[BioC] connecting to ensembl

Wed May 18 21:59:45 CEST 2011

Hi Juerg, Stefan,

Thanks for providing those details, that helps a lot. So it looks
you guys are guilty, like me and the build machines, of keeping
your installation up-to-date.

More precisely we are all using the latest version of RCurl (1.6-1,
from May 15), but the postForm() function in this package seems to
be broken (it doesn't *return* the text from the HTTP response anymore,
it only *displays* it and returns NULL).

One way to workaround the problem is to download and install the
previous version of RCurl (1.6-0) available here:

   http://cran.fhcrc.org/src/contrib/Archive/RCurl/

You will need to download the source tarball manually and then install
it from the command line with:

   R CMD INSTALL RCurl_1.6-0.tar.gz

Another way is to wait for the RCurl maintainer to fix the package
but it might takes a few days before the fix shows up on CRAN...

I'll contact him right now.

Cheers,
H.

On 11-05-18 07:34 AM, Straubhaar, Juerg wrote:
> Hi Herve,
>
> code:
>
> library(biomaRt)
> mart<- useMart("ensembl","rnorvegicus_gene_ensembl")
> attr.g<- c("rgd_symbol","ensembl_gene_id","chromosome_name","start_position",
>            "end_position","strand")
> ensGene<- getBM(attributes=attr.g,mart=mart)
>
> I run the code on the commandline
>
> R --no-save<  processSeq.R 1>process.out 2>error.out
>
> process.out contains
>
> LOC682397	ENSRNOG00000043314	13	1120899	1121213	-1
> LOC304725	ENSRNOG00000031539	13	1192186	2293551	-1
> 	ENSRNOG00000031539	13	1192186	2293551	-1
> 	ENSRNOG00000028603	13	3174383	3175216	1
> 	ENSRNOG00000030028	13	4377731	4379174	-1
> 	ENSRNOG00000040235	13	4866302	4866586	-1
> 	ENSRNOG00000040233	13	5486651	5487388	1
> RGD1561440	ENSRNOG00000033336	13	5488973	5493293	-1
> 	ENSRNOG00000021163	13	5972234	6066767	-1
> 	ENSRNOG00000030239	13	7099478	7102595	1
> ...
>
> all 36669 rows from getBM function which should be stored in the ensGene variable. The ensGene variable is empty
> because of the error.
>
> error.out contains
>
> Error in getBM(attributes = attr.g, mart = mart) :
>    The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.
>
> Connection worked fine until beginning of this week when error appeared.
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] annaffy_1.22.0       KEGG.db_2.4.5        GO.db_2.4.5
>   [4] AnnotationDbi_1.12.1 ShortRead_1.8.2      Rsamtools_1.2.3
>   [7] Biostrings_2.18.4    GenomicRanges_1.2.3  Genominator_1.4.2
> [10] GenomeGraphs_1.10.0  biomaRt_2.6.0        IRanges_1.8.9
> [13] RSQLite_0.9-4        DBI_0.2-5            DESeq_1.2.1
> [16] locfit_1.5-6         lattice_0.19-26      akima_0.5-4
> [19] Biobase_2.10.0       multicore_0.1-5
>
> loaded via a namespace (and not attached):
>   [1] RColorBrewer_1.0-2 RCurl_1.6-1        XML_3.4-0          annotate_1.28.1
>   [5] genefilter_1.32.0  geneplotter_1.28.0 hwriter_1.3        splines_2.12.2
>   [9] survival_2.36-5    xtable_1.5-6
>
>
> Kind regards,
> Juerg Straubhaar
> UMASS Med School
> ________________________________________
> From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Hervé Pagès [hpages at fhcrc.org]
> Sent: Tuesday, May 17, 2011 9:50 PM
> To: s.kroeger at drfz.de
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] connecting to ensembl
>
> Hi Stefan,
>
> On 11-05-17 01:57 AM, Stefan Kroeger wrote:
>> Does anybody else has problem with connecting to ensembl (since yesterday)?
>>
>> example code:
>> myMart<- useMart("ensembl", dataset = "mmusculus_gene_ensembl")
>
> Please show the output or the error message you get.
>
> Yes we see problems in our daily build reports e.g.
>
>
> http://bioconductor.org/checkResults/2.8/bioc-LATEST/GenomicFeatures/lamb1-checksrc.html
>
> AFAICT for at least the last couple of days, biomaRt and all the
> packages that depend on it seem to have problems to connect to the
> ensembl Mart during the builds :-/
>
> H.
>
>>
>> Best
>>    Stefan
>>
>> _______________________________________________
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>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
> _______________________________________________
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>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319