{"action":"created","issue":{"url":"https://api.github.com/repos/thomasp85/mzID/issues/30","labels_url":"https://api.github.com/repos/thomasp85/mzID/issues/30/labels{/name}","comments_url":"https://api.github.com/repos/thomasp85/mzID/issues/30/comments","events_url":"https://api.github.com/repos/thomasp85/mzID/issues/30/events","html_url":"https://github.com/thomasp85/mzID/issues/30","id":90132114,"number":30,"title":"duplicated generics","user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/thomasp85/mzID/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-06-22T15:26:30Z","updated_at":"2015-06-28T11:28:55Z","closed_at":"2015-06-27T17:38:21Z","body":"The [`ProtGenerics`](http://www.bioconductor.org/packages/devel/bioc/html/ProtGenerics.html) package defines generic functions that are used in several proteomics-related packages:\r\n\r\n```r\r\nls('package:ProtGenerics')\r\n [1] \"accessions\"    \"chromatograms\" \"database\"      \"intensity\"    \r\n [5] \"ions\"          \"mass\"          \"modifications\" \"mz\"           \r\n [9] \"peaks\"         \"peptides\"      \"proteins\"      \"psms\"         \r\n[13] \"rtime\"         \"scans\"         \"spectra\"       \"tic\" \r\n```\r\n\r\nGenerics with identical names and different signature, such as `peptides` below, cause errors when `mzID` and, for example `MSnbase` (that uses `ProtGenerics::peptides`) are loaded,\r\n\r\n```r\r\n> peptides\r\nstandardGeneric for \"peptides\" defined from package \"ProtGenerics\"\r\n\r\nfunction (object, ...) \r\nstandardGeneric(\"peptides\")\r\n<environment: 0x4ad4528>\r\nMethods may be defined for arguments: object\r\nUse  showMethods(\"peptides\")  for currently available ones.\r\n```\r\n\r\nWould it be possible import `ProtGenerics` and use these generics to avoid these conflicts?\r\n"},"comment":{"url":"https://api.github.com/repos/thomasp85/mzID/issues/comments/116262262","html_url":"https://github.com/thomasp85/mzID/issues/30#issuecomment-116262262","issue_url":"https://api.github.com/repos/thomasp85/mzID/issues/30","id":116262262,"user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"created_at":"2015-06-28T11:28:55Z","updated_at":"2015-06-28T11:28:55Z","body":"Thanks. Happy to see you feel better."}}