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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor