{"action":"created","issue":{"url":"https://api.github.com/repos/sneumann/xcms/issues/253","repository_url":"https://api.github.com/repos/sneumann/xcms","labels_url":"https://api.github.com/repos/sneumann/xcms/issues/253/labels{/name}","comments_url":"https://api.github.com/repos/sneumann/xcms/issues/253/comments","events_url":"https://api.github.com/repos/sneumann/xcms/issues/253/events","html_url":"https://github.com/sneumann/xcms/issues/253","id":297470327,"number":253,"title":"Error in fillChromPeaks()  ","user":{"login":"bitbarbie","id":3034317,"avatar_url":"https://avatars1.githubusercontent.com/u/3034317?v=4","gravatar_id":"","url":"https://api.github.com/users/bitbarbie","html_url":"https://github.com/bitbarbie","followers_url":"https://api.github.com/users/bitbarbie/followers","following_url":"https://api.github.com/users/bitbarbie/following{/other_user}","gists_url":"https://api.github.com/users/bitbarbie/gists{/gist_id}","starred_url":"https://api.github.com/users/bitbarbie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bitbarbie/subscriptions","organizations_url":"https://api.github.com/users/bitbarbie/orgs","repos_url":"https://api.github.com/users/bitbarbie/repos","events_url":"https://api.github.com/users/bitbarbie/events{/privacy}","received_events_url":"https://api.github.com/users/bitbarbie/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-02-15T14:43:58Z","updated_at":"2018-02-16T09:35:35Z","closed_at":null,"author_association":"NONE","body":"I tried to fill an xset after picking and grouping, but without RT correction. I got the following error, whereas DAY074_007_Q.mzML is the first file it tries to fill. \r\nSteffen is able to asses the data.\r\n\r\n```r\r\nxdata <- fillChromPeaks(xdata, BPPARAM=bpparam() )\r\n\r\nRequesting 234 missing peaks from DAY074_007_Q.mzML ... \r\nError: BiocParallel errors\r\n  element index: 1, 2, 3, 4, 5, 6, ...\r\n  first error: unable to find an inherited method for function ‘mz’ for signature ‘\"NULL\"’\r\nIn addition: Warning message:\r\nstop worker failed:\r\n  'clear_cluster' receive data failed:\r\n  reached elapsed time limit \r\n\r\n```"},"comment":{"url":"https://api.github.com/repos/sneumann/xcms/issues/comments/366186375","html_url":"https://github.com/sneumann/xcms/issues/253#issuecomment-366186375","issue_url":"https://api.github.com/repos/sneumann/xcms/issues/253","id":366186375,"user":{"login":"jotsetung","id":5506112,"avatar_url":"https://avatars3.githubusercontent.com/u/5506112?v=4","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":"2018-02-16T09:35:35Z","updated_at":"2018-02-16T09:35:35Z","author_association":"COLLABORATOR","body":"This is strange - somehow the `spectra` call on your file seems to not return a `list` of `Spectrum1` objects.\r\n2 things: was there any reason to have `mzR` version 2.13.3 installed? That's the current developmental version while all other packages (`xcms` and `MSnbase`) are from the current stable release of Bioconductor 3.6. Second, did you eventually move the original files?"}}
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