{"action":"created","issue":{"url":"https://api.github.com/repos/stencila/r/issues/27","repository_url":"https://api.github.com/repos/stencila/r","labels_url":"https://api.github.com/repos/stencila/r/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/stencila/r/issues/27/comments","events_url":"https://api.github.com/repos/stencila/r/issues/27/events","html_url":"https://github.com/stencila/r/pull/27","id":324245982,"number":27,"title":"Tidyups","user":{"login":"nokome","id":1152336,"avatar_url":"https://avatars0.githubusercontent.com/u/1152336?v=4","gravatar_id":"","url":"https://api.github.com/users/nokome","html_url":"https://github.com/nokome","followers_url":"https://api.github.com/users/nokome/followers","following_url":"https://api.github.com/users/nokome/following{/other_user}","gists_url":"https://api.github.com/users/nokome/gists{/gist_id}","starred_url":"https://api.github.com/users/nokome/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nokome/subscriptions","organizations_url":"https://api.github.com/users/nokome/orgs","repos_url":"https://api.github.com/users/nokome/repos","events_url":"https://api.github.com/users/nokome/events{/privacy}","received_events_url":"https://api.github.com/users/nokome/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2018-05-18T02:08:20Z","updated_at":"2018-05-18T05:12:13Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/stencila/r/pulls/27","html_url":"https://github.com/stencila/r/pull/27","diff_url":"https://github.com/stencila/r/pull/27.diff","patch_url":"https://github.com/stencila/r/pull/27.patch"},"body":"General tidy up of repo including removing on usused code, linting, upgrading of the context API, and documentation."},"comment":{"url":"https://api.github.com/repos/stencila/r/issues/comments/390096418","html_url":"https://github.com/stencila/r/pull/27#issuecomment-390096418","issue_url":"https://api.github.com/repos/stencila/r/issues/27","id":390096418,"user":{"login":"lintr-bot","id":10925265,"avatar_url":"https://avatars3.githubusercontent.com/u/10925265?v=4","gravatar_id":"","url":"https://api.github.com/users/lintr-bot","html_url":"https://github.com/lintr-bot","followers_url":"https://api.github.com/users/lintr-bot/followers","following_url":"https://api.github.com/users/lintr-bot/following{/other_user}","gists_url":"https://api.github.com/users/lintr-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/lintr-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lintr-bot/subscriptions","organizations_url":"https://api.github.com/users/lintr-bot/orgs","repos_url":"https://api.github.com/users/lintr-bot/repos","events_url":"https://api.github.com/users/lintr-bot/events{/privacy}","received_events_url":"https://api.github.com/users/lintr-bot/received_events","type":"User","site_admin":false},"created_at":"2018-05-18T05:12:13Z","updated_at":"2018-05-18T05:12:13Z","author_association":"NONE","body":"[R/addins.R:12:3:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/addins.R#L12) *warning:* **no visible binding for global variable ‘host’, Did you mean 'hist'?**\n```r\n​  host$open(paste0(\"file://\", path))\n  ^~~~\n```\n[R/addins.R:26:3:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/addins.R#L26) *warning:* **no visible global function definition for ‘function_register’**\n```r\n​  function_register(path)\n  ^~~~~~~~~~~~~~~~~\n```\n[R/execute.R:6:34:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/execute.R#L6) *warning:* **no visible binding for global variable ‘functions’, Did you mean 'function'?**\n```r\n​    if (is.null(value)) value <- functions[[operation$name]]\n                                 ^~~~~~~~~\n```\n[R/host-http-server.R:7:1:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/host-http-server.R#L7) *style:* **Variable and function names should be all lowercase.**\n```r\n​HostHttpServer <- R6::R6Class(\"HostHttpServer\",\n^~~~~~~~~~~~~~\n```\n[R/host.R:285:19:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/host.R#L285) *style:* **Variable and function names should be all lowercase.**\n```r\n​        server <- HostHttpServer$new(self, address, port, authorization)\n                  ^~~~~~~~~~~~~~\n```\n[R/json.R:23:1:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/json.R#L23) *style:* **Variable and function names should be all lowercase.**\n```r\n​asJSON <- jsonlite:::asJSON\n^~~~~~\n```\n[R/main.R:41:24:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/main.R#L41) *warning:* **no visible binding for global variable ‘host’, Did you mean 'hist'?**\n```r\n​  cat(jsonlite::toJSON(host$environ(), pretty = TRUE, auto_unbox = TRUE))\n                       ^~~~\n```\n[R/main.R:88:3:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/main.R#L88) *warning:* **no visible binding for '<<-' assignment to ‘host’, Did you mean 'hist'?