{"comment":{"url":"https://api.github.com/repos/steinbaugh/basejump.classes/comments/31120328","html_url":"https://github.com/steinbaugh/basejump.classes/commit/678288b91f7abffff71bba7511e4dad7b603c6a2#commitcomment-31120328","id":31120328,"node_id":"MDEzOkNvbW1pdENvbW1lbnQzMTEyMDMyOA==","user":{"login":"lintr-bot","id":10925265,"node_id":"MDQ6VXNlcjEwOTI1MjY1","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},"position":null,"line":null,"path":null,"commit_id":"678288b91f7abffff71bba7511e4dad7b603c6a2","created_at":"2018-10-31T13:57:32Z","updated_at":"2018-10-31T13:57:32Z","author_association":"NONE","body":"[R/EggNOG.R:10:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L10) *warning:* **no visible global function definition for ‘assert_that’**\n```r\n​        assert_that(has_internet())\n        ^~~~~~~~~~~\n```\n[R/EggNOG.R:10:21:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L10) *warning:* **no visible global function definition for ‘has_internet’**\n```r\n​        assert_that(has_internet())\n                    ^~~~~~~~~~~~\n```\n[R/EggNOG.R:12:13:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L12) *style:* **Variable or function name should be snake_case.**\n```r\n​            categoriesFile <- file.path(basejumpCacheURL, \"cog.txt\")\n            ^~~~~~~~~~~~~~\n```\n[R/EggNOG.R:12:41:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L12) *warning:* **no visible binding for global variable ‘basejumpCacheURL’**\n```r\n​            categoriesFile <- file.path(basejumpCacheURL, \"cog.txt\")\n                                        ^~~~~~~~~~~~~~~~\n```\n[R/EggNOG.R:13:13:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L13) *style:* **Variable or function name should be snake_case.**\n```r\n​            eunogFile <- file.path(basejumpCacheURL, \"eunog.tsv.gz\")\n            ^~~~~~~~~\n```\n[R/EggNOG.R:13:36:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L13) *warning:* **no visible binding for global variable ‘basejumpCacheURL’**\n```r\n​            eunogFile <- file.path(basejumpCacheURL, \"eunog.tsv.gz\")\n                                   ^~~~~~~~~~~~~~~~\n```\n[R/EggNOG.R:14:13:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L14) *style:* **Variable or function name should be snake_case.**\n```r\n​            nogFile <- file.path(basejumpCacheURL, \"nog.tsv.gz\")\n            ^~~~~~~\n```\n[R/EggNOG.R:14:34:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L14) *warning:* **no visible binding for global variable ‘basejumpCacheURL’**\n```r\n​            nogFile <- file.path(basejumpCacheURL, \"nog.tsv.gz\")\n                                 ^~~~~~~~~~~~~~~~\n```\n[R/EggNOG.R:22:13:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L22) *style:* **Variable or function name should be snake_case.**\n```r\n​            categoriesFile <- paste(\n            ^~~~~~~~~~~~~~\n```\n[R/EggNOG.R:27:13:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L27) *style:* **Variable or function name should be snake_case.**\n```r\n​            eunogFile <- paste(\n            ^~~~~~~~~\n```\n[R/EggNOG.R:34:13:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L34) *style:* **Variable or function name should be snake_case.**\n```r\n​            nogFile <- paste(\n            ^~~~~~~\n```\n[R/EggNOG.R:42:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L42) *warning:* **no visible global function definition for ‘assert_is_a_string’**\n```r\n​        assert_is_a_string(categoriesFile)\n        ^~~~~~~~~~~~~~~~~~\n```\n[R/EggNOG.R:43:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L43) *warning:* **no visible global function definition for ‘assert_is_a_string’**\n```r\n​        assert_is_a_string(eunogFile)\n        ^~~~~~~~~~~~~~~~~~\n```\n[R/EggNOG.R:44:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L44) *warning:* **no visible global function definition for ‘assert_is_a_string’**\n```r\n​        assert_is_a_string(nogFile)\n        ^~~~~~~~~~~~~~~~~~\n```\n[R/EggNOG.R:98:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L98) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data) <- .prototypeMetadata\n        ^~~~~~~~\n```\n[R/EggNOG.R:98:27:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/EggNOG.R#L98) *warning:* **no visible binding for global variable ‘.prototypeMetadata’**\n```r\n​        metadata(data) <- .prototypeMetadata\n                          ^~~~~~~~~~~~~~~~~~\n```\n[R/Ensembl2Entrez.R:24:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L24) *warning:* **no visible global function definition for ‘assert_has_rows’**\n```r\n​        assert_has_rows(object)\n        ^~~~~~~~~~~~~~~\n```\n[R/Ensembl2Entrez.R:38:17:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L38) *warning:* **no visible global function definition for ‘expand’**\n```r\n​        data <- expand(data)\n                ^~~~~~\n```\n[R/Ensembl2Entrez.R:42:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L42) *warning:* **no visible global function definition for ‘assert_that’**\n```r\n​        assert_that(!any(duplicated(unmapped)))\n        ^~~~~~~~~~~\n```\n[R/Ensembl2Entrez.R:60:13:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L60) *warning:* **no