Thanks for the hint!
Am 15.06.2012 17:51, schrieb Steffen Durinck:
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:
Was a stupid mistake by myself, I updated all packages globally but
missed that I have local (user) installations of some packages....that's
why I always loaded the old packages & libs.
Sorry and big thanks!
Stefan
> 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]
<mailto:[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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