**\n```r\n​  host <<- Host$new()\n  ^~~~\n```\n[R/main.R:88:12:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/main.R#L88) *warning:* **no visible binding for global variable ‘Host’, Did you mean 'dist'?**\n```r\n​  host <<- Host$new()\n           ^~~~\n```\n[R/register.R:76:15:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L76) *warning:* **no visible global function definition for ‘str_match’**\n```r\n​      pars <- str_match(src, \"function \\\\((.*)\\\\)\")[1, 2]\n              ^~~~~~~~~\n```\n[R/register.R:77:15:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L77) *warning:* **no visible global function definition for ‘str_split’, Did you mean 'strsplit'?**\n```r\n​      pars <- str_split(pars, \",\")[[1]]\n              ^~~~~~~~~\n```\n[R/register.R:78:15:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L78) *warning:* **no visible global function definition for ‘str_match’**\n```r\n​      pars <- str_match(pars, \"(\\\\w+)( = (.+))?\")\n              ^~~~~~~~~\n```\n[R/register.R:99:13:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L99) *warning:* **no visible global function definition for ‘xml_new_root’**\n```r\n​    spec <- xml_new_root(\"function\")\n            ^~~~~~~~~~~~\n```\n[R/register.R:101:35:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L101) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​      if (!is.null(docs[[from]])) xml_add_child(spec, to, docs[[from]])\n                                  ^~~~~~~~~~~~~\n```\n[R/register.R:107:15:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L107) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​    params <- xml_add_child(spec, \"params\")\n              ^~~~~~~~~~~~~\n```\n[R/register.R:109:16:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L109) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​      param <- xml_add_child(params, \"param\", name = arg$arg)\n               ^~~~~~~~~~~~~\n```\n[R/register.R:110:7:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L110) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​      xml_add_child(param, \"description\", arg$description)\n      ^~~~~~~~~~~~~\n```\n[R/register.R:113:5:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L113) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​    xml_add_child(spec, \"return\", docs[[\"value\"]])\n    ^~~~~~~~~~~~~\n```\n[R/register.R:115:16:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L115) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​    implems <- xml_add_child(spec, \"implems\")\n               ^~~~~~~~~~~~~\n```\n[R/register.R:116:5:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L116) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​    xml_add_child(implems, \"implem\", language = \"r\")\n    ^~~~~~~~~~~~~\n```\n[R/register.R:121:19:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L121) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​      examples <- xml_add_child(spec, \"examples\")\n                  ^~~~~~~~~~~~~\n```\n[R/register.R:122:18:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L122) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​      example <- xml_add_child(examples, \"example\")\n                 ^~~~~~~~~~~~~\n```\n[R/register.R:123:7:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L123) *warning:* **no visible global function definition for ‘xml_add_child’**\n```r\n​      xml_add_child(example, \"usage\", docs[[\"examples\"]])\n      ^~~~~~~~~~~~~\n```\n[R/register.R:127:12:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L127) *warning:* **no visible global function definition for ‘xml_serialize’**\n```r\n​    raw <- xml_serialize(spec, NULL)\n           ^~~~~~~~~~~~~\n```\n[R/register.R:130:12:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L130) *warning:* **no visible global function definition for ‘str_sub’**\n```r\n​    xml <- str_sub(char, str_locate(char, \"<function>\")[1], str_locate(char, \"</function>\")[2])\n           ^~~~~~~\n```\n[R/register.R:130:26:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L130) *warning:* **no visible global function definition for ‘str_locate’**\n```r\n​    xml <- str_sub(char, str_locate(char, \"<function>\")[1], str_locate(char, \"</function>\")[2])\n                         ^~~~~~~~~~\n```\n[R/register.R:130:26:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L130) *warning:* **no visible global function definition for ‘str_locate’**\n```r\n​    xml <- str_sub(char, str_locate(char, \"<function>\")[1], str_locate(char, \"</function>\")[2])\n                         ^~~~~~~~~~\n```\n[R/register.R:133:30:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L133) *warning:* **no visible binding for global variable ‘functions’, Did you mean 'function'?