visible global function definition for ‘assert_is_list’**\n```r\n​            assert_is_list(entrez)\n            ^~~~~~~~~~~~~~\n```\n[R/Ensembl2Entrez.R:82:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L82) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data) <- metadata(object)\n        ^~~~~~~~\n```\n[R/Ensembl2Entrez.R:82:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L82) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​        metadata(data) <- metadata(object)\n        ^~~~~~~~\n```\n[R/Ensembl2Entrez.R:83:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L83) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​        metadata(data)[[\"format\"]] <- format\n        ^~~~~~~~\n```\n[R/Ensembl2Entrez.R:83:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L83) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data)[[\"format\"]] <- format\n        ^~~~~~~~\n```\n[R/Ensembl2Entrez.R:92:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L92) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data) <- metadata(object)\n        ^~~~~~~~\n```\n[R/Ensembl2Entrez.R:92:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L92) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​        metadata(data) <- metadata(object)\n        ^~~~~~~~\n```\n[R/Ensembl2Entrez.R:107:19:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L107) *warning:* **no visible global function definition for ‘as.SummarizedExperiment’**\n```r\n​        object <- as.SummarizedExperiment(object)\n                  ^~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/Ensembl2Entrez.R:108:17:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Ensembl2Entrez.R#L108) *warning:* **no visible global function definition for ‘rowData’**\n```r\n​        data <- rowData(object)\n                ^~~~~~~\n```\n[R/Gene2Symbol-methods.R:27:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L27) *warning:* **no visible global function definition for ‘assert_has_rows’**\n```r\n​        assert_has_rows(object)\n        ^~~~~~~~~~~~~~~\n```\n[R/Gene2Symbol-methods.R:69:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L69) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data) <- .genomeMetadata(object)\n        ^~~~~~~~\n```\n[R/Gene2Symbol-methods.R:69:27:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L69) *warning:* **no visible global function definition for ‘.genomeMetadata’**\n```r\n​        metadata(data) <- .genomeMetadata(object)\n                          ^~~~~~~~~~~~~~~\n```\n[R/Gene2Symbol-methods.R:70:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L70) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​        metadata(data)[[\"format\"]] <- format\n        ^~~~~~~~\n```\n[R/Gene2Symbol-methods.R:70:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L70) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data)[[\"format\"]] <- format\n        ^~~~~~~~\n```\n[R/Gene2Symbol-methods.R:91:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L91) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data) <- metadata(object)\n        ^~~~~~~~\n```\n[R/Gene2Symbol-methods.R:91:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L91) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​        metadata(data) <- metadata(object)\n        ^~~~~~~~\n```\n[R/Gene2Symbol-methods.R:117:19:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L117) *warning:* **no visible global function definition for ‘as.SummarizedExperiment’**\n```r\n​        object <- as.SummarizedExperiment(object)\n                  ^~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/Gene2Symbol-methods.R:118:17:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Gene2Symbol-methods.R#L118) *warning:* **no visible global function definition for ‘rowData’**\n```r\n​        data <- rowData(object)\n                ^~~~~~~\n```\n[R/HGNC2Ensembl.R:10:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/HGNC2Ensembl.R#L10) *warning:* **no visible global function definition for ‘assert_that’**\n```r\n​        assert_that(has_internet())\n        ^~~~~~~~~~~\n```\n[R/HGNC2Ensembl.R:10:21:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/HGNC2Ensembl.R#L10) *warning:* **no visible global function definition for ‘has_internet’**\n```r\n​        assert_that(has_internet())\n                    ^~~~~~~~~~~~\n```\n[R/HGNC2Ensembl.R:13:31:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/HGNC2Ensembl.R#L13) *warning:* **no visible binding for global variable ‘basejumpCacheURL’**\n```r\n​            file <- file.path(basejumpCacheURL, \"hgnc.txt.gz\")\n                              ^~~~~~~~~~~~~~~~\n```\n[R/HGNC2Ensembl.R:15:21:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/HGNC2Ensembl.R#L15) *warning:* **no visible binding for global variable ‘.hgncURL’**\n```r\n​            file <- .hgncURL\n                    ^~~~~~~~\n```\n[R/HGNC2Ensembl.R:25:17:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/HGNC2Ensembl.R#L25) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**\n```r\n​        data <- camel(data)\n                ^~~~~\n```\n[R/HGNC2Ensembl.R:32:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/HGNC2Ensembl.R#L32) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data) <- .prototypeMetadata\n        ^~~~~~~~\n```\n[R/HGNC2Ensembl.R:32:27:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/HGNC2Ensembl.R#L32) *warning:* **no visible binding for global variable ‘.prototypeMetadata’**\n```r\n​        metadata(data) <- .prototypeMetadata\n                          ^~~~~~~~~~~~~~~~~~\n```\n[R/HGNC2Ensembl.R:39:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/HGNC2Ensembl.R#L39) *style:* **Variable or function name should be snake_case.