{"action":"created","issue":{"url":"https://api.github.com/repos/Bioconductor/Contributions/issues/900","repository_url":"https://api.github.com/repos/Bioconductor/Contributions","labels_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/900/labels{/name}","comments_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/900/comments","events_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/900/events","html_url":"https://github.com/Bioconductor/Contributions/issues/900","id":366589671,"node_id":"MDU6SXNzdWUzNjY1ODk2NzE=","number":900,"title":"mixOmics","user":{"login":"mixOmicsTeam","id":39628589,"node_id":"MDQ6VXNlcjM5NjI4NTg5","avatar_url":"https://avatars2.githubusercontent.com/u/39628589?v=4","gravatar_id":"","url":"https://api.github.com/users/mixOmicsTeam","html_url":"https://github.com/mixOmicsTeam","followers_url":"https://api.github.com/users/mixOmicsTeam/followers","following_url":"https://api.github.com/users/mixOmicsTeam/following{/other_user}","gists_url":"https://api.github.com/users/mixOmicsTeam/gists{/gist_id}","starred_url":"https://api.github.com/users/mixOmicsTeam/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mixOmicsTeam/subscriptions","organizations_url":"https://api.github.com/users/mixOmicsTeam/orgs","repos_url":"https://api.github.com/users/mixOmicsTeam/repos","events_url":"https://api.github.com/users/mixOmicsTeam/events{/privacy}","received_events_url":"https://api.github.com/users/mixOmicsTeam/received_events","type":"User","site_admin":false},"labels":[{"id":335833554,"node_id":"MDU6TGFiZWwzMzU4MzM1NTQ=","url":"https://api.github.com/repos/Bioconductor/Contributions/labels/2.%20review%20in%20progress","name":"2. review in progress","color":"1881c2","default":false},{"id":335831709,"node_id":"MDU6TGFiZWwzMzU4MzE3MDk=","url":"https://api.github.com/repos/Bioconductor/Contributions/labels/ERROR","name":"ERROR","color":"bb3333","default":false},{"id":335833785,"node_id":"MDU6TGFiZWwzMzU4MzM3ODU=","url":"https://api.github.com/repos/Bioconductor/Contributions/labels/TIMEOUT","name":"TIMEOUT","color":"aa0088","default":false},{"id":335833865,"node_id":"MDU6TGFiZWwzMzU4MzM4NjU=","url":"https://api.github.com/repos/Bioconductor/Contributions/labels/WARNINGS","name":"WARNINGS","color":"dd8822","default":false}],"state":"open","locked":false,"assignee":{"login":"Liubuntu","id":12683977,"node_id":"MDQ6VXNlcjEyNjgzOTc3","avatar_url":"https://avatars1.githubusercontent.com/u/12683977?v=4","gravatar_id":"","url":"https://api.github.com/users/Liubuntu","html_url":"https://github.com/Liubuntu","followers_url":"https://api.github.com/users/Liubuntu/followers","following_url":"https://api.github.com/users/Liubuntu/following{/other_user}","gists_url":"https://api.github.com/users/Liubuntu/gists{/gist_id}","starred_url":"https://api.github.com/users/Liubuntu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Liubuntu/subscriptions","organizations_url":"https://api.github.com/users/Liubuntu/orgs","repos_url":"https://api.github.com/users/Liubuntu/repos","events_url":"https://api.github.com/users/Liubuntu/events{/privacy}","received_events_url":"https://api.github.com/users/Liubuntu/received_events","type":"User","site_admin":false},"assignees":[{"login":"Liubuntu","id":12683977,"node_id":"MDQ6VXNlcjEyNjgzOTc3","avatar_url":"https://avatars1.githubusercontent.com/u/12683977?v=4","gravatar_id":"","url":"https://api.github.com/users/Liubuntu","html_url":"https://github.com/Liubuntu","followers_url":"https://api.github.com/users/Liubuntu/followers","following_url":"https://api.github.com/users/Liubuntu/following{/other_user}","gists_url":"https://api.github.com/users/Liubuntu/gists{/gist_id}","starred_url":"https://api.github.com/users/Liubuntu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Liubuntu/subscriptions","organizations_url":"https://api.github.com/users/Liubuntu/orgs","repos_url":"https://api.github.com/users/Liubuntu/repos","events_url":"https://api.github.com/users/Liubuntu/events{/privacy}","received_events_url":"https://api.github.com/users/Liubuntu/received_events","type":"User","site_admin":false}],"milestone":null,"comments":11,"created_at":"2018-10-04T01:35:24Z","updated_at":"2018-10-09T23:10:59Z","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/mixOmicsTeam/mixOmics\r\n\r\n> mixOmics has been on CRAN since 2009 and we finally decided to convert to bioC. It is a big move for us and we are aware that our current submission needs further improvements. We hope to be able to stage some of our developments gradually. The future improvements we envisage in particular are to set up setGeneric and setMethods functions to fit in MultiAssayExperiments. We have not been successful so far and we need more time.