[R/convertUCSCBuildToEnsembl.R:14:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/convertUCSCBuildToEnsembl.R#L14) *style:* **Variable or function name should be snake_case.**
```r
convertUCSCBuildToEnsembl <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertUCSCBuildToEnsembl.R:15:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/convertUCSCBuildToEnsembl.R#L15) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(object)
    ^~~~~~~~~~~~~~~~~~~
```
[R/emptyRanges.R:31:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/emptyRanges.R#L31) *style:* **Variable or function name should be snake_case.**
```r
emptyRanges <- function(
^~~~~~~~~~~
```
[R/emptyRanges.R:34:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/emptyRanges.R#L34) *style:* **Variable or function name should be snake_case.**
```r
    mcolsNames = NULL
    ^~~~~~~~~~
```
[R/emptyRanges.R:36:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/emptyRanges.R#L36) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(names)
    ^~~~~~~~~~~~~~~~~~~
```
[R/emptyRanges.R:37:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/emptyRanges.R#L37) *warning:* **no visible global function definition for ‘assert_all_are_non_missing_nor_empty_character’**
```r
    assert_all_are_non_missing_nor_empty_character(names)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/emptyRanges.R:39:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/emptyRanges.R#L39) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(mcolsNames, c("character", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/emptyRanges.R:65:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/emptyRanges.R#L65) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
    mcols(gr) <- mcols
    ^~~~~
```
[R/geneSynonyms.R:20:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/geneSynonyms.R#L20) *style:* **Variable or function name should be snake_case.**
```r
geneSynonyms <- function(organism) {
^~~~~~~~~~~~
```
[R/geneSynonyms.R:21:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/geneSynonyms.R#L21) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(has_internet())
    ^~~~~~~~~~~
```
[R/geneSynonyms.R:21:17:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/geneSynonyms.R#L21) *warning:* **no visible global function definition for ‘has_internet’**
```r
    assert_that(has_internet())
                ^~~~~~~~~~~~
```
[R/geneSynonyms.R:38:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/geneSynonyms.R#L38) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(organism == "Homo sapiens")
        ^~~~~~~~~~~
```
[R/geneSynonyms.R:60:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/geneSynonyms.R#L60) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
    assert_is_non_empty(data)
    ^~~~~~~~~~~~~~~~~~~
```
[R/geneSynonyms.R:95:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/geneSynonyms.R#L95) *style:* **Variable or function name should be snake_case.**
```r
.geneSynonymsOrganisms <- c(
^~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGene2Symbol.R:44:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L44) *style:* **Variable or function name should be snake_case.**
```r
makeGene2SymbolFromEnsembl <-
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGene2Symbol.R:52:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L52) *warning:* **no visible global function definition for ‘Gene2Symbol’**
```r
        Gene2Symbol(gr)
        ^~~~~~~~~~~
```
[R/makeGene2Symbol.R:62:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L62) *style:* **Variable or function name should be snake_case.**
```r
makeGene2SymbolFromEnsDb <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGene2Symbol.R:63:11:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L63) *warning:* **no visible global function definition for ‘makeGRangesFromEnsDb’**
```r
    gr <- makeGRangesFromEnsDb(object)
          ^~~~~~~~~~~~~~~~~~~~
```
[R/makeGene2Symbol.R:64:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L64) *warning:* **no visible global function definition for ‘Gene2Symbol’**
```r
    Gene2Symbol(gr)
    ^~~~~~~~~~~
```
[R/makeGene2Symbol.R:71:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L71) *style:* **Variable or function name should be snake_case.**
```r
makeGene2SymbolFromGFF <- function(file) {
^~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGene2Symbol.R:72:11:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L72) *warning:* **no visible global function definition for ‘makeGRangesFromGFF’**
```r
    gr <- makeGRangesFromGFF(file, level = "genes")
          ^~~~~~~~~~~~~~~~~~
```
[R/makeGene2Symbol.R:73:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L73) *warning:* **no visible global function definition for ‘Gene2Symbol’**
```r
    Gene2Symbol(gr)
    ^~~~~~~~~~~
```
[R/makeGene2Symbol.R:82:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGene2Symbol.R#L82) *style:* **Variable or function name should be snake_case.**
```r
makeGene2SymbolFromGTF <- makeGene2SymbolFromGFF
^~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:87:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L87) *style:* **Variable or function name should be snake_case.**
```r
.defineBroadClass <- function(object) {
^~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:88:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L88) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "GRanges")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:91:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L91) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(names)
    ^~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:92:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L92) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
    assert_is_non_empty(names)
