{"action":"created","issue":{"url":"https://api.github.com/repos/Bioconductor/Contributions/issues/481","repository_url":"https://api.github.com/repos/Bioconductor/Contributions","labels_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/481/labels{/name}","comments_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/481/comments","events_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/481/events","html_url":"https://github.com/Bioconductor/Contributions/issues/481","id":257674104,"number":481,"title":"panelcn.mops","user":{"login":"gpovysil","id":10186153,"avatar_url":"https://avatars1.githubusercontent.com/u/10186153?v=4","gravatar_id":"","url":"https://api.github.com/users/gpovysil","html_url":"https://github.com/gpovysil","followers_url":"https://api.github.com/users/gpovysil/followers","following_url":"https://api.github.com/users/gpovysil/following{/other_user}","gists_url":"https://api.github.com/users/gpovysil/gists{/gist_id}","starred_url":"https://api.github.com/users/gpovysil/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gpovysil/subscriptions","organizations_url":"https://api.github.com/users/gpovysil/orgs","repos_url":"https://api.github.com/users/gpovysil/repos","events_url":"https://api.github.com/users/gpovysil/events{/privacy}","received_events_url":"https://api.github.com/users/gpovysil/received_events","type":"User","site_admin":false},"labels":[{"id":335833554,"url":"https://api.github.com/repos/Bioconductor/Contributions/labels/2.%20review%20in%20progress","name":"2. review in progress","color":"1881c2","default":false},{"id":335833326,"url":"https://api.github.com/repos/Bioconductor/Contributions/labels/OK","name":"OK","color":"228822","default":false}],"state":"open","locked":false,"assignee":{"login":"lshep","id":18724380,"avatar_url":"https://avatars3.githubusercontent.com/u/18724380?v=4","gravatar_id":"","url":"https://api.github.com/users/lshep","html_url":"https://github.com/lshep","followers_url":"https://api.github.com/users/lshep/followers","following_url":"https://api.github.com/users/lshep/following{/other_user}","gists_url":"https://api.github.com/users/lshep/gists{/gist_id}","starred_url":"https://api.github.com/users/lshep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lshep/subscriptions","organizations_url":"https://api.github.com/users/lshep/orgs","repos_url":"https://api.github.com/users/lshep/repos","events_url":"https://api.github.com/users/lshep/events{/privacy}","received_events_url":"https://api.github.com/users/lshep/received_events","type":"User","site_admin":false},"assignees":[{"login":"lshep","id":18724380,"avatar_url":"https://avatars3.githubusercontent.com/u/18724380?v=4","gravatar_id":"","url":"https://api.github.com/users/lshep","html_url":"https://github.com/lshep","followers_url":"https://api.github.com/users/lshep/followers","following_url":"https://api.github.com/users/lshep/following{/other_user}","gists_url":"https://api.github.com/users/lshep/gists{/gist_id}","starred_url":"https://api.github.com/users/lshep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lshep/subscriptions","organizations_url":"https://api.github.com/users/lshep/orgs","repos_url":"https://api.github.com/users/lshep/repos","events_url":"https://api.github.com/users/lshep/events{/privacy}","received_events_url":"https://api.github.com/users/lshep/received_events","type":"User","site_admin":false}],"milestone":null,"comments":3,"created_at":"2017-09-14T10:42:48Z","updated_at":"2017-09-22T13:12:10Z","closed_at":null,"author_association":"NONE","body":"Update the following URL to point to the GitHub repository of\r\nthe package you wish to submit to _Bioconductor_\r\n\r\n- Repository: https://github.com/bioinf-jku/panelcn.mops\r\n\r\nConfirm the following by editing each check box to '[x]'\r\n\r\n- [x] I understand that by submitting my package to _Bioconductor_,\r\n  the package source and all review commentary are visible to the\r\n  general public.\r\n\r\n- [x] I have read the _Bioconductor_ [Package Submission][2]\r\n  instructions. My package is consistent with the _Bioconductor_\r\n  [Package Guidelines][1].\r\n\r\n- [x] I understand that a minimum requirement for package acceptance \r\n  is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. \r\n  Passing these checks does not result in automatic acceptance. The \r\n  package will then undergo a formal review and recommendations for \r\n  acceptance regarding other Bioconductor standards will be addressed.\r\n\r\n- [x] My package addresses statistical or bioinformatic issues related\r\n  to the analysis and comprehension of high throughput genomic data.\r\n\r\n- [x] I am committed to the long-term maintenance of my package. This\r\n  includes monitoring the [support site][3] for issues that users may\r\n  have, subscribing to the [bioc-devel][4] mailing list to stay aware\r\n  of developments in the _Bioconductor_ community, responding promptly\r\n  to requests for updates from the Core team in response to changes in\r\n  _R_ or underlying software.