[BioC] KEGGSOAP (installation?) problem

Paolo Sonego paolo.sonego at gmail.com
Fri Apr 24 16:06:13 CEST 2009


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



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