgnc_symbol
1       TSSK1B
2       YTHDC2
3          MCC
4         DCP2
5        ZRSR1
6        REEP5
7        SRP19
8          APC
9     EPB41L4A
10     C5orf13
11      STARD4
12       CAMK4
13       WDR36
14        TSLP
15    SLC25A46

 > sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-23 r51373)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=C              LC_NUMERIC=C            LC_TIME=C 

  [4] LC_COLLATE=C            LC_MONETARY=C 
LC_MESSAGES=it_IT.UTF-8
  [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C 

[10] LC_TELEPHONE=C          LC_MEASUREMENT=C        LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_2.3.4  fortunes_1.3-7

loaded via a namespace (and not attached):
[1] RCurl_1.3-1 XML_2.8-1



  Ferrari ha scritto:
> (Sorry if you received this email twice)
> 
> Hi all,
> 
> I am currently experiencing problems running biomaRt package.
> I have a simple task to do which consists in retrieving all hgnc symbols
> between two genomic positions on a chromosome.
> 
> My genomic positions are mapped to NCBI36/hg18 so I want to use an archived
> version of ensembl database to be able to query this human genome version.
> 
> I am behind a proxy. I am using a windows PC, pentium 4, 3.2 Ghz, 1 Go RAM.
> 
> I have already been through the archived mailing list to find useful
> information about problems running biomaRt. And this allowed me to get
> started and below you will find the scripts I used and my sessionInfo().
> 
> 
> I can connect to the release 54 (NCBI36) of ensembl database, create a
> 'biomart object' but the getBM function fails. A traceback() call indicates
> that the error comes from a call to tryCatch(..). The error is the following
> :
> 
> *Erreur dans 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.
> De plus : Message d'avis :
> In getStatus(status) : NAs introduits lors de la conversion automatique*
> 
> But it seems that my internet connection is not down and neither is biomart
> web service.
> 
> Does anyone know why I am getting this message ?
> Any help would be appreciated. Thank you very much.
> 
> 
> Anthony Ferrari
> 
> 
> 
> 
>> Sys.time()
> [1] "2010-03-24 09:57:42 CET"
>> library(biomaRt);
>> Sys.setenv("http_proxy"="http://195.220.67.254:8247");
>>
>> listMarts(host="may2009.archive.ensembl.org",path="/
> biomart/martservice",archive=FALSE);
>                biomart              version
> 1 ENSEMBL_MART_ENSEMBL           Ensembl 54
> 2     ENSEMBL_MART_SNP Ensembl Variation 54
> 3    ENSEMBL_MART_VEGA              Vega 35
> 4             REACTOME   Reactome(CSHL US)
> 5     wormbase_current   WormBase (CSHL US)
> 6                pride       PRIDE (EBI UK)
>> ensembl =
> useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="
> may2009.archive.ensembl.org",path="/biomart/martservice",archive=FALSE);
> Checking attributes ... ok
> Checking filters ... ok
>> chrom <- 5;
>> chr.start <- 110000000;
>> chr.stop  <- 113000000;
>>
>>
> getBM(attributes="hgnc_symbol",filters=c("chromosome_name","start","end"),values=list(chrom,chr.start,chr.stop),mart=ensembl);
> Erreur dans 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.
> De plus : Message d'avis :
> In getStatus(status) : NAs introduits lors de la conversion automatique
>> traceback()
> 6: stop("Request to BioMart web service failed. Verify if you are still
> connected to the internet.  Alternatively the BioMart web service is
> temporarily down.")
> 5: value[[3L]](cond)
> 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 3: tryCatchList(expr, classes, parentenv, handlers)
> 2: tryCatch(postForm(paste(martHost(mart), "?", sep = ""), query =
> xmlQuery),
>        error = function(e) {
>            stop("Request to BioMart web service failed. Verify if you are
> still connected to the internet.  Alternatively the BioMart web service is
> temporarily down.")
>        })
> 1: getBM(attributes = "hgnc_symbol", filters = c("chromosome_name",
>        "start", "end"), values = list(chrom, chr.start, chr.stop),
>        mart = ensembl)
>> Sys.time()
> [1] "2010-03-24 09:57:47 CET"
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
> 
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biomaRt_2.2.0
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.3-1 XML_2.8-1
> 
> 	[[alternative HTML version deleted]]
> 
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-- 

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact



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