{"comment":{"url":"https://api.github.com/repos/richelbilderbeek/Cer2016/comments/18076492","html_url":"https://github.com/richelbilderbeek/Cer2016/commit/b1144cf23cc2fb363e441beaf55ed786b7702a97#commitcomment-18076492","id":18076492,"user":{"login":"lintr-bot","id":10925265,"avatar_url":"https://avatars.githubusercontent.com/u/10925265?v=3","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},"position":null,"line":null,"path":null,"commit_id":"b1144cf23cc2fb363e441beaf55ed786b7702a97","created_at":"2016-06-30T10:22:34Z","updated_at":"2016-06-30T10:22:34Z","body":"[R/add_alignments.R:19:20:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/add_alignments.R#L19) *warning:* **no visible global function definition for ‘is_phylogeny’**\n```r\n​    testit::assert(is_phylogeny(species_tree))\n                   ^~~~~~~~~~~~\n```\n[R/add_alignments.R:32:21:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/add_alignments.R#L32) *warning:* **no visible global function definition for ‘get_species_tree_by_index’**\n```r\n​    species_tree <- get_species_tree_by_index(file = file, sti = sti)\n                    ^~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/add_alignments.R:37:41:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/add_alignments.R#L37) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​      this_seed <- rng_seed - 1 + ai + ((sti - 1) * 2)\n                                        ^\n```\n[R/add_alignments.R:59:18:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/add_alignments.R#L59) *warning:* **no visible global function definition for ‘has_alignments’**\n```r\n​  testit::assert(has_alignments(file))\n                 ^~~~~~~~~~~~~~\n```\n[R/add_posteriors.R:49:25:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/add_posteriors.R#L49) *warning:* **no visible global function definition for ‘is_beast_posterior’**\n```r\n​        testit::assert(!is_beast_posterior(posterior))\n                        ^~~~~~~~~~~~~~~~~~\n```\n[R/add_posteriors.R:69:12:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/add_posteriors.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​          ((sti - 1) * n_alignments * 2)\n           ^\n```\n[R/add_species_trees.R:36:28:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/add_species_trees.R#L36) *warning:* **no visible binding for global variable ‘i’, Did you mean 'C'?**\n```r\n​          message(\"add_species_trees: species_tree #\", i, \" already exists\")\n                           ^\n```\n[R/collect_file_nrbss.R:84:11:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/collect_file_nrbss.R#L84) *warning:* **no visible global function definition for ‘get_species_tree_by_index’**\n```r\n​    st <- get_species_tree_by_index(file = file, sti = sti) # st: species tree\n          ^~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/collect_file_nrbss.R:88:1:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/collect_file_nrbss.R#L88) *style:* **lines should not be more than 80 characters.**\n```r\n​    pt <- Cer2016::get_posterior(file, sti = sti, ai = ai, pi = pi)[[state_index]] # pt: posterior state tree, of type phylo\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/collect_species_tree_gammas.R:30:18:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/collect_species_tree_gammas.R#L30) *warning:* **no visible global function definition for ‘get_species_tree_by_index’**\n```r\n​    phylogeny <- get_species_tree_by_index(file = file, sti = sti)\n                 ^~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/get_alignment.R:51:12:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/get_alignment.R#L51) *warning:* **no visible global function definition for ‘extract_napst’**\n```r\n​  napst <- extract_napst(file = file)\n           ^~~~~~~~~~~~~\n```\n[R/get_alignment.R:55:13:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/get_alignment.R#L55) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​  i <- 1 + ((sti - 1) * napst) + (ai - 1)\n            ^\n```\n[R/get_posterior.R:57:12:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/get_posterior.R#L57) *warning:* **no visible global function definition for ‘extract_napst’**\n```r\n​  napst <- extract_napst(file = file)\n           ^~~~~~~~~~~~~\n```\n[R/get_posterior.R:64:11:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/get_posterior.R#L64) *warning:* **no visible global function definition for ‘extract_nppa’**\n```r\n​  nppa <- extract_nppa(file = file)\n          ^~~~~~~~~~~~\n```\n[R/get_posterior.R:71:6:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/get_posterior.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​    ((sti - 1) * napst * 2)\n     ^\n```\n[R/get_species_tree.R:12:1:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/get_species_tree.R#L12) *style:* **lines should not be more than 80 characters.