Hi Stefan,
It looks like you are running an old version of biomaRt, the current
release version is 2.12 and you seem to be running 1.14
Can you update your biomaRt package and try again? things work for me:
> library(biomaRt)
> listMarts()
biomart
1 ensembl
2 snp
3 functional_genomics
4 vega
5 bacteria_mart_13
6 fungi_mart_13
7 fungi_variations_10
8 metazoa_mart_13
9 metazoa_variations_10
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.13.1
loaded via a namespace (and not attached):
[1] RCurl_1.91-1 XML_3.9-4
Cheers,
Steffen
On Fri, Jun 15, 2012 at 2:42 AM, Stefan Kroeger <[email protected]> wrote:
> Hi, since a few days I got the following problem, when trying to use
> biomaRt service in R:
>
> > library(biomaRt)
> > listMarts()
> Opening and ending tag mismatch: link line 6 and head
> Opening and ending tag mismatch: br line 17 and div
> Opening and ending tag mismatch: br line 17 and td
> Opening and ending tag mismatch: div line 17 and tr
> Opening and ending tag mismatch: img line 24 and td
> Opening and ending tag mismatch: td line 23 and tr
> Opening and ending tag mismatch: td line 92 and tr
> Opening and ending tag mismatch: tr line 91 and tbody
> Opening and ending tag mismatch: tr line 21 and table
> Opening and ending tag mismatch: img line 16 and body
> Opening and ending tag mismatch: td line 15 and html
> Premature end of data in tag tr line 14
> Premature end of data in tag tbody line 13
> Premature end of data in tag table line 12
> Premature end of data in tag body line 10
> Premature end of data in tag meta line 4
> Premature end of data in tag head line 3
> Premature end of data in tag html line 2
> Fehler: 1: Opening and ending tag mismatch: link line 6 and head
> 2: Opening and ending tag mismatch: br line 17 and div
> 3: Opening and ending tag mismatch: br line 17 and td
> 4: Opening and ending tag mismatch: div line 17 and tr
> 5: Opening and ending tag mismatch: img line 24 and td
> 6: Opening and ending tag mismatch: td line 23 and tr
> 7: Opening and ending tag mismatch: td line 92 and tr
> 8: Opening and ending tag mismatch: tr line 91 and tbody
> 9: Opening and ending tag mismatch: tr line 21 and table
> 10: Opening and ending tag mismatch: img line 16 and body
> 11: Opening and ending tag mismatch: td line 15 and html
> 12: Premature end of data in tag tr line 14
> 13: Premature end of data in tag tbody line 13
> 14: Premature end of data in tag table line 12
> 15: Premature end of data in tag body line 10
> 16: Premature end of data in tag meta line 4
> 17: Premature end of data in tag head line 3
> 18: Premature end of data in tag html line 2
>
>
> same happens when executing:
> > mart <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")
>
>
> I don't have any idea what's the problem.
> - I already recompiled/reinstalled: RCurl, bitops, biomaRt
> - I can access martview web services
>
> Can anybody help?
>
> Thanks
> Stefan
>
>
> Addiotionally my current sessionInfo()
> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
> [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_1.14.1 RCurl_1.91-1 bitops_1.0-4.1 xps_1.16.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0 XML_3.9-4
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