{"action":"created","issue":{"url":"https://api.github.com/repos/sneumann/xcms/issues/15","labels_url":"https://api.github.com/repos/sneumann/xcms/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/sneumann/xcms/issues/15/comments","events_url":"https://api.github.com/repos/sneumann/xcms/issues/15/events","html_url":"https://github.com/sneumann/xcms/issues/15","id":76130021,"number":15,"title":"xcmsSet crashes session when loading mzXML files","user":{"login":"jvondollen","id":2341664,"avatar_url":"https://avatars.githubusercontent.com/u/2341664?v=3","gravatar_id":"","url":"https://api.github.com/users/jvondollen","html_url":"https://github.com/jvondollen","followers_url":"https://api.github.com/users/jvondollen/followers","following_url":"https://api.github.com/users/jvondollen/following{/other_user}","gists_url":"https://api.github.com/users/jvondollen/gists{/gist_id}","starred_url":"https://api.github.com/users/jvondollen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jvondollen/subscriptions","organizations_url":"https://api.github.com/users/jvondollen/orgs","repos_url":"https://api.github.com/users/jvondollen/repos","events_url":"https://api.github.com/users/jvondollen/events{/privacy}","received_events_url":"https://api.github.com/users/jvondollen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-05-13T21:30:36Z","updated_at":"2015-05-14T16:52:54Z","closed_at":null,"body":"Happens when running the xcms package from the bioconductor site, as well as when running the current github version.\r\n\r\nUsing mzXML files, I tried to group them into sets following the folder structure recommended in the documentation. I even tried a pair of files instead of the whole batch and got the same result.\r\n\r\nSImply calling the xcmsSet('my_file') command caused the bomb icon popped up with a message of\r\n\"R Session Aborted\r\nR encountered a fatal error.\r\nThe session was terminated.\"\r\n\r\nA test file that crashes for me is:\r\nhttp://csb.stanford.edu/nirka/100505_NKalisman_Freidman_S1.mzXML\r\n"},"comment":{"url":"https://api.github.com/repos/sneumann/xcms/issues/comments/102101266","html_url":"https://github.com/sneumann/xcms/issues/15#issuecomment-102101266","issue_url":"https://api.github.com/repos/sneumann/xcms/issues/15","id":102101266,"user":{"login":"jvondollen","id":2341664,"avatar_url":"https://avatars.githubusercontent.com/u/2341664?v=3","gravatar_id":"","url":"https://api.github.com/users/jvondollen","html_url":"https://github.com/jvondollen","followers_url":"https://api.github.com/users/jvondollen/followers","following_url":"https://api.github.com/users/jvondollen/following{/other_user}","gists_url":"https://api.github.com/users/jvondollen/gists{/gist_id}","starred_url":"https://api.github.com/users/jvondollen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jvondollen/subscriptions","organizations_url":"https://api.github.com/users/jvondollen/orgs","repos_url":"https://api.github.com/users/jvondollen/repos","events_url":"https://api.github.com/users/jvondollen/events{/privacy}","received_events_url":"https://api.github.com/users/jvondollen/received_events","type":"User","site_admin":false},"created_at":"2015-05-14T16:52:54Z","updated_at":"2015-05-14T16:52:54Z","body":"Thanks for the feedback! I wonder what the problem could be then. Below is\nthe code that causes the crash, followed by my session info:\n\n####################\n> library(xcms)\n> mzXML_files <- list.files('~/projects/test/', recursive=T, full.names=T)\n> print(mzXML_files)\n[1] \"/Users/jvondollen/projects/test//100505_NKalisman_Freidman_S1.mzXML\"\nxset = xcmsSet(mzXML_files)\n\n*****R SESSION HAS ABORTED****\n\n###################\n> sessionInfo()\nR version 3.1.2 (2014-10-31)\nPlatform: x86_64-apple-darwin10.8.0 (64-bit)\n\nlocale:\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\n\nattached base packages:\n[1] parallel  stats     graphics  grDevices utils     datasets  methods\nbase\n\nother attached packages:\n[1] xcms_1.40.0         Biobase_2.26.0      BiocGenerics_0.12.1 mzR_2.0.0\n        Rcpp_0.11.3\n\nloaded via a namespace (and not attached):\n[1] codetools_0.2-11 tools_3.1.2\n\n\nI'm on a macbook Pro, MacOSX 10.8.5.\nAny ideas? Thanks\n\n~john\n\nOn Thu, May 14, 2015 at 2:54 AM, Jan Stanstrup <notifications@github.com>\nwrote:\n\n> Works here:\n>\n> > xset\n> An \"xcmsSet\" object with 1 samples\n>\n> Time range: 435.9-3482.4 seconds (7.3-58 minutes)\n> Mass range: 400.2133-1799.0789 m/z\n> Peaks: 3136 (about 3136 per sample)\n> Peak Groups: 0\n> Sample classes: temp\n>\n> Profile settings: method = bin\n>                   step = 0.1\n>\n> Memory usage: 0.342 MB\n>\n> > sessionInfo()\n> R version 3.2.0 (2015-04-16)\n> Platform: x86_64-w64-mingw32/x64 (64-bit)\n> Running under: Windows 7 x64 (build 7601) Service Pack 1\n>\n> locale:\n> [1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252    LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C\n> [5] LC_TIME=Danish_Denmark.1252\n>\n> attached base packages:\n> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base\n>\n> other attached packages:\n> [1] xcms_1.45.1         Biobase_2.29.0      ProtGenerics_1.1.0  BiocGenerics_0.15.0 mzR_2.3.0           Rcpp_0.11.5\n>\n> loaded via a namespace (and not attached):\n> [1] tools_3.2.0      codetools_0.2-11\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/sneumann/xcms/issues/15#issuecomment-101988886>.\n>\n"}}