**\n```r\n​    stop(\"get_species_tree_by_index: index must be less than number of species_trees\")\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/has_alignments.R:20:31:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/has_alignments.R#L20) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**\n```r\n​        error = function(msg) {}\n                              ^\n```\n[R/has_alignments.R:20:32:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/has_alignments.R#L20) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**\n```r\n​        error = function(msg) {}\n                               ^\n```\n[R/has_alignments.R:22:17:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/has_alignments.R#L22) *warning:* **no visible global function definition for ‘is_alignment’**\n```r\n​      v <- c(v, is_alignment(alignment))\n                ^~~~~~~~~~~~\n```\n[R/plot_alignments.R:16:40:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/plot_alignments.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​      alignment_index <- 1 + ai - 1 + ((sti - 1) * 2)\n                                       ^\n```\n[R/set_alignment.R:46:12:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/set_alignment.R#L46) *warning:* **no visible global function definition for ‘extract_napst’**\n```r\n​  napst <- extract_napst(file = file)\n           ^~~~~~~~~~~~~\n```\n[R/set_alignment.R:54:13:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/set_alignment.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​  i <- 1 + ((sti - 1) * napst) + (ai - 1)\n            ^\n```\n[R/set_posterior.R:42:12:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/set_posterior.R#L42) *warning:* **no visible global function definition for ‘extract_napst’**\n```r\n​  napst <- extract_napst(file = file)\n           ^~~~~~~~~~~~~\n```\n[R/set_posterior.R:52:11:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/set_posterior.R#L52) *warning:* **no visible global function definition for ‘extract_nppa’**\n```r\n​  nppa <- extract_nppa(file = file)\n          ^~~~~~~~~~~~\n```\n[R/set_posterior.R:62:6:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/set_posterior.R#L62) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​    ((sti - 1) * napst * 2)\n     ^\n```\n[R/set_species_tree.R:17:1:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/R/set_species_tree.R#L17) *style:* **lines should not be more than 80 characters.**\n```r\n​    stop(\"set_species_tree_by_index: index must be less than number of species_trees\")\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-add_alignments.R:48:1:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-add_alignments.R#L48) *style:* **lines should not be more than 80 characters.**\n```r\n​  expect_true(is_alignment(get_alignment(file = read_file(filename = filename), sti = 1, ai = 1)))\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-add_alignments.R:49:1:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-add_alignments.R#L49) *style:* **lines should not be more than 80 characters.**\n```r\n​  expect_true(is_alignment(get_alignment(file = read_file(filename = filename), sti = 2, ai = 1)))\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-collect_files_nltts.R:15:4:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-collect_files_nltts.R#L15) *style:* **Commented code should be removed.**\n```r\n​  #expect_equal(nrow(df$species_tree_nltts), 18)\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-collect_files_nltts.R:16:4:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-collect_files_nltts.R#L16) *style:* **Commented code should be removed.**\n```r\n​  #expect_equal(nrow(df$posterior_nltts), 540)\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-collect_species_tree_gammas.R:41:1:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-collect_species_tree_gammas.R#L41) *style:* **lines should not be more than 80 characters.**\n```r\n​  file <- set_species_tree_by_index(file = file, sti = 1, species_tree = \"Not a phylogeny\")\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-do_simulation.R:33:6:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-do_simulation.R#L33) *style:* **Commented code should be removed.**\n```r\n​    #file.remove(filename)\n     ^~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-get_alignments.R:8:4:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-get_alignments.R#L8) *style:* **Commented code should be removed.**\n```r\n​  #expect_equal(length(alignments), 2)\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-get_alignments.R:9:4:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-get_alignments.R#L9) *style:* **Commented code should be removed.**\n```r\n​  #expect_true(is_alignment(alignments[[1]][[1]]))\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-get_alignments.R:10:4:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-get_alignments.R#L10) *style:* **Commented code should be removed.**\n```r\n​  #expect_true(is_alignment(alignments[[2]][[1]]))\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-get_alignments.R:18:4:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-get_alignments.R#L18) *style:* **Commented code should be removed.**\n```r\n​  #expect_equal(length(alignments), 8)\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-get_alignments.R:19:4:](https://github.com/richelbilderbeek/Cer2016/blob/b1144cf23cc2fb363e441beaf55ed786b7702a97/tests/testthat/test-get_alignments.R#L19) *style:* **Commented code should be removed.**\n```r\n​  #expect_true(is_alignment(alignments[[8]][[1]]))\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```"}}
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