**\n```r\n​.hgncURL <- paste(\n^~~~~~~~\n```\n[R/internal.R:16:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L16) *style:* **Variable or function name should be snake_case.**\n```r\n​.prototypeMetadata <- list(\n^~~~~~~~~~~~~~~~~~\n```\n[R/internal.R:21:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L21) *style:* **Variable or function name should be snake_case.**\n```r\n​.hasPrototypeMetadata <- function(object) {\n^~~~~~~~~~~~~~~~~~~~~\n```\n[R/internal.R:28:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L28) *style:* **Variable or function name should be snake_case.**\n```r\n​.assertHasPrototypeMetadata <- function(object) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/internal.R:38:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L38) *style:* **Variable or function name should be snake_case.**\n```r\n​.prototypeGenomeMetadata <- c(\n^~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/internal.R:47:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L47) *style:* **Variable or function name should be snake_case.**\n```r\n​.genomeMetadata <- function(object) {\n^~~~~~~~~~~~~~~\n```\n[R/internal.R:49:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L49) *style:* **Variable or function name should be snake_case.**\n```r\n​    prototypeMetadata <- .prototypeGenomeMetadata %>%\n    ^~~~~~~~~~~~~~~~~\n```\n[R/internal.R:54:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L54) *style:* **Variable or function name should be snake_case.**\n```r\n​.hasGenomeMetadata <- function(object) {\n^~~~~~~~~~~~~~~~~~\n```\n[R/internal.R:55:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L55) *warning:* **no visible binding for global variable ‘genomeMetadataNames’**\n```r\n​    all(genomeMetadataNames %in% names(metadata(object)))\n        ^~~~~~~~~~~~~~~~~~~\n```\n[R/internal.R:55:40:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L55) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​    all(genomeMetadataNames %in% names(metadata(object)))\n                                       ^~~~~~~~\n```\n[R/internal.R:58:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L58) *style:* **Variable or function name should be snake_case.**\n```r\n​.assertHasGenomeMetadata <- function(object) {\n^~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/internal.R:65:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/internal.R#L65) *warning:* **no visible global function definition for ‘.assertHasPrototypeMetadata’**\n```r\n​    .assertHasPrototypeMetadata(object)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/MGI2Ensembl.R:13:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/MGI2Ensembl.R#L13) *style:* **Variable or function name should be snake_case.**\n```r\n​MGI2Ensembl <- function() {\n^~~~~~~~~~~\n```\n[R/MGI2Ensembl.R:14:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/MGI2Ensembl.R#L14) *warning:* **no visible global function definition for ‘assert_that’**\n```r\n​    assert_that(has_internet())\n    ^~~~~~~~~~~\n```\n[R/MGI2Ensembl.R:14:17:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/MGI2Ensembl.R#L14) *warning:* **no visible global function definition for ‘has_internet’**\n```r\n​    assert_that(has_internet())\n                ^~~~~~~~~~~~\n```\n[R/MGI2Ensembl.R:17:27:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/MGI2Ensembl.R#L17) *warning:* **no visible binding for global variable ‘basejumpCacheURL’**\n```r\n​        file <- file.path(basejumpCacheURL, \"mgi.rpt.gz\")\n                          ^~~~~~~~~~~~~~~~\n```\n[R/MGI2Ensembl.R:19:17:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/MGI2Ensembl.R#L19) *warning:* **no visible binding for global variable ‘.mgiURL’**\n```r\n​        file <- .mgiURL\n                ^~~~~~~\n```\n[R/MGI2Ensembl.R:37:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/MGI2Ensembl.R#L37) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​    metadata(data) <- .prototypeMetadata\n    ^~~~~~~~\n```\n[R/MGI2Ensembl.R:37:23:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/MGI2Ensembl.R#L37) *warning:* **no visible binding for global variable ‘.prototypeMetadata’**\n```r\n​    metadata(data) <- .prototypeMetadata\n                      ^~~~~~~~~~~~~~~~~~\n```\n[R/MGI2Ensembl.R:44:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/MGI2Ensembl.R#L44) *style:* **Variable or function name should be snake_case.**\n```r\n​.mgiURL <- paste(\n^~~~~~~\n```\n[R/PANTHER.R:23:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L23) *style:* **Variable or function name should be snake_case.