    ^~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:94:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L94) *warning:* **no visible global function definition for ‘as_tibble’**
```r
    data <- as_tibble(object)
            ^~~~~~~~~
```
[R/makeGRanges.R:104:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L104) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
    assert_is_subset("geneName", colnames(data))
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:105:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L105) *style:* **Variable or function name should be snake_case.**
```r
    geneName <- data[["geneName"]]
    ^~~~~~~~
```
[R/makeGRanges.R:109:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L109) *style:* **Variable or function name should be snake_case.**
```r
    biotypeCol <- grep(
    ^~~~~~~~~~
```
[R/makeGRanges.R:116:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L116) *style:* **Variable or function name should be snake_case.**
```r
        biotypeCol <- biotypeCol[[1L]]
        ^~~~~~~~~~
```
[R/makeGRanges.R:126:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L126) *style:* **Variable or function name should be snake_case.**
```r
    seqnameCol <- grep(
    ^~~~~~~~~~
```
[R/makeGRanges.R:133:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L133) *style:* **Variable or function name should be snake_case.**
```r
        seqnameCol <- seqnameCol[[1L]]
        ^~~~~~~~~~
```
[R/makeGRanges.R:214:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L214) *style:* **Variable or function name should be snake_case.**
```r
.annotationHub <- function() {
^~~~~~~~~~~~~~
```
[R/makeGRanges.R:215:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L215) *style:* **Variable or function name should be snake_case.**
```r
    userAttached <- .packages()
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:219:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L219) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(ah, "AnnotationHub")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:220:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L220) *warning:* **no visible global function definition for ‘.forceDetach’**
```r
    .forceDetach(keep = userAttached)
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:232:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L232) *style:* **Variable or function name should be snake_case.**
```r
.forceDetach <- function(keep = NULL) {
^~~~~~~~~~~~
```
[R/makeGRanges.R:249:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L249) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
    assert_are_identical(.packages(), keep)
    ^~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:257:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L257) *style:* **Variable or function name should be snake_case.**
```r
.getAnnotationHubID <- function(
^~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:259:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L259) *style:* **Variable or function name should be snake_case.**
```r
    genomeBuild = NULL,
    ^~~~~~~~~~~
```
[R/makeGRanges.R:260:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L260) *style:* **Variable or function name should be snake_case.**
```r
    ensemblRelease = NULL,
    ^~~~~~~~~~~~~~
```
[R/makeGRanges.R:263:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L263) *style:* **Variable or function name should be snake_case.**
```r
    userAttached <- .packages()
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:264:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L264) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
    assert_is_a_string(organism)
    ^~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:266:32:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L266) *warning:* **no visible global function definition for ‘makeNames’, Did you mean 'make.names'?**
```r
    organism <- gsub("_", " ", makeNames(organism))
                               ^~~~~~~~~
```
[R/makeGRanges.R:267:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L267) *warning:* **no visible global function definition for ‘assertIsAStringOrNULL’**
```r
    assertIsAStringOrNULL(genomeBuild)
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:270:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L270) *style:* **Variable or function name should be snake_case.**
```r
        ucscCheck <- tryCatch(
        ^~~~~~~~~
```
[R/makeGRanges.R:282:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L282) *warning:* **no visible global function definition for ‘assertIsAnImplicitIntegerOrNULL’**
```r
    assertIsAnImplicitIntegerOrNULL(ensemblRelease)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:285:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L285) *warning:* **no visible global function definition for ‘assert_all_are_positive’**
```r
        assert_all_are_positive(ensemblRelease)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:286:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L286) *style:* **Variable or function name should be snake_case.**
```r
        ensemblRelease <- as.integer(ensemblRelease)
        ^~~~~~~~~~~~~~
```
[R/makeGRanges.R:298:15:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L298) *warning:* **no visible global function definition for ‘.annotationHub’**
```r
        ah <- .annotationHub()
              ^~~~~~~~~~~~~~
```
[R/makeGRanges.R:338:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L338) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset("genome", colnames(mcols))
        ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:344:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L344) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset("title", colnames(mcols))
        ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:350:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L350) *warning:* **no visible global function definition for ‘assert_is_of_length’**
```r
        assert_is_of_length(nrow(mcols), 1L)
        ^~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:368:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L368) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
    assert_is_a_string(id)
    ^~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:369:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L369) *warning:* **no visible global function definition for ‘assert_all_are_matching_regex’**
```r
    assert_all_are_matching_regex(x = id, pattern = "^AH[[:digit:]]+$")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:371:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L371) *warning:* **no visible global function definition for ‘.forceDetach’**
```r
    .forceDetach(keep = userAttached)
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:381:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L381) *style:* **Variable or function name should be snake_case.**
```r
.getEnsDbFromAnnotationHub <- function(id, ah = NULL) {
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:382:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L382) *style:* **Variable or function name should be snake_case.**
```r
    userAttached <- .packages()
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:385:15:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L385) *warning:* **no visible global function definition for ‘.annotationHub’**
```r
        ah <- .annotationHub()
              ^~~~~~~~~~~~~~
```
[R/makeGRanges.R:387:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L387) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(ah, "AnnotationHub")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:395:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L395) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(edb, "EnsDb")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:396:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L396) *warning:* **no visible global function definition for ‘.forceDetach’**
```r
    .forceDetach(keep = userAttached)
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:405:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L405) *style:* **Variable or function name should be snake_case.**
```r
.getEnsDbFromPackage <- function(package) {
^~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:407:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L407) *style:* **Variable or function name should be snake_case.**
```r
    userAttached <- .packages()
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:408:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L408) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
    assert_is_a_string(package)
    ^~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:415:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L415) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(edb, "EnsDb")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:416:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L416) *warning:* **no visible global function definition for ‘.forceDetach’**
```r
    .forceDetach(keep = userAttached)
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:440:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L440) *style:* **Variable or function name should be snake_case.**
```r
makeGRangesFromEnsembl <- function(
^~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:443:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L443) *style:* **Variable or function name should be snake_case.**
```r
    genomeBuild = NULL,
    ^~~~~~~~~~~
```
[R/makeGRanges.R:447:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L447) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
    assert_is_a_string(organism)
    ^~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:457:16:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L457) *warning:* **no visible global function definition for ‘.getEnsDbFromPackage’**
```r
        edb <- .getEnsDbFromPackage(package = id)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:464:16:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L464) *warning:* **no visible global function definition for ‘.getEnsDbFromAnnotationHub’**
```r
        edb <- .getEnsDbFromAnnotationHub(id = id)
               ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:466:11:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L466) *warning:* **no visible global function definition for ‘makeGRangesFromEnsDb’**
```r
    gr <- makeGRangesFromEnsDb(object = edb, level = level)
          ^~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:467:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L467) *warning:* **no visible global function definition for ‘metadata’**
```r
    metadata(gr)[["id"]] <- id
    ^~~~~~~~
```
[R/makeGRanges.R:467:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L467) *warning:* **no visible global function definition for ‘metadata<-’**
```r
    metadata(gr)[["id"]] <- id
    ^~~~~~~~
```
[R/makeGRanges.R:476:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L476) *style:* **Variable or function name should be snake_case.**
```r
makeGRangesFromEnsDb <- function(object, level) {
^~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:478:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L478) *style:* **Variable or function name should be snake_case.**
```r
    userAttached <- .packages()
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:490:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L490) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "EnsDb"))
    ^~~~~~~~~~~
```
