[BioC] KEGGSOAP (installation?) problem

Marc Carlson mcarlson at fhcrc.org
Fri Apr 24 18:37:37 CEST 2009


Hi Paolo,

I am not able to reproduce this using the same R version and packages
listed in your sessionInfo().  Also, the output really looks like this
was caused by the web belching some bad hypertext at your R session. 
Can you please try it again and let us know if the problem persists?


  Marc




Paolo Sonego wrote:
> Dear all,
>
> I'm not sure if this could be considered a bug...
>
> I need to use the KEGGSOAP package to retrieve some KEGG pathway
> diagrams.
>
> Below is the procedure I followed to check the KEGGSOAP package:
>
> library(KEGGSOAP)
> ## from the mark.pathway.by.objects help page
> > url <- color.pathway.by.objects("path:eco00260",
> +                             c("eco:b0002", "eco:c00263"),
> +                             c("#ff0000", "#00ff00"), c("#ffff00",
> "yellow"))
> Opening and ending tag mismatch: META line 2 and HEAD
> Specification mandate value for attribute noshade
> attributes construct error
> Couldn't find end of Start Tag HR line 8
> Opening and ending tag mismatch: LI line 27 and UL
> Opening and ending tag mismatch: LI line 41 and UL
> Specification mandate value for attribute noshade
> attributes construct error
> Couldn't find end of Start Tag HR line 46
> Opening and ending tag mismatch: BR line 45 and BODY
> Opening and ending tag mismatch: P line 43 and HTML
> Premature end of data in tag LI line 40
> Premature end of data in tag LI line 39
> Premature end of data in tag LI line 38
> Premature end of data in tag LI line 37
> Premature end of data in tag LI line 36
> Premature end of data in tag UL line 35
> Premature end of data in tag P line 33
> Premature end of data in tag UL line 26
> Premature end of data in tag P line 24
> 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: Opening and ending tag mismatch: META line 2 and HEAD
> 2: Specification mandate value for attribute noshade
> 3: attributes construct error
> 4: Couldn't find end of Start Tag HR line 8
> 5: Opening and ending tag mismatch: LI line 27 and UL
> 6: Opening and ending tag mismatch: LI line 41 and UL
> 7: Specification mandate value for attribute noshade
> 8: attributes construct error
> 9: Couldn't find end of Start Tag HR line 46
> 10: Opening and ending tag mismatch: BR line 45 and BODY
> 11: Opening and ending tag mismatch: P line 43 and HTML
> 12: Premature end of data in tag LI line 40
> 13: Premature end of data in tag LI line 39
> 14: Premature end of data in tag LI line 38
> 15: Premature end of data in tag LI line 37
> 16: Premature end of data in tag LI line 36
> 17: Premature end of data in tag UL line 35
> 18: Premature end of data in tag P line 33
> 19: Premature end of data in tag UL line 26
> 20: Premature end of data in tag P line 24
> 21: Premature end of data in tag P line 9
> 22: Premature end of da
> >
>
> ----------------------------
> My R session info:
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base   
> other attached packages:
> [1] KEGGSOAP_1.18.0 fortunes_1.3-6
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 SSOAP_0.4-6  XML_2.3-0
>
> ------------------------------
>
> My system information:
>
> uname -a
>
> Linux 2.6.25-gentoo-r7 #2 SMP Wed Nov 5 17:56:30 CET 2008 x86_64
> Intel(R) Xeon(TM) CPU 3.40GHz GenuineIntel GNU/Linux
>
>
> Any help would be appreciated.
>
> Regards,
>
> Paolo
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



More information about the Bioconductor mailing list