**\n```r\n​.pantherMappings <- c(\n^~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:32:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L32) *style:* **Variable or function name should be snake_case.**\n```r\n​.splitTerms <- function(vec, progress = TRUE) {\n^~~~~~~~~~~\n```\n[R/PANTHER.R:35:19:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L35) *warning:* **no visible binding for global variable ‘pblapply’, Did you mean 'lapply'?**\n```r\n​        lapply <- pblapply\n                  ^~~~~~~~\n```\n[R/PANTHER.R:58:25:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L58) *warning:* **no visible global function definition for ‘HGNC2Ensembl’**\n```r\n​        hgnc2ensembl <- HGNC2Ensembl()\n                        ^~~~~~~~~~~~\n```\n[R/PANTHER.R:91:24:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L91) *warning:* **no visible global function definition for ‘MGI2Ensembl’**\n```r\n​        mgi2ensembl <- MGI2Ensembl()\n                       ^~~~~~~~~~~\n```\n[R/PANTHER.R:122:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L122) *warning:* **no visible global function definition for ‘mutate’**\n```r\n​        mutate(data, geneID = str_extract(!!sym(\"keys\"), \"FBgn\\\\d{7}$\"))\n        ^~~~~~\n```\n[R/PANTHER.R:122:31:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L122) *warning:* **no visible global function definition for ‘str_extract’**\n```r\n​        mutate(data, geneID = str_extract(!!sym(\"keys\"), \"FBgn\\\\d{7}$\"))\n                              ^~~~~~~~~~~\n```\n[R/PANTHER.R:122:45:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L122) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**\n```r\n​        mutate(data, geneID = str_extract(!!sym(\"keys\"), \"FBgn\\\\d{7}$\"))\n                                            ^~~\n```\n[R/PANTHER.R:129:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L129) *warning:* **no visible global function definition for ‘mutate’**\n```r\n​        mutate(data, geneID = str_extract(!!sym(\"keys\"), \"WBGene\\\\d{8}$\"))\n        ^~~~~~\n```\n[R/PANTHER.R:129:31:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L129) *warning:* **no visible global function definition for ‘str_extract’**\n```r\n​        mutate(data, geneID = str_extract(!!sym(\"keys\"), \"WBGene\\\\d{8}$\"))\n                              ^~~~~~~~~~~\n```\n[R/PANTHER.R:129:45:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L129) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**\n```r\n​        mutate(data, geneID = str_extract(!!sym(\"keys\"), \"WBGene\\\\d{8}$\"))\n                                            ^~~\n```\n[R/PANTHER.R:142:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L142) *warning:* **no visible global function definition for ‘assert_that’**\n```r\n​    assert_that(has_internet())\n    ^~~~~~~~~~~\n```\n[R/PANTHER.R:142:17:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L142) *warning:* **no visible global function definition for ‘has_internet’**\n```r\n​    assert_that(has_internet())\n                ^~~~~~~~~~~~\n```\n[R/PANTHER.R:147:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L147) *style:* **Variable or function name should be snake_case.**\n```r\n​    pantherName <-  .pantherMappings[[organism]]\n    ^~~~~~~~~~~\n```\n[R/PANTHER.R:147:21:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L147) *warning:* **no visible binding for global variable ‘.pantherMappings’**\n```r\n​    pantherName <-  .pantherMappings[[organism]]\n                    ^~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:148:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L148) *warning:* **no visible global function definition for ‘assert_is_a_string’**\n```r\n​    assert_is_a_string(pantherName)\n    ^~~~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:152:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L152) *warning:* **no visible global function definition for ‘assert_is_a_string’**\n```r\n​    assert_is_a_string(release)\n    ^~~~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:153:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L153) *warning:* **no visible global function definition for ‘assert_is_a_bool’**\n```r\n​    assert_is_a_bool(progress)\n    ^~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:180:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L180) *warning:* **no visible global function definition for ‘assert_is_a_string’**\n```r\n​    assert_is_a_string(file)\n    ^~~~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:211:37:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L211) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**\n```r\n​    fun <- get(paste(\"\", \"PANTHER\", camel(organism), sep = \".