\r\n\r\nI am familiar with the essential aspects of _Bioconductor_ software\r\nmanagement, including:\r\n\r\n- [x] The 'devel' branch for new packages and features.\r\n- [x] The stable 'release' branch, made available every six\r\n      months, for bug fixes.\r\n- [x] _Bioconductor_ version control using [Subversion][5]\r\n  (optionally [via GitHub][6]).\r\n\r\nFor help with submitting your package, please subscribe and post questions\r\nto the [bioc-devel][4] mailing list.\r\n\r\n[1]: https://bioconductor.org/developers/package-guidelines/\r\n[2]: https://bioconductor.org/developers/package-submission/\r\n[3]: https://support.bioconductor.org\r\n[4]: https://stat.ethz.ch/mailman/listinfo/bioc-devel\r\n[5]: http://bioconductor.org/developers/how-to/source-control/\r\n[6]: http://bioconductor.org/developers/how-to/git-mirrors/\r\n"},"comment":{"url":"https://api.github.com/repos/Bioconductor/Contributions/issues/comments/331442607","html_url":"https://github.com/Bioconductor/Contributions/issues/481#issuecomment-331442607","issue_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/481","id":331442607,"user":{"login":"lshep","id":18724380,"avatar_url":"https://avatars3.githubusercontent.com/u/18724380?v=4","gravatar_id":"","url":"https://api.github.com/users/lshep","html_url":"https://github.com/lshep","followers_url":"https://api.github.com/users/lshep/followers","following_url":"https://api.github.com/users/lshep/following{/other_user}","gists_url":"https://api.github.com/users/lshep/gists{/gist_id}","starred_url":"https://api.github.com/users/lshep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lshep/subscriptions","organizations_url":"https://api.github.com/users/lshep/orgs","repos_url":"https://api.github.com/users/lshep/repos","events_url":"https://api.github.com/users/lshep/events{/privacy}","received_events_url":"https://api.github.com/users/lshep/received_events","type":"User","site_admin":false},"created_at":"2017-09-22T13:12:10Z","updated_at":"2017-09-22T13:12:10Z","author_association":"CONTRIBUTOR","body":"Hello, \r\nThank you for your interest in submitting to Bioconductor.  Some comments and questions to be addressed: \r\n\r\n**Build report:** \r\n- [ ] Please add unit tests\r\n\r\n**Vignette:** \r\n- [ ] I can't run the code to reproduce this vignette? Provide example files and actually run the code.  \r\ni.e testbam SAMPLE1.bam is not a real file so test is NULL is the section that you are evaluating things? You then load data and have a test already generated? perhaps you meant to load the data earlier to provide pregenerated data objects? \r\n- [ ] please define acronyms at first occurrence (RC, ROI, etc.)\r\n- [ ] In resultstable example you haven't defined selectedGenes to show the output you give\r\n- [ ] resultlist used XandCB and countWindows - why not store this information so you don't have to have the user reinput it in createResultTable? \r\n- [ ] Can more than one result from resultlist be passed into intergerCopyNumber? Can more than one be passed into plotBoxplot? I feel like the index of interest should be passed as an argument instead of\r\nforcing the user to subset before use? \r\n- [ ] In running the code it appears a file newBed.bed gets created. For vignettes, if this is part of the code that is executed, we encourage writing any output created to a temporary directory to keep user directories clean. \r\n\r\n**MAN:** \r\n- [ ] For data man pages, give more information on how it was generated. And show the data(panelcn.mops) call in an example. \r\n- [ ] panelcn.mops.Rd / runPanelcnMopds better description, its too generic. Describe more about what is being done\r\n- [ ] Why have the overly complicated structure when you currently only have one file \r\n```\r\n bed <- list.files(system.file(\"extdata\", package = \"panelcn.mops\"),\r\n                         pattern = \".bed$\", full.names = TRUE)\r\n```\r\n**INST/EXTDATA**\r\n- [ ] What is this? document it with a man page on where it came from. \r\n\r\n**R CODE:** \r\n- [ ] we don't encourage the . in function name as it indicates S3 object implementation. change panelcn.mops function to camelcase or underscore. \r\n- [ ] Please see: [efficient coding](http://bioconductor.org/developers/how-to/efficient-code/)\r\na. Write seq_len(n) or seq_along(x) rather than 1:n or 1:length(x). This protects against the case when n or length(x) is 0 (which often occurs as an unexpected ‘edge case’ in real code) or negative.\r\nb. There are some for loops where you could better pre-allocate and fill. \r\n\r\n\r\nPlease update the package, ensure you have your webhook set up to get new build reports on version bumps, and comment back here with how the above have been addressed or clarification to questions.  We look forward to getting your package accepted into Bioconductor. \r\n\r\nCheers, \r\nLori \r\n\r\n\r\n"}}
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