{"comment":{"url":"https://api.github.com/repos/richelbilderbeek/Cer2016/comments/17434792","html_url":"https://github.com/richelbilderbeek/Cer2016/commit/58a17b80dd797412d37685c122ee37c7b47d8318#commitcomment-17434792","id":17434792,"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":"58a17b80dd797412d37685c122ee37c7b47d8318","created_at":"2016-05-11T14:23:47Z","updated_at":"2016-05-11T14:23:47Z","body":"[R/branch_sorter.R:10:54:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/branch_sorter.R#L10) *style:* **Put spaces around all infix operators.**\n```r\n​    edgeorder    <- data.table::data.table(table, key=\"V2\")\n                                                    ~^~\n```\n[R/branch_sorter.R:12:39:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/branch_sorter.R#L12) *warning:* **no visible binding for global variable 'V2', Did you mean '^'?**\n```r\n​    edgeorder    <- subset(edgeorder, V2 < (length(filename$tip.label) + 1))\n                                      ^~\n```\n[R/collect_posterior_filenames.R:26:1:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/collect_posterior_filenames.R#L26) *style:* **lines should not be more than 80 characters.**\n```r\n​  n_species_trees_samples <- as.numeric(file$parameters$n_species_trees_samples[2])\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/collect_posterior_filenames.R:36:25:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/collect_posterior_filenames.R#L36) *style:* **Commas should always have a space after.**\n```r\n​          base_filename,\"_\", i, \"_\", j, \"_\", k, \".trees\", sep = \"\"\n                        ^\n```\n[R/test.R:3:4:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L3) *style:* **Commented code should be removed.**\n```r\n​  ## ------------------------------------------------------------------------\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/test.R:7:4:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L7) *style:* **Commented code should be removed.**\n```r\n​  ## ------------------------------------------------------------------------\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/test.R:8:10:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L8) *warning:* **Do not use absolute paths.**\n```r\n​  setwd(\"d:/Peregrine/\")\n         ^~~~~~~~~~~~~\n```\n[R/test.R:9:31:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L9) *warning:* **Do not use absolute paths.**\n```r\n​  testit::assert(file.exists(\"d:/Peregrine\"))\n                              ^~~~~~~~~~~~\n```\n[R/test.R:12:1:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L12) *style:* **lines should not be more than 80 characters.**\n```r\n​  all_parameters <- Sys.glob(\"*.RDa\") #alternative, but longer: all_parameters <- list.files(pattern = \"\\\\.RDa$\", ignore.case=TRUE)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/test.R:15:13:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L15) *style:* **Use <-, not =, for assignment.**\n```r\n​  filenames = \"all_parameters\"\n            ^\n```\n[R/test.R:19:10:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L19) *warning:* **Do not use absolute paths.**\n```r\n​  setwd(\"c:/Users/Aline/Cer2016\")\n         ^~~~~~~~~~~~~~~~~~~~~~\n```\n[R/test.R:21:4:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L21) *style:* **Commented code should be removed.**\n```r\n​  ## ------------------------------------------------------------------------\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/test.R:22:22:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L22) *style:* **Commas should always have a space after.**\n```r\n​  rng_seeds <- seq(1,4)\n                     ^\n```\n[R/test.R:54:4:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/R/test.R#L54) *style:* **Commented code should be removed.**\n```r\n​  ## ------------------------------------------------------------------------\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-branch_sorter.R:8:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-branch_sorter.R#L8) *style:* **Commented code should be removed.**\n```r\n​  # expect_equal(count(names(df),\"branch_length\"), 1)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-branch_sorter.R:9:4:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-branch_sorter.R#L9) *style:* **Commented code should be removed.**\n```r\n​  #expect_equal(count(names(df),\"taxon_name\"), 1)\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-branch_sorter.R:10:4:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-branch_sorter.R#L10) *style:* **Commented code should be removed.**\n```r\n​  #expect_equal(count(names(df),\"branch_length\"), 1)\n   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-branch_sorter.R:13:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-branch_sorter.R#L13) *style:* **Commented code should be removed.**\n```r\n​  # expect_equal(length(df$taxon_name), 3)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-branch_sorter.R:14:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-branch_sorter.R#L14) *style:* **Commented code should be removed.**\n```r\n​  # expect_equal(length(df$branch_length), 3)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-branch_sorter.R:15:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-branch_sorter.R#L15) *style:* **Commented code should be removed.**\n```r\n​  # expected <- df(taxon_name = c(\"A\", \"B\", \"C\"), branch_length = c(1,1,2))\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-branch_sorter.R:16:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-branch_sorter.R#L16) *style:* **Commented code should be removed.**\n```r\n​  # expect_equal(df, expected)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-collect_posterior_filenames.R:28:7:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-collect_posterior_filenames.R#L28) *style:* **Commented code should be removed.**\n```r\n​  #   find_path(\"toy_example_4_2_2_2.trees\")\n      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-collect_posterior_filenames.R:30:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-collect_posterior_filenames.R#L30) *style:* **Commented code should be removed.**\n```r\n​  # expected <- sort(expected)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-collect_posterior_filenames.R:31:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-collect_posterior_filenames.R#L31) *style:* **Commented code should be removed.**\n```r\n​  # posterior_filenames <- sort(posterior_filenames)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-collect_posterior_filenames.R:32:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-collect_posterior_filenames.R#L32) *style:* **Commented code should be removed.**\n```r\n​  # expect_true(posterior_filenames == expected)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-normalized_rooted_branch_score.R:4:5:](https://github.com/richelbilderbeek/Cer2016/blob/58a17b80dd797412d37685c122ee37c7b47d8318/tests/testthat/test-normalized_rooted_branch_score.R#L4) *style:* **Commented code should be removed.**\n```r\n​#   expect_equal(normalized_rooted_branch_score(c(1), c(1)), 0)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```"}}