[BioC] getBM no connection but listMarts has
James W. MacDonald
jmacdon at med.umich.edu
Mon Dec 7 21:47:21 CET 2009
Hi Cristobal,
Earlier I was using my Windows box. For comparison I switched to our
ROCKS cluster:
$ xml2-config --version
2.6.23
Not sure that is correct - I seem to recall having to link against a
newer version of libxml2, but I don't see one in my home directory.
$ curl --version
curl 7.19.5 (i686-pc-linux-gnu) libcurl/7.19.5 OpenSSL/0.9.7a zlib/1.2.1.2
Protocols: tftp ftp telnet dict ldap http file https ftps
Features: IPv6 Largefile NTLM SSL libz
> getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters =
"affy_hg_u133_plus_2", values = affyids, mart = ensembl)
affy_hg_u133_plus_2 entrezgene
1 202763_at 836
2 202763_at NA
3 209310_s_at 837
4 209310_s_at NA
5 207500_at 838
6 207500_at NA
> sessionInfo()
R version 2.10.0 alpha (2009-09-30 r49906)
i686-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=en_US.iso885915 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.1.0
loaded via a namespace (and not attached):
[1] RCurl_1.2-0 XML_2.6-0
Best,
Jim
Cristobal Fresno Rodríguez wrote:
> Hi Jim,
>
> I updated the packages as recommended, and still have the same error.
>
> > library(biomaRt)
> > sessionInfo()
> R version 2.10.1 RC (2009-12-06 r50681)
> i686-pc-linux-gnu
>
> 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_2.2.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.3-0 XML_2.6-0
> > ensembl <- useMart("ensembl", "hsapiens_gene_ensembl")
> Checking attributes ... ok
> Checking filters ... ok
> > 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)
> 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.
> >
>
> Can you tell me what curl and xml are on your system?
> I have
> $ xml2-config --version
> 2.7.5
> $ curl --version
> curl 7.19.7 (i686-pc-linux-gnu) libcurl/7.19.7
> Protocols: tftp ftp telnet dict http file
> Features: IPv6 Largefile
>
> Best,
> Cristobal
>
>
>
> El 7 de diciembre de 2009 14:37, James W. MacDonald
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>> escribió:
>
> Hi Cristobal,
>
>
> Cristobal Fresno Rodríguez wrote:
>
> Hi,
>
> I'm trying to use biomaRt but get the following error, when I
> try getBM
> statement but the connectivity seems ok according to listMarts().
>
> library("biomaRt")
> listMarts()[1:4,]
> biomart
> version
> 1 ensembl ENSEMBL 56 GENES (SANGER UK)
> 2 snp ENSEMBL 56 VARIATION (SANGER UK)
> 3 functional_genomics ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK)
> 4 vega VEGA 36 (SANGER UK)
> ensembl = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
> Checking attributes ... ok
> Checking filters ... ok
> 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)
> 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.
> Calls: getBM ... tryCatch -> tryCatchList -> tryCatchOne ->
> <Anonymous>
>
>
> I search a little bit and found that on the postForm call on
> getBM got the
> error; probably RCurl compatibility issue?
>
>
> Possibly. You have a previous version of R and a current version of
> biomaRt and RCurl. This works for me with packages installed using
> biocLite():
>
> > library(biomaRt)
> > ensembl <- useMart("ensembl", "hsapiens_gene_ensembl")
>
> Checking attributes ... ok
> Checking filters ... ok
> > 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)
> affy_hg_u133_plus_2 entrezgene
> 1 202763_at 836
> 2 202763_at NA
> 3 209310_s_at 837
> 4 209310_s_at NA
> 5 207500_at 838
> 6 207500_at NA
> > > > sessionInfo()
> R version 2.10.0 Patched (2009-11-05 r50317)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
>
> other attached packages:
> [1] biomaRt_2.2.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.2-1 XML_2.6-0
>
> Best,
>
> Jim
>
>
>
> sessionInfo()
>
> R version 2.9.2 (2009-08-24)
> i486-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_2.2.0 rkward_0.5.1
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.3-0 tools_2.9.2 XML_2.6-0
>
>
> Thanks,
>
> Cristobal
>
> [[alternative HTML version deleted]]
>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should
> not be used for urgent or sensitive issues
>
>
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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