{"action":"created","issue":{"url":"https://api.github.com/repos/JinmiaoChenLab/cytofkit/issues/1","repository_url":"https://api.github.com/repos/JinmiaoChenLab/cytofkit","labels_url":"https://api.github.com/repos/JinmiaoChenLab/cytofkit/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/JinmiaoChenLab/cytofkit/issues/1/comments","events_url":"https://api.github.com/repos/JinmiaoChenLab/cytofkit/issues/1/events","html_url":"https://github.com/JinmiaoChenLab/cytofkit/issues/1","id":180134362,"number":1,"title":"Installation problems","user":{"login":"mleipold","id":1111114,"avatar_url":"https://avatars.githubusercontent.com/u/1111114?v=3","gravatar_id":"","url":"https://api.github.com/users/mleipold","html_url":"https://github.com/mleipold","followers_url":"https://api.github.com/users/mleipold/followers","following_url":"https://api.github.com/users/mleipold/following{/other_user}","gists_url":"https://api.github.com/users/mleipold/gists{/gist_id}","starred_url":"https://api.github.com/users/mleipold/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mleipold/subscriptions","organizations_url":"https://api.github.com/users/mleipold/orgs","repos_url":"https://api.github.com/users/mleipold/repos","events_url":"https://api.github.com/users/mleipold/events{/privacy}","received_events_url":"https://api.github.com/users/mleipold/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-09-29T19:02:06Z","updated_at":"2016-10-05T06:51:24Z","closed_at":null,"body":"I'm trying to install the cytofkit software.  I am running Mac OSX 10.10.3, XQuartz 2.7.9 (freshly updated during installation attempts), and R 3.2.3 (or RStudio Version 0.98.1103).\r\n\r\nI was able to download it from Bioconductor, and it looked like it installed:\r\n-----\r\n> source(\"https://bioconductor.org/biocLite.R\")\r\nBioconductor version 3.1 (BiocInstaller 1.18.5), ?biocLite for help\r\nA newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help\r\n> biocLite(\"cytofkit\")\r\nBioC_mirror: http://bioconductor.org\r\nUsing Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.3.\r\nInstalling package(s) ‘cytofkit’\r\ntrying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/cytofkit_1.1.0.tgz'\r\nContent type 'application/x-gzip' length 1812061 bytes (1.7 MB)\r\n==================================================\r\ndownloaded 1.7 MB\r\n\r\n\r\nThe downloaded binary packages are in\r\n\t/var/folders/ln/_r_qkh8j1wz_wlrx0gw3mp100000gq/T//RtmpAu0vRJ/downloaded_packages\r\nOld packages: 'manipulate'\r\nUpdate all/some/none? [a/s/n]: \r\na\r\ntrying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/manipulate_1.0.1.tgz'\r\nContent type 'application/x-gzip' length 34143 bytes (33 KB)\r\n==================================================\r\ndownloaded 33 KB\r\n\r\n\r\nThe downloaded binary packages are in\r\n\t/var/folders/ln/_r_qkh8j1wz_wlrx0gw3mp100000gq/T//RtmpAu0vRJ/downloaded_packages\r\n-----\r\n\r\nI can see \"cytofkit\" as a package in RStudio.  As shown above, a few packages had to be updated, but all that happened fine as far as I can tell.  Similarly, during the first installation attempt, XQuartz wanted an update, so I did that.  I even restarted my computer after the XQuartz update to make sure that wouldn't be an issue.\r\n\r\nWhen I move on to the next step:\r\n>library(\"cytofkit\")\r\n\r\nIt pauses, XQuartz opens, and then I get the \">\" back.\r\n\r\n\r\nAfter that, though, I can't get anything to work.  \r\n\r\n-------\r\n> ?cytofkit-package\r\nError in eval(expr, envir, enclos) : object 'cytofkit' not found\r\nError in .helpForCall(topicExpr, parent.frame()) : \r\n  error in trying to evaluate the expression for argument ‘e1’ (cytofkit)\r\n> cytofkit_GUI()\r\nError: could not find function \"cytofkit_GUI\"\r\n> \r\n------\r\n\r\nIn short:  the GUI never opens...it seems like there's an error earlier in the process.\r\n\r\n\r\nSuggestions?\r\n\r\n-Mike, HIMC"},"comment":{"url":"https://api.github.com/repos/JinmiaoChenLab/cytofkit/issues/comments/251596202","html_url":"https://github.com/JinmiaoChenLab/cytofkit/issues/1#issuecomment-251596202","issue_url":"https://api.github.com/repos/JinmiaoChenLab/cytofkit/issues/1","id":251596202,"user":{"login":"haoeric","id":3971838,"avatar_url":"https://avatars.githubusercontent.com/u/3971838?v=3","gravatar_id":"","url":"https://api.github.com/users/haoeric","html_url":"https://github.com/haoeric","followers_url":"https://api.github.com/users/haoeric/followers","following_url":"https://api.github.com/users/haoeric/following{/other_user}","gists_url":"https://api.github.com/users/haoeric/gists{/gist_id}","starred_url":"https://api.github.com/users/haoeric/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/haoeric/subscriptions","organizations_url":"https://api.github.com/users/haoeric/orgs","repos_url":"https://api.github.com/users/haoeric/repos","events_url":"https://api.github.com/users/haoeric/events{/privacy}","received_events_url":"https://api.github.com/users/haoeric/received_events","type":"User","site_admin":false},"created_at":"2016-10-05T06:51:24Z","updated_at":"2016-10-05T06:51:24Z","body":"Dear @ghowell2812,\r\n\r\nThanks for your feedback. From your information, I may guess that cytofkit is not installed properly on your side. Could you check your R version (type `version` on R console will print your R version) and make sure it is version 3.3.0 or above. Then update BiocInstaller and install cytofkit with codes below:\r\n\r\n```R\r\nsource(\"https://bioconductor.org/biocLite.R\")\r\nbiocLite(\"BiocInstaller\")\r\n\r\nsource(\"https://bioconductor.org/biocLite.R\")\r\nbiocLite(\"cytofkit\")\r\n```\r\n"}}
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