{"action":"created","issue":{"url":"https://api.github.com/repos/ropensci/RNeXML/issues/128","labels_url":"https://api.github.com/repos/ropensci/RNeXML/issues/128/labels{/name}","comments_url":"https://api.github.com/repos/ropensci/RNeXML/issues/128/comments","events_url":"https://api.github.com/repos/ropensci/RNeXML/issues/128/events","html_url":"https://github.com/ropensci/RNeXML/issues/128","id":109184655,"number":128,"title":"nexml_validate issues warnings on validating valid NeXML","user":{"login":"hlapp","id":51458,"avatar_url":"https://avatars.githubusercontent.com/u/51458?v=3","gravatar_id":"","url":"https://api.github.com/users/hlapp","html_url":"https://github.com/hlapp","followers_url":"https://api.github.com/users/hlapp/followers","following_url":"https://api.github.com/users/hlapp/following{/other_user}","gists_url":"https://api.github.com/users/hlapp/gists{/gist_id}","starred_url":"https://api.github.com/users/hlapp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hlapp/subscriptions","organizations_url":"https://api.github.com/users/hlapp/orgs","repos_url":"https://api.github.com/users/hlapp/repos","events_url":"https://api.github.com/users/hlapp/events{/privacy}","received_events_url":"https://api.github.com/users/hlapp/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-09-30T21:37:26Z","updated_at":"2015-10-01T12:05:40Z","closed_at":null,"body":"Here's the log:\r\n\r\n```R\r\n> nexml_validate(\"./inst/examples/test_original.xml\")\r\n[1] FALSE\r\nWarning message:\r\nIn nexml_validate(\"./inst/examples/test_original.xml\") :\r\n  Validation failed, error messages: \r\n                    'http://purl.obolibrary.org/obo/VTO_0036225' is not a valid xml NCName for Bio::Phylo::Taxa::Taxon=SCALAR(0x1ce5440)            Validation failed, error messages: \r\n                    'http://purl.obolibrary.org/obo/VTO_0036225' is not a valid xml NCName for Bio::Phylo::Taxa::Taxon=SCALAR(0x1ce5440)\r\n```\r\n\r\nThe [file](https://github.com/xu-hong/rphenoscape/blob/master/inst/examples/test_original.xml) is the original NeXML returned by the Phenocape API.\r\n\r\nOne thing that might come into play here is the use of HTTP URIs as local identifiers. I have filed issue phenoscape/phenoscape-kb-services#15 for whether this is on purpose, and what motivates it."},"comment":{"url":"https://api.github.com/repos/ropensci/RNeXML/issues/comments/144707458","html_url":"https://github.com/ropensci/RNeXML/issues/128#issuecomment-144707458","issue_url":"https://api.github.com/repos/ropensci/RNeXML/issues/128","id":144707458,"user":{"login":"hlapp","id":51458,"avatar_url":"https://avatars.githubusercontent.com/u/51458?v=3","gravatar_id":"","url":"https://api.github.com/users/hlapp","html_url":"https://github.com/hlapp","followers_url":"https://api.github.com/users/hlapp/followers","following_url":"https://api.github.com/users/hlapp/following{/other_user}","gists_url":"https://api.github.com/users/hlapp/gists{/gist_id}","starred_url":"https://api.github.com/users/hlapp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hlapp/subscriptions","organizations_url":"https://api.github.com/users/hlapp/orgs","repos_url":"https://api.github.com/users/hlapp/repos","events_url":"https://api.github.com/users/hlapp/events{/privacy}","received_events_url":"https://api.github.com/users/hlapp/received_events","type":"User","site_admin":false},"created_at":"2015-10-01T12:05:40Z","updated_at":"2015-10-01T12:05:40Z","body":"The XML isn't valid. See @balhoff's comments on phenoscape/phenoscape-kb-services#15"}}