[R/makeGRanges.R:492:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L492) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "EnsDb")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:496:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L496) *style:* **Variable or function name should be snake_case.**
```r
    genomeBuild <- metadata(object) %>%
    ^~~~~~~~~~~
```
[R/makeGRanges.R:500:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L500) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
    assert_is_a_string(genomeBuild)
    ^~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:543:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L543) *style:* **Variable or function name should be snake_case.**
```r
        txData <- mcols(tx)
        ^~~~~~
```
[R/makeGRanges.R:543:19:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L543) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        txData <- mcols(tx)
                  ^~~~~
```
[R/makeGRanges.R:544:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L544) *style:* **Variable or function name should be snake_case.**
```r
        geneData <- mcols(gene)
        ^~~~~~~~
```
[R/makeGRanges.R:544:21:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L544) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        geneData <- mcols(gene)
                    ^~~~~
```
[R/makeGRanges.R:557:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L557) *warning:* **no visible global function definition for ‘mcols<-’**
```r
        mcols(tx) <- as(data, "DataFrame")
        ^~~~~
```
[R/makeGRanges.R:561:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L561) *warning:* **no visible global function definition for ‘metadata<-’, Did you mean 'metadata'?**
```r
    metadata(gr) <- metadata
    ^~~~~~~~
```
[R/makeGRanges.R:562:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L562) *warning:* **no visible global function definition for ‘.forceDetach’**
```r
    .forceDetach(keep = userAttached)
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:563:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L563) *warning:* **no visible global function definition for ‘.makeGRanges’**
```r
    .makeGRanges(gr)
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:572:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L572) *style:* **Variable or function name should be snake_case.**
```r
.gffSource <- function(gff) {
^~~~~~~~~~
```
[R/makeGRanges.R:573:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L573) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
    assert_is_subset("source", colnames(mcols(gff)))
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:573:41:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L573) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
    assert_is_subset("source", colnames(mcols(gff)))
                                        ^~~~~
```
[R/makeGRanges.R:594:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L594) *style:* **Variable or function name should be snake_case.**
```r
.gffType <- function(gff) {
^~~~~~~~
```
[R/makeGRanges.R:595:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L595) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(gff, "GRanges"))
    ^~~~~~~~~~~
```
[R/makeGRanges.R:596:12:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L596) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**
```r
    gff <- camel(gff)
           ^~~~~
```
[R/makeGRanges.R:617:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L617) *style:* **Variable or function name should be snake_case.**
```r
makeGRangesFromGFF <- function(
^~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:626:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L626) *warning:* **no visible global function definition for ‘localOrRemoteFile’**
```r
    file <- localOrRemoteFile(file)
            ^~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:627:12:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L627) *warning:* **no visible global function definition for ‘import’**
```r
    gff <- import(file)
           ^~~~~~
```
[R/makeGRanges.R:628:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L628) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(gff, "GRanges")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:629:12:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L629) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**
```r
    gff <- camel(gff)
           ^~~~~
```
[R/makeGRanges.R:631:15:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L631) *warning:* **no visible global function definition for ‘.gffSource’**
```r
    source <- .gffSource(gff)
              ^~~~~~~~~~
```
[R/makeGRanges.R:632:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L632) *warning:* **no visible global function definition for ‘.gffType’**
```r
    type <- .gffType(gff)
            ^~~~~~~~
```
[R/makeGRanges.R:662:21:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L662) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
    gn <- gn[!is.na(mcols(gn)[["geneID"]])]
                    ^~~~~
```
[R/makeGRanges.R:663:20:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L663) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
    gn <- gn[is.na(mcols(gn)[["transcriptID"]])]
                   ^~~~~
```
[R/makeGRanges.R:666:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L666) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset("name", colnames(mcols(gn)))
        ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:666:43:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L666) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        assert_is_subset("name", colnames(mcols(gn)))
                                          ^~~~~
```
[R/makeGRanges.R:667:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L667) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["geneName"]] <- mcols(gn)[["name"]]
