[BioC] Entity 'nbsp' not defined using biomaRt

[Hans-Rudolf Hotz]

Hi Severine


Looks like there are two problems.....

Currently, 'mart = useMart("ensembl")'  doesn't work for me at all. The 
web site 'www.biomart.org' is currently down.


Hence, I use a different host, eg 'host = "www.ensembl.org")', and then

mart2 = useMart("ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org")

and this works fine for me.


The kind of error, you see, I only get if a use a wrong host address, eg:

mart3 = useMart("ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org/foo")



Regards, Hans




On 07/04/2011 12:21 PM, Affeldt Severine wrote:
> Dear list,
>
> I am using biomaRt for a few months now, and I have recently encountered a problem while using the 'useMart' function.
>
> ----------------------------
> Here is my code:
>
> library("biomaRt")
> mart = useMart("ensembl")
>
> I get the following error messages:
>
> Entity 'nbsp' not defined
> Entity 'eacute' not defined
> Entity 'ecirc' not defined
> Entity 'eacute' not defined
> Opening and ending tag mismatch: META line 2 and HEAD
> Entity 'eacute' not defined
> Entity 'ecirc' not defined
> Entity 'eacute' not defined
> Specification mandate value for attribute noshade
> attributes construct error
> Couldn't find end of Start Tag HR line 8
> Entity 'nbsp' not defined
> Entity 'eacute' not defined
> Entity 'eacute' not defined
> Entity 'eacute' not defined
> Entity 'nbsp' not defined
> Opening and ending tag mismatch: LI line 15 and UL
> Entity 'egrave' not defined
> Entity 'eacute' not defined
> Entity 'nbsp' not defined
> Entity 'eacute' not defined
> Entity 'eacute' not defined
> Entity 'eacute' not defined
> Entity 'eacute' not defined
> Entity 'ecirc' not defined
> Specification mandate value for attribute noshade
> attributes construct error
> Couldn't find end of Start Tag HR line 31
> Opening and ending tag mismatch: BR line 30 and BODY
> Opening and ending tag mismatch: P line 21 and HTML
> Premature end of data in tag UL line 14
> Premature end of data in tag P line 12
> Premature end of data in tag P line 9
> Premature end of data in tag BODY line 5
> Premature end of data in tag HEAD line 2
> Premature end of data in tag HTML line 2
> Error: 1: Entity 'nbsp' not defined
> 2: Entity 'eacute' not defined
> 3: Entity 'ecirc' not defined
> 4: Entity 'eacute' not defined
> 5: Opening and ending tag mismatch: META line 2 and HEAD
> 6: Entity 'eacute' not defined
> 7: Entity 'ecirc' not defined
> 8: Entity 'eacute' not defined
> 9: Specification mandate value for attribute noshade
> 10: attributes construct error
> 11: Couldn't find end of Start Tag HR line 8
> 12: Entity 'nbsp' not defined
> 13: Entity 'eacute' not defined
> 14: Entity 'eacute' not defined
> 15: Entity 'eacute' not defined
> 16: Entity 'nbsp' not defined
> 17: Opening and ending tag mismatch: LI line 15 and UL
> 18: Entity 'egrave' not defined
> 19: Entity 'eacute' not defined
> 20: Entity 'nbsp' not defined
> 21: Entity 'eacute' not defined
> 22: Entity 'eacute' not defined
> 23: Entity 'eacute' not defined
> 24: Entity 'eacute' not defined
> 25: Entity 'ecirc' not defined
> 26: Specification mandate value for attribute noshade
> 27: attributes construct error
> 28: Couldn't find end of Start Tag HR line 3
> ----------------------------
>
> Here is the session information:
>
> R version 2.13.0 (2011-04-13)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.8.1
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.6-6  tools_2.13.0 XML_3.4-0
> ----------------------------
>
> Thank you in advance for any help on this,
> Regards,
>
> Severine
>
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