**\n```r\n​  assign(name, func, envir = functions)\n                             ^~~~~~~~~\n```\n[R/register.R:134:29:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L134) *warning:* **no visible binding for global variable ‘functions_xml’**\n```r\n​  assign(name, xml, envir = functions_xml)\n                            ^~~~~~~~~~~~~\n```\n[R/register.R:149:6:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L149) *warning:* **no visible binding for global variable ‘functions’, Did you mean 'function'?**\n```r\n​  ls(functions)\n     ^~~~~~~~~\n```\n[R/register.R:163:23:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L163) *warning:* **no visible global function definition for ‘function_register’**\n```r\n​  for (file in files) function_register(file)\n                      ^~~~~~~~~~~~~~~~~\n```\n[R/register.R:175:19:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L175) *warning:* **no visible global function definition for ‘function_register’**\n```r\n​    registered <- function_register(file)\n                  ^~~~~~~~~~~~~~~~~\n```\n[R/register.R:203:19:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L203) *warning:* **no visible global function definition for ‘function_register’**\n```r\n​    registered <- function_register(file)\n                  ^~~~~~~~~~~~~~~~~\n```\n[R/register.R:205:5:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/R/register.R#L205) *warning:* **no visible global function definition for ‘function_document’**\n```r\n​    function_document(registered$xml, file.path(path, \"docs\", paste0(registered$name, \".md\")))\n    ^~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:4:9:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L4) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s1 <- HostHttpServer$new(NULL)\n        ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:5:9:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L5) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s2 <- HostHttpServer$new(NULL)\n        ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:23:8:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L23) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s <- HostHttpServer$new(NULL)\n       ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:42:8:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L42) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s <- HostHttpServer$new(host)\n       ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:114:8:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L114) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s <- HostHttpServer$new(host)\n       ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:122:8:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L122) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s <- HostHttpServer$new(host)\n       ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:134:8:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L134) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s <- HostHttpServer$new(host)\n       ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:149:8:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L149) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s <- HostHttpServer$new(host)\n       ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:157:8:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L157) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s <- HostHttpServer$new(host)\n       ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-host-http-server.R:169:8:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-host-http-server.R#L169) *style:* **Variable and function names should be all lowercase.**\n```r\n​  s <- HostHttpServer$new(host)\n       ^~~~~~~~~~~~~~\n```\n[tests/testthat/test-sqlite-context.R:8:10:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-sqlite-context.R#L8) *style:* **Variable and function names should be all lowercase.**\n```r\n​    c <- SqliteContext$new()\n         ^~~~~~~~~~~~~\n```\n[tests/testthat/test-sqlite-context.R:14:10:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-sqlite-context.R#L14) *style:* **Variable and function names should be all lowercase.**\n```r\n​    c <- SqliteContext$new(dir = \"test-dir-2\")\n         ^~~~~~~~~~~~~\n```\n[tests/testthat/test-sqlite-context.R:22:10:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-sqlite-context.R#L22) *style:* **Variable and function names should be all lowercase.**\n```r\n​    c <- SqliteContext$new()\n         ^~~~~~~~~~~~~\n```\n[tests/testthat/test-sqlite-context.R:60:10:](https://github.com/stencila/r/blob/3215c903a6293a56387cd64693099cd2f62a2236/tests/testthat/test-sqlite-context.R#L60) *style:* **Variable and function names should be all lowercase.**\n```r\n​    c <- SqliteContext$new()\n         ^~~~~~~~~~~~~\n```"}}
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