{"action":"created","issue":{"url":"https://api.github.com/repos/lgatto/MSnbase/issues/170","repository_url":"https://api.github.com/repos/lgatto/MSnbase","labels_url":"https://api.github.com/repos/lgatto/MSnbase/issues/170/labels{/name}","comments_url":"https://api.github.com/repos/lgatto/MSnbase/issues/170/comments","events_url":"https://api.github.com/repos/lgatto/MSnbase/issues/170/events","html_url":"https://github.com/lgatto/MSnbase/issues/170","id":190051853,"number":170,"title":"[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match.","user":{"login":"jotsetung","id":5506112,"avatar_url":"https://avatars.githubusercontent.com/u/5506112?v=3","gravatar_id":"","url":"https://api.github.com/users/jotsetung","html_url":"https://github.com/jotsetung","followers_url":"https://api.github.com/users/jotsetung/followers","following_url":"https://api.github.com/users/jotsetung/following{/other_user}","gists_url":"https://api.github.com/users/jotsetung/gists{/gist_id}","starred_url":"https://api.github.com/users/jotsetung/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jotsetung/subscriptions","organizations_url":"https://api.github.com/users/jotsetung/orgs","repos_url":"https://api.github.com/users/jotsetung/repos","events_url":"https://api.github.com/users/jotsetung/events{/privacy}","received_events_url":"https://api.github.com/users/jotsetung/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2016-11-17T13:50:16Z","updated_at":"2016-11-21T08:21:33Z","closed_at":null,"body":"I'm experiencing some random errors again:\r\nI have a set of 690 mzML files, select 12 of them for further analysis, filter on retention time and get the following error when calling `spectra` on the `OnDiskMSnExp`:\r\n```{r}\r\nError: BiocParallel errors\r\n  element index: 6\r\n  first error: [MSData::Spectrum::getMZIntensityPairs()] Sizes do not match.\r\n```\r\nAt first I thought that it must be my files, but when I select randomly selected 12 other files the same error occurred. So it's most likely not these specific files, also, the element index is not always 6.\r\nAlso without filtering I get errors.\r\n\r\nAnd what makes me really wondering is that sometimes, especially if called repeatedly, the function works without errors."},"comment":{"url":"https://api.github.com/repos/lgatto/MSnbase/issues/comments/261872465","html_url":"https://github.com/lgatto/MSnbase/issues/170#issuecomment-261872465","issue_url":"https://api.github.com/repos/lgatto/MSnbase/issues/170","id":261872465,"user":{"login":"jotsetung","id":5506112,"avatar_url":"https://avatars.githubusercontent.com/u/5506112?v=3","gravatar_id":"","url":"https://api.github.com/users/jotsetung","html_url":"https://github.com/jotsetung","followers_url":"https://api.github.com/users/jotsetung/followers","following_url":"https://api.github.com/users/jotsetung/following{/other_user}","gists_url":"https://api.github.com/users/jotsetung/gists{/gist_id}","starred_url":"https://api.github.com/users/jotsetung/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jotsetung/subscriptions","organizations_url":"https://api.github.com/users/jotsetung/orgs","repos_url":"https://api.github.com/users/jotsetung/repos","events_url":"https://api.github.com/users/jotsetung/events{/privacy}","received_events_url":"https://api.github.com/users/jotsetung/received_events","type":"User","site_admin":false},"created_at":"2016-11-21T08:21:33Z","updated_at":"2016-11-21T08:21:33Z","body":"GOT IT!\r\nIn the function to read the spectrum values _on the fly_ (invoked by `spectrapply`) I was using the `mzR::peaks` method without first reading the spectras' headers. Now, if I add a `mzR::header` call before the `mzR::peaks` (even without needing the header information), it works.\r\nEventually that way the C++ code silently reads additional information (e.g. on how the spectrum data is encoded) that is missing if the header information is not read.\r\n\r\nI'll do some more tests and push the changes once fixed. "}}
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