\"))\n                                    ^~~~~\n```\n[R/PANTHER.R:212:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L212) *warning:* **no visible global function definition for ‘assert_is_function’**\n```r\n​    assert_is_function(fun)\n    ^~~~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:214:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L214) *warning:* **no visible global function definition for ‘assert_has_rows’**\n```r\n​    assert_has_rows(data)\n    ^~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:226:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L226) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**\n```r\n​    assert_has_no_duplicates(data[[\"geneID\"]])\n    ^~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:246:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L246) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​    metadata(data) <- .prototypeMetadata\n    ^~~~~~~~\n```\n[R/PANTHER.R:246:23:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L246) *warning:* **no visible binding for global variable ‘.prototypeMetadata’**\n```r\n​    metadata(data) <- .prototypeMetadata\n                      ^~~~~~~~~~~~~~~~~~\n```\n[R/PANTHER.R:247:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L247) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​    metadata(data)[[\"organism\"]] <- organism\n    ^~~~~~~~\n```\n[R/PANTHER.R:247:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L247) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​    metadata(data)[[\"organism\"]] <- organism\n    ^~~~~~~~\n```\n[R/PANTHER.R:248:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L248) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​    metadata(data)[[\"release\"]] <- release\n    ^~~~~~~~\n```\n[R/PANTHER.R:248:5:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L248) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​    metadata(data)[[\"release\"]] <- release\n    ^~~~~~~~\n```\n[R/show-methods.R:27:1:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/show-methods.R#L27) *style:* **Variable or function name should be snake_case.**\n```r\n​.showHeader <- function(object) {\n^~~~~~~~~~~\n```\n[R/show-methods.R:28:30:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/show-methods.R#L28) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​    cat(paste(class(object), metadata(object)[[\"version\"]]), sep = \"\\n\")\n                             ^~~~~~~~\n```\n[R/show-methods.R:35:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/show-methods.R#L35) *warning:* **no visible global function definition for ‘.showHeader’**\n```r\n​        .showHeader(object)\n        ^~~~~~~~~~~\n```\n[R/show-methods.R:45:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/show-methods.R#L45) *warning:* **no visible global function definition for ‘.showHeader’**\n```r\n​        .showHeader(object)\n        ^~~~~~~~~~~\n```\n[R/show-methods.R:84:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/show-methods.R#L84) *warning:* **no visible global function definition for ‘show.DataFrame’**\n```r\n​        show.DataFrame(object)\n        ^~~~~~~~~~~~~~\n```\n[R/show-methods.R:128:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/show-methods.R#L128) *warning:* **no visible global function definition for ‘.showHeader’**\n```r\n​        .showHeader(object)\n        ^~~~~~~~~~~\n```\n[R/show-methods.R:151:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/show-methods.R#L151) *warning:* **no visible global function definition for ‘show.DataFrame’**\n```r\n​        show.DataFrame(object)\n        ^~~~~~~~~~~~~~\n```\n[R/Tx2Gene-methods.R:17:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Tx2Gene-methods.R#L17) *warning:* **no visible global function definition for ‘assert_has_rows’**\n```r\n​        assert_has_rows(object)\n        ^~~~~~~~~~~~~~~\n```\n[R/Tx2Gene-methods.R:34:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Tx2Gene-methods.R#L34) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data) <- .genomeMetadata(object)\n        ^~~~~~~~\n```\n[R/Tx2Gene-methods.R:34:27:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Tx2Gene-methods.R#L34) *warning:* **no visible global function definition for ‘.genomeMetadata’**\n```r\n​        metadata(data) <- .genomeMetadata(object)\n                          ^~~~~~~~~~~~~~~\n```\n[R/Tx2Gene-methods.R:56:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Tx2Gene-methods.R#L56) *warning:* **no visible global function definition for ‘metadata<-’**\n```r\n​        metadata(data) <- metadata(object)\n        ^~~~~~~~\n```\n[R/Tx2Gene-methods.R:56:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Tx2Gene-methods.R#L56) *warning:* **no visible global function definition for ‘metadata’**\n```r\n​        metadata(data) <- metadata(object)\n        ^~~~~~~~\n```\n[R/Tx2Gene-methods.R:75:19:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Tx2Gene-methods.R#L75) *warning:* **no visible global function definition for ‘as.SummarizedExperiment’**\n```r\n​        object <- as.SummarizedExperiment(object)\n                  ^~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/Tx2Gene-methods.R:76:17:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/Tx2Gene-methods.R#L76) *warning:* **no visible global function definition for ‘rowData’**\n```r\n​        data <- rowData(object)\n                ^~~~~~~\n```"}}
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