        ^~~~~
```
[R/makeGRanges.R:667:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L667) *warning:* **no visible global function definition for ‘mcols<-’**
```r
        mcols(gn)[["geneName"]] <- mcols(gn)[["name"]]
        ^~~~~
```
[R/makeGRanges.R:667:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L667) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["geneName"]] <- mcols(gn)[["name"]]
        ^~~~~
```
[R/makeGRanges.R:668:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L668) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["name"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:668:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L668) *warning:* **no visible global function definition for ‘mcols<-’**
```r
        mcols(gn)[["name"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:670:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L670) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset("biotype", colnames(mcols(gn)))
        ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:670:46:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L670) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        assert_is_subset("biotype", colnames(mcols(gn)))
                                             ^~~~~
```
[R/makeGRanges.R:671:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L671) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["geneBiotype"]] <- mcols(gn)[["biotype"]]
        ^~~~~
```
[R/makeGRanges.R:671:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L671) *warning:* **no visible global function definition for ‘mcols<-’**
```r
        mcols(gn)[["geneBiotype"]] <- mcols(gn)[["biotype"]]
        ^~~~~
```
[R/makeGRanges.R:671:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L671) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["geneBiotype"]] <- mcols(gn)[["biotype"]]
        ^~~~~
```
[R/makeGRanges.R:672:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L672) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["biotype"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:672:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L672) *warning:* **no visible global function definition for ‘mcols<-’**
```r
        mcols(gn)[["biotype"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:674:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L674) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["alias"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:674:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L674) *warning:* **no visible global function definition for ‘mcols<-’**
```r
        mcols(gn)[["alias"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:675:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L675) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["id"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:675:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L675) *warning:* **no visible global function definition for ‘mcols<-’**
```r
        mcols(gn)[["id"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:676:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L676) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcols(gn)[["parent"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:676:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L676) *warning:* **no visible global function definition for ‘mcols<-’**
```r
        mcols(gn)[["parent"]] <- NULL
        ^~~~~
```
[R/makeGRanges.R:678:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L678) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**
```r
    assert_has_no_duplicates(mcols(gn)[["geneID"]])
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:678:30:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L678) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
    assert_has_no_duplicates(mcols(gn)[["geneID"]])
                             ^~~~~
```
[R/makeGRanges.R:679:18:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L679) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
    names(gn) <- mcols(gn)[["geneID"]]
                 ^~~~~
```
[R/makeGRanges.R:696:25:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L696) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        tx <- tx[!is.na(mcols(tx)[["transcriptID"]])]
                        ^~~~~
```
[R/makeGRanges.R:710:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L710) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
            assert_is_subset("name", colnames(mcols(tx)))
            ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:710:47:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L710) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            assert_is_subset("name", colnames(mcols(tx)))
                                              ^~~~~
```
[R/makeGRanges.R:711:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L711) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["transcriptName"]] <- mcols(tx)[["name"]]
            ^~~~~
```
[R/makeGRanges.R:711:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L711) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(tx)[["transcriptName"]] <- mcols(tx)[["name"]]
            ^~~~~
```
[R/makeGRanges.R:711:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L711) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["transcriptName"]] <- mcols(tx)[["name"]]
            ^~~~~
```
[R/makeGRanges.R:712:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L712) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["name"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:712:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L712) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(tx)[["name"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:714:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L714) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
