[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(
^~~~~~~~~~~~~~~~~~
```


@markwhitfeld what do you think about https://github.com/ngxs/store/pull/628?


Created multidev environment [visualizing-faculty-research#ci-140](https://dashboard.pantheon.io/sites/3f330315-1192-4ce1-93ac-1446fdb4b97a#ci-140).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-140-visualizing-faculty-research.pantheonsite.io/)


Hi ifenglin,
Your code is very good!
Can you tell me the how to get the "data/cm_alldata.mat" and "data/cm_labels.mat" in case I have the real data and the imagery data? Or can you tell me the format?
Thank you very much and looking forward to your early reply.

Best regards,
Zellar209


It seems "retransmit" is only used for failed pairs now.. Which shouldn't happen in this case? Can you confirm ?


Why is manifest a move-only type?


缅怀


@mauritsvanrees Jenkins CI reporting about code analysis
See the full report here: https://jenkins.plone.org/job/package-plone.app.iterate/81/violations
```
plone/app/iterate/__init__.py:48:78: C812 missing trailing comma
plone/app/iterate/archiver.py:26:1: I004 isort found an unexpected blank line in imports
plone/app/iterate/archiver.py:27:1: I001 isort found an import in the wrong position
plone/app/iterate/base.py:160:22: W292 no newline at end of file
plone/app/iterate/containers.py:72:50: C812 missing trailing comma
plone/app/iterate/containers.py:73:14: C812 missing trailing comma
plone/app/iterate/copier.py:37:1: I001 isort found an import in the wrong position
plone/app/iterate/event.py:28:1: I004 isort found an unexpected blank line in imports
plone/app/iterate/event.py:29:1: I001 isort found an import in the wrong position
plone/app/iterate/interfaces.py:321:23: C812 missing trailing comma
plone/app/iterate/interfaces.py:328:22: C812 missing trailing comma
plone/app/iterate/permissions.py:26:1: I003 isort expected 1 blank line in imports, found 0
plone/app/iterate/policy.py:57:45: C812 missing trailing comma
plone/app/iterate/policy.py:66:11: T000 Todo note found.
plone/app/iterate/setuphandlers.py:11:27: C812 missing trailing comma
plone/app/iterate/testing.py:151:80: E501 line too long (83 > 79 characters)
plone/app/iterate/browser/checkout.py:70:33: C812 missing trailing comma
plone/app/iterate/dexterity/copier.py:5:1: I001 isort found an import in the wrong position
plone/app/iterate/dexterity/copier.py:67:19: T000 Todo note found.
plone/app/iterate/dexterity/copier.py:157:50: C812 missing trailing comma
plone/app/iterate/dexterity/utils.py:25:18: C812 missing trailing comma
plone/app/iterate/tests/test_doctests.py:6:1: I003 isort expected 1 blank line in imports, found 0
plone/app/iterate/tests/test_doctests.py:7:1: I003 isort expected 1 blank line in imports, found 0
plone/app/iterate/tests/test_doctests.py:9:5: F401 'Products.ATContentTypes' imported but unused
plone/app/iterate/tests/test_doctests.py:26:54: C812 missing trailing comma
plone/app/iterate/tests/test_doctests.py:34:53: C812 missing trailing comma
plone/app/iterate/tests/test_iterate.py:171:80: E501 line too long (97 > 79 characters)
plone/app/iterate/tests/test_iterate_at.py:35:1: I003 isort expected 1 blank line in imports, found 0
plone/app/iterate/tests/test_iterate_at.py:42:5: E301 expected 1 blank line, found 0
plone/app/iterate/tests/test_iterate_at.py:52:80: E501 line too long (85 > 79 characters)
plone/app/iterate/tests/test_iterate_at.py:154:11: T000 Todo note found.
plone/app/iterate/tests/test_iterate_at.py:302:80: E501 line too long (97 > 79 characters)
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


Why is validator token a move-only type?


[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’**
```r
        assert_that(has_internet())
        ^~~~~~~~~~~
```
[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’**
```r
        assert_that(has_internet())
                    ^~~~~~~~~~~~
```
[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.**
```r
            categoriesFile <- file.path(basejumpCacheURL, "cog.txt")
            ^~~~~~~~~~~~~~
```
[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’**
```r
            categoriesFile <- file.path(basejumpCacheURL, "cog.txt")
                                        ^~~~~~~~~~~~~~~~
```
[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.**
```r
            eunogFile <- file.path(basejumpCacheURL, "eunog.tsv.gz")
            ^~~~~~~~~
```
[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’**
```r
            eunogFile <- file.path(basejumpCacheURL, "eunog.tsv.gz")
                                   ^~~~~~~~~~~~~~~~
```
[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.**
```r
            nogFile <- file.path(basejumpCacheURL, "nog.tsv.gz")
            ^~~~~~~
```
[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’**
```r
            nogFile <- file.path(basejumpCacheURL, "nog.tsv.gz")
                                 ^~~~~~~~~~~~~~~~
```
[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.**
```r
            categoriesFile <- paste(
            ^~~~~~~~~~~~~~
```
[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.**
```r
            eunogFile <- paste(
            ^~~~~~~~~
```
[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.**
```r
            nogFile <- paste(
            ^~~~~~~
```
[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’**
```r
        assert_is_a_string(categoriesFile)
        ^~~~~~~~~~~~~~~~~~
```
[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’**
```r
        assert_is_a_string(eunogFile)
        ^~~~~~~~~~~~~~~~~~
```
[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’**
```r
        assert_is_a_string(nogFile)
        ^~~~~~~~~~~~~~~~~~
```
[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<-’**
```r
        metadata(data) <- .prototypeMetadata
        ^~~~~~~~
```
[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’**
```r
        metadata(data) <- .prototypeMetadata
                          ^~~~~~~~~~~~~~~~~~
```
[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’**
```r
        assert_has_rows(object)
        ^~~~~~~~~~~~~~~
```
[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’**
```r
        data <- expand(data)
                ^~~~~~
```
[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’**
```r
        assert_that(!any(duplicated(unmapped)))
        ^~~~~~~~~~~
```
[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’**
```r
            assert_is_list(entrez)
            ^~~~~~~~~~~~~~
