{"comment":{"url":"https://api.github.com/repos/seninp-bioinfo/MetaComp/comments/19138874","html_url":"https://github.com/seninp-bioinfo/MetaComp/commit/d72b6a15846c3e7deb23513a61856baf4ca90a51#commitcomment-19138874","id":19138874,"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":"d72b6a15846c3e7deb23513a61856baf4ca90a51","created_at":"2016-09-23T00:07:03Z","updated_at":"2016-09-23T00:07:03Z","body":"[R/convert_to_taxa_table.R:52:71:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/R/convert_to_taxa_table.R#L52) *style:* **Put spaces around all infix operators.**\n```r\n​  ncbi_taxa_filepath <- system.file(\"extdata/taxonomy.tsv.gz\", package=\"MetaComp\")\n                                                                     ~^~\n```\n[R/convert_to_taxa_table.R:57:1:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/R/convert_to_taxa_table.R#L57) *style:* **lines should not be more than 100 characters.**\n```r\n​  data <- base::as.data.frame(data.table::fread(base::sprintf('gunzip -c %s', ncbi_taxa_filepath), header=T))\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/convert_to_taxa_table.R:57:106:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/R/convert_to_taxa_table.R#L57) *style:* **Put spaces around all infix operators.**\n```r\n​  data <- base::as.data.frame(data.table::fread(base::sprintf('gunzip -c %s', ncbi_taxa_filepath), header=T))\n                                                                                                        ~^~\n```\n[R/convert_to_taxa_table.R:102:1:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/R/convert_to_taxa_table.R#L102) *style:* **lines should not be more than 100 characters.**\n```r\n​        # get parent_taxID and loop through until parent_taxID doesnt equal to 131567 (highest classification)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/convert_to_taxa_table.R:116:1:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/R/convert_to_taxa_table.R#L116) *style:* **lines should not be more than 100 characters.**\n```r\n​  base::colnames(taxa_table) <- c(\"Domain\", \"Phylum\", \"Class\", \"Order\", \"Family\", \"Genus\", \"Species\")\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/convert_to_taxa_table.R:117:1:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/R/convert_to_taxa_table.R#L117) *style:* **lines should not be more than 100 characters.**\n```r\n​  base::subset(taxa_table, select=c(\"Domain\", \"Phylum\", \"Class\", \"Order\", \"Family\", \"Genus\", \"Species\"))\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/convert_to_taxa_table.R:117:34:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/R/convert_to_taxa_table.R#L117) *style:* **Put spaces around all infix operators.**\n```r\n​  base::subset(taxa_table, select=c(\"Domain\", \"Phylum\", \"Class\", \"Order\", \"Family\", \"Genus\", \"Species\"))\n                                ~^~\n```\n[tests/testthat/test_convert_to_otu_table.R:21:22:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/tests/testthat/test_convert_to_otu_table.R#L21) *style:* **Commas should always have a space after.**\n```r\n​expect_that(sum(dat[,1]), equals(1.0))\n                     ^\n```\n[tests/testthat/test_convert_to_otu_table.R:26:1:](https://github.com/seninp-bioinfo/MetaComp/blob/d72b6a15846c3e7deb23513a61856baf4ca90a51/tests/testthat/test_convert_to_otu_table.R#L26) *style:* **lines should not be more than 100 characters.**\n```r\n​expect_that(convert_to_otu_table(\"../test_data/merged_table.tsv\", \"non_existent_taxa_level\"), throws_error())\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```"}}
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