{"action":"created","comment":{"url":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/comments/64686721","id":64686721,"diff_hunk":"@@ -1,21 +1,20 @@\n # IO parsing for TCs and RTCs\n-library(jsonlite)\n \n # Should grab this from DESCRIPTION\n PB_COMMANDR_VERSION <- \"0.2.1\"\n \n #' General func to load JSON from a file\n #' @export\n loadJsonFromFile <- function(path) {\n-  loginfo(paste(\"Loading tool contract from\", path))\n+  logging::loginfo(paste(\"Loading tool contract from\", path))\n   if (file.exists(path)) {\n     s <- readChar(path, file.info(path)$size)\n-    d <- fromJSON(s)\n+    d <- jsonlite::fromJSON(s, simplifyDataFrame = FALSE)","path":"R/io.R","position":15,"original_position":15,"commit_id":"855fa3786fcca2e5d0863c1c8314135c42317c9b","original_commit_id":"855fa3786fcca2e5d0863c1c8314135c42317c9b","user":{"login":"evolvedmicrobe","id":1330626,"avatar_url":"https://avatars.githubusercontent.com/u/1330626?v=3","gravatar_id":"","url":"https://api.github.com/users/evolvedmicrobe","html_url":"https://github.com/evolvedmicrobe","followers_url":"https://api.github.com/users/evolvedmicrobe/followers","following_url":"https://api.github.com/users/evolvedmicrobe/following{/other_user}","gists_url":"https://api.github.com/users/evolvedmicrobe/gists{/gist_id}","starred_url":"https://api.github.com/users/evolvedmicrobe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/evolvedmicrobe/subscriptions","organizations_url":"https://api.github.com/users/evolvedmicrobe/orgs","repos_url":"https://api.github.com/users/evolvedmicrobe/repos","events_url":"https://api.github.com/users/evolvedmicrobe/events{/privacy}","received_events_url":"https://api.github.com/users/evolvedmicrobe/received_events","type":"User","site_admin":false},"body":"I think jsonlite made an update that changed this option, not having this load as a simplified data frame seemed to help.","created_at":"2016-05-26T03:13:40Z","updated_at":"2016-05-26T03:13:40Z","html_url":"https://github.com/mpkocher/pbcommandR/pull/7#discussion_r64686721","pull_request_url":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/7","_links":{"self":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/comments/64686721"},"html":{"href":"https://github.com/mpkocher/pbcommandR/pull/7#discussion_r64686721"},"pull_request":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/7"}}},"pull_request":{"url":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/7","id":71494469,"html_url":"https://github.com/mpkocher/pbcommandR/pull/7","diff_url":"https://github.com/mpkocher/pbcommandR/pull/7.diff","patch_url":"https://github.com/mpkocher/pbcommandR/pull/7.patch","issue_url":"https://api.github.com/repos/mpkocher/pbcommandR/issues/7","number":7,"state":"open","locked":false,"title":"Fixnamespace","user":{"login":"evolvedmicrobe","id":1330626,"avatar_url":"https://avatars.githubusercontent.com/u/1330626?v=3","gravatar_id":"","url":"https://api.github.com/users/evolvedmicrobe","html_url":"https://github.com/evolvedmicrobe","followers_url":"https://api.github.com/users/evolvedmicrobe/followers","following_url":"https://api.github.com/users/evolvedmicrobe/following{/other_user}","gists_url":"https://api.github.com/users/evolvedmicrobe/gists{/gist_id}","starred_url":"https://api.github.com/users/evolvedmicrobe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/evolvedmicrobe/subscriptions","organizations_url":"https://api.github.com/users/evolvedmicrobe/orgs","repos_url":"https://api.github.com/users/evolvedmicrobe/repos","events_url":"https://api.github.com/users/evolvedmicrobe/events{/privacy}","received_events_url":"https://api.github.com/users/evolvedmicrobe/received_events","type":"User","site_admin":false},"body":"R packages usually like to avoid any library() calls in the R code,\r\npreferring to use package prefixes (e.g. jsonlite::) along with\r\nIMPORTs, rather than using DEPENDS and a library() call at the start of\r\neach file (see: http://r-pkgs.had.co.nz/namespace.html#namespace), so I\r\nchanged this.