            assert_is_subset("biotype", colnames(mcols(tx)))
            ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:714:50:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L714) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            assert_is_subset("biotype", colnames(mcols(tx)))
                                                 ^~~~~
```
[R/makeGRanges.R:715:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L715) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["transcriptBiotype"]] <- mcols(tx)[["biotype"]]
            ^~~~~
```
[R/makeGRanges.R:715:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L715) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(tx)[["transcriptBiotype"]] <- mcols(tx)[["biotype"]]
            ^~~~~
```
[R/makeGRanges.R:715:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L715) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["transcriptBiotype"]] <- mcols(tx)[["biotype"]]
            ^~~~~
```
[R/makeGRanges.R:716:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L716) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["biotype"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:716:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L716) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(tx)[["biotype"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:718:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L718) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
            assert_is_subset("parent", colnames(mcols(tx)))
            ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:718:49:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L718) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            assert_is_subset("parent", colnames(mcols(tx)))
                                                ^~~~~
```
[R/makeGRanges.R:719:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L719) *warning:* **no visible global function definition for ‘assert_that’**
```r
            assert_that(all(grepl("^gene:", mcols(tx)[["parent"]])))
            ^~~~~~~~~~~
```
[R/makeGRanges.R:719:45:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L719) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            assert_that(all(grepl("^gene:", mcols(tx)[["parent"]])))
                                            ^~~~~
```
[R/makeGRanges.R:720:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L720) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["geneID"]] <- as.character(mcols(tx)[["parent"]])
            ^~~~~
```
[R/makeGRanges.R:720:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L720) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(tx)[["geneID"]] <- as.character(mcols(tx)[["parent"]])
            ^~~~~
```
[R/makeGRanges.R:720:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L720) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["geneID"]] <- as.character(mcols(tx)[["parent"]])
            ^~~~~
```
[R/makeGRanges.R:727:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L727) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["alias"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:727:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L727) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(tx)[["alias"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:728:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L728) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["id"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:728:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L728) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(tx)[["id"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:729:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L729) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
            mcols(tx)[["parent"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:729:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L729) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(tx)[["parent"]] <- NULL
            ^~~~~
```
[R/makeGRanges.R:731:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L731) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**
```r
        assert_has_no_duplicates(mcols(tx)[["transcriptID"]])
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:731:34:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L731) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        assert_has_no_duplicates(mcols(tx)[["transcriptID"]])
                                 ^~~~~
```
[R/makeGRanges.R:732:22:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L732) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        names(tx) <- mcols(tx)[["transcriptID"]]
                     ^~~~~
```
[R/makeGRanges.R:745:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L745) *style:* **Variable or function name should be snake_case.**
```r
        geneCols <- setdiff(
        ^~~~~~~~
```
[R/makeGRanges.R:750:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L750) *style:* **Variable or function name should be snake_case.**
```r
            geneCols <- c("geneID", geneCols)
            ^~~~~~~~
```
[R/makeGRanges.R:763:13:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L763) *warning:* **no visible global function definition for ‘mcols<-’**
```r
            mcols(gr) <- merge
            ^~~~~
```
[R/makeGRanges.R:783:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L783) *warning:* **no visible global function definition for ‘.makeGRanges’**
```r
    .makeGRanges(gr)
    ^~~~~~~~~~~~
```
[R/makeGRanges.R:789:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L789) *style:* **Variable or function name should be snake_case.**
