{"action":"created","issue":{"url":"https://api.github.com/repos/RamsinghLab/arkas/issues/28","repository_url":"https://api.github.com/repos/RamsinghLab/arkas","labels_url":"https://api.github.com/repos/RamsinghLab/arkas/issues/28/labels{/name}","comments_url":"https://api.github.com/repos/RamsinghLab/arkas/issues/28/comments","events_url":"https://api.github.com/repos/RamsinghLab/arkas/issues/28/events","html_url":"https://github.com/RamsinghLab/arkas/issues/28","id":170282533,"number":28,"title":"R CMD Check checking dependencies in R code","user":{"login":"arcolombo","id":5473099,"avatar_url":"https://avatars.githubusercontent.com/u/5473099?v=3","gravatar_id":"","url":"https://api.github.com/users/arcolombo","html_url":"https://github.com/arcolombo","followers_url":"https://api.github.com/users/arcolombo/followers","following_url":"https://api.github.com/users/arcolombo/following{/other_user}","gists_url":"https://api.github.com/users/arcolombo/gists{/gist_id}","starred_url":"https://api.github.com/users/arcolombo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arcolombo/subscriptions","organizations_url":"https://api.github.com/users/arcolombo/orgs","repos_url":"https://api.github.com/users/arcolombo/repos","events_url":"https://api.github.com/users/arcolombo/events{/privacy}","received_events_url":"https://api.github.com/users/arcolombo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-08-09T22:04:45Z","updated_at":"2016-08-10T20:02:28Z","closed_at":null,"body":"here is one\r\n\r\n* checking dependencies in R code ... WARNING\r\nLoading required package: rtracklayer\r\nLoading required package: knitr\r\nLoading required package: stringdist\r\nLoading required package: biomaRt\r\nWarning: replacing previous import ‘Biostrings::tail’ by ‘utils::tail’ when loading ‘TxDbLite’\r\nWarning: replacing previous import ‘Biostrings::head’ by ‘utils::head’ when loading ‘TxDbLite’\r\nLoading required package: SummarizedExperiment\r\nLoading required package: Rsamtools\r\nLoading required package: XVector\r\nLoading required package: Biostrings\r\nLoading required package: beeswarm\r\nLoading required package: tools\r\nLoading required package: ComplexHeatmap\r\nLoading required package: grid\r\nLoading required package: grDevices\r\n\r\nAttaching package: ‘ComplexHeatmap’\r\n\r\nThe following object is masked from ‘package:biomaRt’:\r\n\r\n    select\r\n\r\nThe following object is masked from ‘package:AnnotationDbi’:\r\n\r\n    select\r\nAttaching package: ‘arkas’\r\n\r\nThe following object is masked from ‘package:TxDbLite’:\r\n\r\n    strpop\r\n\r\n'::' or ':::' import not declared from: ‘BiocGenerics’\r\n'library' or 'require' call not declared from: ‘biomaRt’\r\n'library' or 'require' call to ‘biomaRt’ in package code.\r\n  Please use :: or requireNamespace() instead.\r\n  See section 'Suggested packages' in the 'Writing R Extensions' manual.\r\nNamespace in Imports field not imported from: ‘Matrix’\r\n  All declared Imports should be used.\r\nPackages in Depends field not imported from:\r\n  ‘SummarizedExperiment’ ‘beeswarm’ ‘ggplot2’ ‘jsonlite’ ‘parallel’\r\n  ‘qusage’\r\n  These packages need to be imported from (in the NAMESPACE file)\r\n  for when this namespace is loaded but not attached.\r\nUnexported objects imported by ':::' calls:\r\n  ‘BiocGenerics:::replaceSlots’\r\n  ‘SummarizedExperiment:::.valid.SummarizedExperiment0.assays_ncol’\r\n  ‘SummarizedExperiment:::.valid.SummarizedExperiment0.assays_nrow’\r\n  See the note in ?`:::` about the use of this operator.\r\npackage 'methods' is used but not declared\r\n"},"comment":{"url":"https://api.github.com/repos/RamsinghLab/arkas/issues/comments/238986407","html_url":"https://github.com/RamsinghLab/arkas/issues/28#issuecomment-238986407","issue_url":"https://api.github.com/repos/RamsinghLab/arkas/issues/28","id":238986407,"user":{"login":"arcolombo","id":5473099,"avatar_url":"https://avatars.githubusercontent.com/u/5473099?v=3","gravatar_id":"","url":"https://api.github.com/users/arcolombo","html_url":"https://github.com/arcolombo","followers_url":"https://api.github.com/users/arcolombo/followers","following_url":"https://api.github.com/users/arcolombo/following{/other_user}","gists_url":"https://api.github.com/users/arcolombo/gists{/gist_id}","starred_url":"https://api.github.com/users/arcolombo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arcolombo/subscriptions","organizations_url":"https://api.github.com/users/arcolombo/orgs","repos_url":"https://api.github.com/users/arcolombo/repos","events_url":"https://api.github.com/users/arcolombo/events{/privacy}","received_events_url":"https://api.github.com/users/arcolombo/received_events","type":"User","site_admin":false},"created_at":"2016-08-10T20:02:28Z","updated_at":"2016-08-10T20:02:28Z","body":"why not copy the function replaceSlots into arkas itself?  yes this is generating one's own electricity, but is this a bad approach? "}}
{"actor":{"display_login":"arcolombo"}}