\r\n\r\nAdditionally, I added test files directly, and changed some of the code\r\nso the tests will pass.  I am not sure if I am following the schema\r\nthough, I will highlight the places I was uncertain about below.\r\n\r\nApologies for the white-space edits, I normally try to leave those out.","created_at":"2016-05-26T03:12:16Z","updated_at":"2016-05-26T03:13:40Z","closed_at":null,"merged_at":null,"merge_commit_sha":"704ab57fb6bd5a75ba3a147505fef2ad8e2e2c0e","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/7/commits","review_comments_url":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/7/comments","review_comment_url":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/comments{/number}","comments_url":"https://api.github.com/repos/mpkocher/pbcommandR/issues/7/comments","statuses_url":"https://api.github.com/repos/mpkocher/pbcommandR/statuses/855fa3786fcca2e5d0863c1c8314135c42317c9b","head":{"label":"mpkocher:fixnamespace","ref":"fixnamespace","sha":"855fa3786fcca2e5d0863c1c8314135c42317c9b","user":{"login":"mpkocher","id":868552,"avatar_url":"https://avatars.githubusercontent.com/u/868552?v=3","gravatar_id":"","url":"https://api.github.com/users/mpkocher","html_url":"https://github.com/mpkocher","followers_url":"https://api.github.com/users/mpkocher/followers","following_url":"https://api.github.com/users/mpkocher/following{/other_user}","gists_url":"https://api.github.com/users/mpkocher/gists{/gist_id}","starred_url":"https://api.github.com/users/mpkocher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpkocher/subscriptions","organizations_url":"https://api.github.com/users/mpkocher/orgs","repos_url":"https://api.github.com/users/mpkocher/repos","events_url":"https://api.github.com/users/mpkocher/events{/privacy}","received_events_url":"https://api.github.com/users/mpkocher/received_events","type":"User","site_admin":false},"repo":{"id":30176443,"name":"pbcommandR","full_name":"mpkocher/pbcommandR","owner":{"login":"mpkocher","id":868552,"avatar_url":"https://avatars.githubusercontent.com/u/868552?v=3","gravatar_id":"","url":"https://api.github.com/users/mpkocher","html_url":"https://github.com/mpkocher","followers_url":"https://api.github.com/users/mpkocher/followers","following_url":"https://api.github.com/users/mpkocher/following{/other_user}","gists_url":"https://api.github.com/users/mpkocher/gists{/gist_id}","starred_url":"https://api.github.com/users/mpkocher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpkocher/subscriptions","organizations_url":"https://api.github.com/users/mpkocher/orgs","repos_url":"https://api.github.com/users/mpkocher/repos","events_url":"https://api.github.com/users/mpkocher/events{/privacy}","received_events_url":"https://api.github.com/users/mpkocher/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/mpkocher/pbcommandR","description":"R interface for pbsmrtpipe workflow engine","fork":false,"url":"https://api.github.com/repos/mpkocher/pbcommandR","forks_url":"https://api.github.com/repos/mpkocher/pbcommandR/forks","keys_url":"https://api.github.com/repos/mpkocher/pbcommandR/keys{/key_id}","collaborators_url":"https://api.github.com/repos/mpkocher/pbcommandR/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/mpkocher/pbcommandR/teams","hooks_url":"https://api.github.com/repos/mpkocher/pbcommandR/hooks","issue_events_url":"https://api.github.com/repos/mpkocher/pbcommandR/issues/events{/number}","events_url":"https://api.github.com/repos/mpkocher/pbcommandR/events","assignees_url":"https://api.github.com/repos/mpkocher/pbcommandR/assignees{/user}","branches_url":"https://api.github.com/repos/mpkocher/pbcommandR/branches{/branch}","tags_url":"https://api.github.com/repos/mpkocher/pbcommandR/tags","blobs_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/refs{/sha}","trees_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/trees{/sha}","statuses_url":"https://api.github.com/repos/mpkocher/pbcommandR/statuses/{sha}","languages_url":"https://api.github.com/repos