xml Parsing Error

[slancast]

When I run the following code:

HmdbEntry(prefix = "http://www.hmdb.ca/metabolites/", id = "HMDB61677")

I get the following very long error. Please help.

error parsing attribute name
attributes construct error
Couldn't find end of Start Tag n.length line 3
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag x.length line 3
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag n.allowed_origins.length line 3
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag l line 3
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
StartTag: invalid element name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag l line 3
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag n.length-1 line 3
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
StartTag: invalid element name
xmlParseEntityRef: no name
EntityRef: expecting ';'
StartTag: invalid element name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag o.length line 3
EntityRef: expecting ';'
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag t line 3
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag r.length line 3
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
StartTag: invalid element name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag i line 3
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag f line 3
xmlParseEntityRef: no name
EntityRef: expecting ';'
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag n.length line 3
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag e.length line 3
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
EntityRef: expecting ';'
xmlParseEntityRef: no name
xmlParseEntityRef: no name
error parsing attribute name
attributes construct error
Couldn't find end of Start Tag t line 3
Entity 'times' not defined
Unescaped '<' not allowed in attributes values
attributes construct error
Couldn't find end of Start Tag a line 52
AttValue: " or ' expected
attributes construct error
Couldn't find end of Start Tag div line 52
AttValue: " or ' expected
attributes construct error
Couldn't find end of Start Tag div line 52
AttValue: " or ' expected
attributes construct error
Couldn't find end of Start Tag div line 52
Opening and ending tag mismatch: li line 0 and div
Opening and ending tag mismatch: ul line 0 and div
Opening and ending tag mismatch: ul line 0 and div
Opening and ending tag mismatch: td line 0 and a
Opening and ending tag mismatch: tr line 0 and li
Opening and ending tag mismatch: tbody line 0 and ul
Opening and ending tag mismatch: table line 0 and ul
Unescaped '<' not allowed in attributes values
attributes construct error
Couldn't find end of Start Tag a line 52
AttValue: " or ' expected
attributes construct error
Couldn't find end of Start Tag div line 52
AttValue: " or ' expected
attributes construct error
Couldn't find end of Start Tag div line 52
AttValue: " or ' expected
attributes construct error
Couldn't find end of Start Tag div line 52
Opening and ending tag mismatch: li line 0 and div
Opening and ending tag mismatch: ul line 0 and div
Opening and ending tag mismatch: main line 0 and div
Opening and ending tag mismatch: body line 0 and a
Opening and ending tag mismatch: html line 0 and li
Extra content at the end of the document
Error: 1: error parsing attribute name
2: attributes construct error
3: Couldn't find end of Start Tag n.length line 3
4: xmlParseEntityRef: no name
5: EntityRef: expecting ';'
6: xmlParseEntityRef: no name
7: xmlParseEntityRef: no name
8: xmlParseEntityRef: no name
9: xmlParseEntityRef: no name
10: xmlParseEntityRef: no name
11: xmlParseEntityRef: no name
12: xmlParseEntityRef: no name
13: xmlParseEntityRef: no name
14: xmlParseEntityRef: no name
15: EntityRef: expecting ';'
16: xmlParseEntityRef: no name
17: EntityRef: expecting ';'
18: xmlParseEntityRef: no name
19: xmlParseEntityRef: no name
20: xmlParseEntityRef: no name
21: EntityRef: expecting ';'
22: xmlParseEntityRef: no name
23: xmlParseEntityRef: no name
24: xmlParseEntityRef: no name
25: EntityRef: expecting ';'
26: xmlParseEntityRef: no name
27: EntityRef: expecting ';'
28: xmlParseEntityRef: no name
29: xmlParseEntityRef: no name
30: xmlParseEntityRef: no name
31: xmlParseEntityRef: no name
32: xmlParseEntityRef: no name
In addition: Warning message:
In readLines(.hmxPath(prefix = prefix, id = id, ...)) :
incomplete final line found on 'http://www.hmdb.ca/metabolites/HMDB61677.xml'

[vjcitn]

That's too bad. You can try HMDB0061677 and you will get a list as an answer with a warning ... the record for that entry is not typical. You could contact HMDB to have them normalize the information.