\r\n> We hope that mixOmics will benefit the bioC community and attract more users! You can see our engagement and commitment with the computational biology community at www.mixOmics.org\r\n\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- [see below] 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> Please note the following:\r\n> - R CMD check --as-cran gives 3 NOTES, all OK for bioconductor \r\n> - R CMD BiocCheck gives:\r\n>   - 1 ERROR (remove package from CRAN as our package still needs to be live on CRAN\r\n>   - 1 WARNING: that we cannot address because it's relative to when we use the `cpus` argument in some of our functions, let me know if there is a work around this\r\n>  - 4 NOTES: those include unit tests and aesthetics of the code. Our package includes > 100 R functions and we are unsure how to implement the unit tests at this stage. We welcome any feedback from you.\r\n\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 [Git][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/git/\r\n[6]: http://bioconductor.org/developers/how-to/git/sync-existing-repositories/\r\n"},"comment":{"url":"https://api.github.com/repos/Bioconductor/Contributions/issues/comments/428383860","html_url":"https://github.com/Bioconductor/Contributions/issues/900#issuecomment-428383860","issue_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/900","id":428383860,"node_id":"MDEyOklzc3VlQ29tbWVudDQyODM4Mzg2MA==","user":{"login":"mixOmicsTeam","id":39628589,"node_id":"MDQ6VXNlcjM5NjI4NTg5","avatar_url":"https://avatars2.githubusercontent.com/u/39628589?v=4","gravatar_id":"","url":"https://api.github.com/users/mixOmicsTeam","html_url":"https://github.com/mixOmicsTeam","followers_url":"https://api.github.com/users/mixOmicsTeam/followers","following_url":"https://api.github.com/users/mixOmicsTeam/following{/other_user}","gists_url":"https://api.github.com/users/mixOmicsTeam/gists{/gist_id}","starred_url":"https://api.github.com/users/mixOmicsTeam/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mixOmicsTeam/subscriptions","organizations_url":"https://api.github.com/users/mixOmicsTeam/orgs","repos_url":"https://api.github.com/users/mixOmicsTeam/repos","events_url":"https://api.github.com/users/mixOmicsTeam/events{/privacy}","received_events_url":"https://api.github.com/users/mixOmicsTeam/received_events","type":"User","site_admin":false},"created_at":"2018-10-09T23:10:59Z","updated_at":"2018-10-09T23:10:59Z","author_association":"NONE","body":"Hi Lluis,\r\n\r\nThanks for your support/help :)\r\nWe already have all our examples as tests (and some more, https://github.com/mixOmicsTeam/mixOmics-CRAN/tree/master/running_scripts); we run them everytime to make sure the package is not broken, but it does not check for consistency between version, just that the code runs without errors.\r\nI'm not sure how to make tests using testthat (from what I saw the examples are quite simple) without saving a lot of mixOmics objects of the previous version and checking that the new versions give the same objects/outputs..\r\n\r\nBest,\r\n--\r\nDr. Florian Rohart\r\nResearch Fellow - Applied Statistician\r\nCourse coordinator\r\n\r\nInstitute for Molecular Bioscience\r\nThe University of Queensland\r\nSt Lucia, Brisbane, QLD 4072\r\nhttp://florian.rohart.free.fr/\r\nhttp://www.flickr.com/frohart/<https://www.flickr.com/photos/119717703@N02/>\r\n\r\nOn 10 Oct 2018, at 3:06 am, Lluís <notifications@github.com<mailto:notifications@github.com>> wrote:\r\n\r\n\r\nSorry if my comments weren't helpful. As a user of mixOmics I am excited to see the package coming to Bioconductor. I was only trying to help you with the process.\r\n\r\nI want to offer my help regarding the unit tests. One good point to start with is conerting the examples into tests. I would recommend to add tests using testthat. If you want I could submit a pull request.\r\n\r\n—\r\nYou are receiving this because you were mentioned.\r\nReply to this email directly, view it on GitHub<https://github.com/Bioconductor/Contributions/issues/900#issuecomment-428272642>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AlyvLS1-Mk30anVMusWZo5KtrrWten3wks5ujNehgaJpZM4XHN8b>.\r\n\r\n"}}
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