/mpkocher/pbcommandR/languages","stargazers_url":"https://api.github.com/repos/mpkocher/pbcommandR/stargazers","contributors_url":"https://api.github.com/repos/mpkocher/pbcommandR/contributors","subscribers_url":"https://api.github.com/repos/mpkocher/pbcommandR/subscribers","subscription_url":"https://api.github.com/repos/mpkocher/pbcommandR/subscription","commits_url":"https://api.github.com/repos/mpkocher/pbcommandR/commits{/sha}","git_commits_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/commits{/sha}","comments_url":"https://api.github.com/repos/mpkocher/pbcommandR/comments{/number}","issue_comment_url":"https://api.github.com/repos/mpkocher/pbcommandR/issues/comments{/number}","contents_url":"https://api.github.com/repos/mpkocher/pbcommandR/contents/{+path}","compare_url":"https://api.github.com/repos/mpkocher/pbcommandR/compare/{base}...{head}","merges_url":"https://api.github.com/repos/mpkocher/pbcommandR/merges","archive_url":"https://api.github.com/repos/mpkocher/pbcommandR/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/mpkocher/pbcommandR/downloads","issues_url":"https://api.github.com/repos/mpkocher/pbcommandR/issues{/number}","pulls_url":"https://api.github.com/repos/mpkocher/pbcommandR/pulls{/number}","milestones_url":"https://api.github.com/repos/mpkocher/pbcommandR/milestones{/number}","notifications_url":"https://api.github.com/repos/mpkocher/pbcommandR/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/mpkocher/pbcommandR/labels{/name}","releases_url":"https://api.github.com/repos/mpkocher/pbcommandR/releases{/id}","deployments_url":"https://api.github.com/repos/mpkocher/pbcommandR/deployments","created_at":"2015-02-02T07:41:43Z","updated_at":"2016-01-18T12:25:06Z","pushed_at":"2016-05-26T03:12:17Z","git_url":"git://github.com/mpkocher/pbcommandR.git","ssh_url":"git@github.com:mpkocher/pbcommandR.git","clone_url":"https://github.com/mpkocher/pbcommandR.git","svn_url":"https://github.com/mpkocher/pbcommandR","homepage":null,"size":63,"stargazers_count":2,"watchers_count":2,"language":"R","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":5,"forks":0,"open_issues":5,"watchers":2,"default_branch":"master"}},"base":{"label":"mpkocher:master","ref":"master","sha":"deeff13378a5b0ad53f62bb967fbbb46ea820aba","user":{"login":"mpkocher","id":868552,"avatar_url":"https://avatars.githubusercontent.com/u/868552?v=3","gravatar_id":"","url":"https://api.github.com/users/mpkocher","html_url":"https://github.com/mpkocher","followers_url":"https://api.github.com/users/mpkocher/followers","following_url":"https://api.github.com/users/mpkocher/following{/other_user}","gists_url":"https://api.github.com/users/mpkocher/gists{/gist_id}","starred_url":"https://api.github.com/users/mpkocher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpkocher/subscriptions","organizations_url":"https://api.github.com/users/mpkocher/orgs","repos_url":"https://api.github.com/users/mpkocher/repos","events_url":"https://api.github.com/users/mpkocher/events{/privacy}","received_events_url":"https://api.github.com/users/mpkocher/received_events","type":"User","site_admin":false},"repo":{"id":30176443,"name":"pbcommandR","full_name":"mpkocher/pbcommandR","owner":{"login":"mpkocher","id":868552,"avatar_url":"https://avatars.githubusercontent.com/u/868552?v=3","gravatar_id":"","url":"https://api.github.com/users/mpkocher","html_url":"https://github.com/mpkocher","followers_url":"https://api.github.com/users/mpkocher/followers","following_url":"https://api.github.com/users/mpkocher/following{/other_user}","gists_url":"https://api.github.com/users/mpkocher/gists{/gist_id}","starred_url":"https://api.github.com/users/mpkocher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpkocher/subscriptions","organizations_url":"https://api.github.com/users/mpkocher/orgs","repos_url":"https://api.github.com/users/mpkocher/repos","events_url":"https://api.github.com/users/mpkocher/events{/privacy}","received_events_url":"https://api.github.com/users/mpkocher/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/mpkocher/pbcommandR","description":"R