```r
.makeGRanges <- function(object) {
^~~~~~~~~~~~
```
[R/makeGRanges.R:790:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L790) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "GRanges")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:791:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L791) *warning:* **no visible global function definition for ‘assert_has_names’**
```r
    assert_has_names(object)
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:796:14:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L796) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**
```r
    mcols <- camel(mcols)
             ^~~~~
```
[R/makeGRanges.R:806:14:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L806) *warning:* **no visible global function definition for ‘removeNA’, Did you mean 'remove'?**
```r
    mcols <- removeNA(mcols)
             ^~~~~~~~
```
[R/makeGRanges.R:812:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L812) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset("geneID", colnames(mcols))
        ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:852:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L852) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
    mcols(object) <- mcols
    ^~~~~
```
[R/makeGRanges.R:861:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L861) *style:* **Variable or function name should be snake_case.**
```r
        idCol <- "transcriptID"
        ^~~~~
```
[R/makeGRanges.R:863:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L863) *style:* **Variable or function name should be snake_case.**
```r
        idCol <- "geneID"
        ^~~~~
```
[R/makeGRanges.R:868:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L868) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
    mcols(object)[["broadClass"]] <- .defineBroadClass(object)
    ^~~~~
```
[R/makeGRanges.R:868:38:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L868) *warning:* **no visible global function definition for ‘.defineBroadClass’**
```r
    mcols(object)[["broadClass"]] <- .defineBroadClass(object)
                                     ^~~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:871:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L871) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
    mcols(object) <- mcols(object)[, sort(colnames(mcols(object)))]
    ^~~~~
```
[R/makeGRanges.R:877:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L877) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "GRanges")
    ^~~~~~~~~~~~~~~~
```
[R/makeGRanges.R:895:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L895) *warning:* **no visible global function definition for ‘as_tibble’**
```r
        as_tibble(gr, rownames = NULL)
        ^~~~~~~~~
```
[R/makeGRanges.R:905:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeGRanges.R#L905) *style:* **Variable or function name should be snake_case.**
```r
makeGRangesFromGTF <- makeGRangesFromGFF
^~~~~~~~~~~~~~~~~~
```
[R/makeTx2Gene.R:43:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L43) *style:* **Variable or function name should be snake_case.**
```r
makeTx2GeneFromEnsembl <-
^~~~~~~~~~~~~~~~~~~~~~
```
[R/makeTx2Gene.R:49:9:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L49) *warning:* **no visible global function definition for ‘Tx2Gene’**
```r
        Tx2Gene(gr)
        ^~~~~~~
```
[R/makeTx2Gene.R:59:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L59) *style:* **Variable or function name should be snake_case.**
```r
makeTx2GeneFromEnsDb <- function(object) {
^~~~~~~~~~~~~~~~~~~~
```
[R/makeTx2Gene.R:60:11:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L60) *warning:* **no visible global function definition for ‘makeGRangesFromEnsDb’**
```r
    gr <- makeGRangesFromEnsDb(object, level = "transcripts")
          ^~~~~~~~~~~~~~~~~~~~
```
[R/makeTx2Gene.R:61:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L61) *warning:* **no visible global function definition for ‘Tx2Gene’**
```r
    Tx2Gene(gr)
    ^~~~~~~
```
[R/makeTx2Gene.R:68:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L68) *style:* **Variable or function name should be snake_case.**
```r
makeTx2GeneFromGFF <- function(file) {
^~~~~~~~~~~~~~~~~~
```
[R/makeTx2Gene.R:69:11:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L69) *warning:* **no visible global function definition for ‘makeGRangesFromGFF’**
```r
    gr <- makeGRangesFromGFF(file, level = "transcripts")
          ^~~~~~~~~~~~~~~~~~
```
[R/makeTx2Gene.R:70:5:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L70) *warning:* **no visible global function definition for ‘Tx2Gene’**
```r
    Tx2Gene(gr)
    ^~~~~~~
```
[R/makeTx2Gene.R:79:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/makeTx2Gene.R#L79) *style:* **Variable or function name should be snake_case.**
```r
makeTx2GeneFromGTF <- makeTx2GeneFromGFF
^~~~~~~~~~~~~~~~~~
```
[R/package.R:44:1:](https://github.com/steinbaugh/basejump.annotations/blob/975c9c1a6222ac1427da0320b445bee9c61f6962/R/package.R#L44) *style:* **Variable or function name should be snake_case.**
```r
.prototypeMetadata <- list(
^~~~~~~~~~~~~~~~~~
```


How is this different than what is already checked in ? Looks like an older version of the code... Please use a PR with the latest code


Aren't interfaces' methods always public?


I mean for them we could unconditionally use `getMethod`


:x: 1 / 8 Rules Failed

      :cold_sweat: It's not you, it's your code. It may not be aligned with your organization's best practices

      :point_right: You can review your rules settings at smart policy management :point_left:

:point_right: click here to view a full list of the events :point_left:


vogel/stellar-core/fix-ioservice-balance = ecd315d2 merged ok, testing candidate = f91df46d