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vjcitn / hmdbQuery

utilities for querying Human Metabolome Database
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xml Parsing Error #5

Open slancast opened 3 years ago

slancast commented 3 years ago

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 commented 3 years ago

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.