interface for pbsmrtpipe workflow engine","fork":false,"url":"https://api.github.com/repos/mpkocher/pbcommandR","forks_url":"https://api.github.com/repos/mpkocher/pbcommandR/forks","keys_url":"https://api.github.com/repos/mpkocher/pbcommandR/keys{/key_id}","collaborators_url":"https://api.github.com/repos/mpkocher/pbcommandR/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/mpkocher/pbcommandR/teams","hooks_url":"https://api.github.com/repos/mpkocher/pbcommandR/hooks","issue_events_url":"https://api.github.com/repos/mpkocher/pbcommandR/issues/events{/number}","events_url":"https://api.github.com/repos/mpkocher/pbcommandR/events","assignees_url":"https://api.github.com/repos/mpkocher/pbcommandR/assignees{/user}","branches_url":"https://api.github.com/repos/mpkocher/pbcommandR/branches{/branch}","tags_url":"https://api.github.com/repos/mpkocher/pbcommandR/tags","blobs_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/refs{/sha}","trees_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/trees{/sha}","statuses_url":"https://api.github.com/repos/mpkocher/pbcommandR/statuses/{sha}","languages_url":"https://api.github.com/repos/mpkocher/pbcommandR/languages","stargazers_url":"https://api.github.com/repos/mpkocher/pbcommandR/stargazers","contributors_url":"https://api.github.com/repos/mpkocher/pbcommandR/contributors","subscribers_url":"https://api.github.com/repos/mpkocher/pbcommandR/subscribers","subscription_url":"https://api.github.com/repos/mpkocher/pbcommandR/subscription","commits_url":"https://api.github.com/repos/mpkocher/pbcommandR/commits{/sha}","git_commits_url":"https://api.github.com/repos/mpkocher/pbcommandR/git/commits{/sha}","comments_url":"https://api.github.com/repos/mpkocher/pbcommandR/comments{/number}","issue_comment_url":"https://api.github.com/repos/mpkocher/pbcommandR/issues/comments{/number}","contents_url":"https://api.github.com/repos/mpkocher/pbcommandR/contents/{+path}","compare_url":"https://api.github.com/repos/mpkocher/pbcommandR/compare/{base}...{head}","merges_url":"https://api.github.com/repos/mpkocher/pbcommandR/merges","archive_url":"https://api.github.com/repos/mpkocher/pbcommandR/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/mpkocher/pbcommandR/downloads","issues_url":"https://api.github.com/repos/mpkocher/pbcommandR/issues{/number}","pulls_url":"https://api.github.com/repos/mpkocher/pbcommandR/pulls{/number}","milestones_url":"https://api.github.com/repos/mpkocher/pbcommandR/milestones{/number}","notifications_url":"https://api.github.com/repos/mpkocher/pbcommandR/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/mpkocher/pbcommandR/labels{/name}","releases_url":"https://api.github.com/repos/mpkocher/pbcommandR/releases{/id}","deployments_url":"https://api.github.com/repos/mpkocher/pbcommandR/deployments","created_at":"2015-02-02T07:41:43Z","updated_at":"2016-01-18T12:25:06Z","pushed_at":"2016-05-26T03:12:17Z","git_url":"git://github.com/mpkocher/pbcommandR.git","ssh_url":"git@github.com:mpkocher/pbcommandR.git","clone_url":"https://github.com/mpkocher/pbcommandR.git","svn_url":"https://github.com/mpkocher/pbcommandR","homepage":null,"size":63,"stargazers_count":2,"watchers_count":2,"language":"R","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":5,"forks":0,"open_issues":5,"watchers":2,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/7"},"html":{"href":"https://github.com/mpkocher/pbcommandR/pull/7"},"issue":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/issues/7"},"comments":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/issues/7/comments"},"review_comments":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/7/comments"},"review_comment":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/pulls/7/commits"},"statuses":{"href":"https://api.github.com/repos/mpkocher/pbcommandR/statuses/855fa3786fcca2e5d0863c1c8314135c42317c9b"}}}}
{"actor":{"display_login":"evolvedmicrobe"}}