```
[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<-’**
```r
        metadata(data) <- metadata(object)
        ^~~~~~~~
```
[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’**
```r
        metadata(data) <- metadata(object)
        ^~~~~~~~
```
[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’**
```r
        metadata(data)[["format"]] <- format
        ^~~~~~~~
```
[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<-’**
```r
        metadata(data)[["format"]] <- format
        ^~~~~~~~
```
[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<-’**
```r
        metadata(data) <- metadata(object)
        ^~~~~~~~
```
[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’**
```r
        metadata(data) <- metadata(object)
        ^~~~~~~~
```
[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’**
```r
        object <- as.SummarizedExperiment(object)
                  ^~~~~~~~~~~~~~~~~~~~~~~
```
[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’**
```r
        data <- rowData(object)
                ^~~~~~~
```
[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’**
```r
        assert_has_rows(object)
        ^~~~~~~~~~~~~~~
```
[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<-’**
```r
        metadata(data) <- .genomeMetadata(object)
        ^~~~~~~~
```
[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’**
```r
        metadata(data) <- .genomeMetadata(object)
                          ^~~~~~~~~~~~~~~
```
[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’**
```r
        metadata(data)[["format"]] <- format
        ^~~~~~~~
```
[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<-’**
```r
        metadata(data)[["format"]] <- format
        ^~~~~~~~
```
[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<-’**
```r
        metadata(data) <- metadata(object)
        ^~~~~~~~
```
[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’**
```r
        metadata(data) <- metadata(object)
        ^~~~~~~~
```
[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’**
```r
        object <- as.SummarizedExperiment(object)
                  ^~~~~~~~~~~~~~~~~~~~~~~
```
[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’**
```r
        data <- rowData(object)
                ^~~~~~~
```
[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’**
```r
        assert_that(has_internet())
        ^~~~~~~~~~~
```
[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’**
```r
        assert_that(has_internet())
                    ^~~~~~~~~~~~
```
[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’**
```r
            file <- file.path(basejumpCacheURL, "hgnc.txt.gz")
                              ^~~~~~~~~~~~~~~~
```
[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’**
```r
            file <- .hgncURL
                    ^~~~~~~~
```
[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'?**
```r
        data <- camel(data)
                ^~~~~
```
[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<-’**
```r
        metadata(data) <- .prototypeMetadata
        ^~~~~~~~
```
[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’**
```r
        metadata(data) <- .prototypeMetadata
                          ^~~~~~~~~~~~~~~~~~
```
[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.**
```r
.hgncURL <- paste(
^~~~~~~~
```
[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.**
```r
.prototypeMetadata <- list(
^~~~~~~~~~~~~~~~~~
```
[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.**
```r
.hasPrototypeMetadata <- function(object) {
^~~~~~~~~~~~~~~~~~~~~
```
[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.**
```r
.assertHasPrototypeMetadata <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[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.**
```r
.prototypeGenomeMetadata <- c(
^~~~~~~~~~~~~~~~~~~~~~~~
```
[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.**
```r
.genomeMetadata <- function(object) {
^~~~~~~~~~~~~~~
```
[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.**
```r
    prototypeMetadata <- .prototypeGenomeMetadata %>%
    ^~~~~~~~~~~~~~~~~
```
[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.**
```r
.hasGenomeMetadata <- function(object) {
^~~~~~~~~~~~~~~~~~
```
[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’**
```r
    all(genomeMetadataNames %in% names(metadata(object)))
        ^~~~~~~~~~~~~~~~~~~
```
[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’**
```r
    all(genomeMetadataNames %in% names(metadata(object)))
                                       ^~~~~~~~
```
[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.**
```r
.assertHasGenomeMetadata <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~
```
[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’**
```r
    .assertHasPrototypeMetadata(object)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[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.**
```r
MGI2Ensembl <- function() {
^~~~~~~~~~~
```
[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’**
```r
    assert_that(has_internet())
    ^~~~~~~~~~~
```
[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’**
```r
    assert_that(has_internet())
                ^~~~~~~~~~~~
```
[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’**
```r
        file <- file.path(basejumpCacheURL, "mgi.rpt.gz")
                          ^~~~~~~~~~~~~~~~
```
[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’**
```r
        file <- .mgiURL
                ^~~~~~~
```
[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<-’**
```r
    metadata(data) <- .prototypeMetadata
    ^~~~~~~~
```
[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’**
```r
    metadata(data) <- .prototypeMetadata
                      ^~~~~~~~~~~~~~~~~~
```
[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.**
```r
.mgiURL <- paste(
^~~~~~~
```
[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.**
```r
.pantherMappings <- c(
^~~~~~~~~~~~~~~~
```
[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.**
```r
.splitTerms <- function(vec, progress = TRUE) {
^~~~~~~~~~~
```
[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'?**
```r
        lapply <- pblapply
                  ^~~~~~~~
```
[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’**
```r
        hgnc2ensembl <- HGNC2Ensembl()
                        ^~~~~~~~~~~~
```
[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’**
```r
        mgi2ensembl <- MGI2Ensembl()
                       ^~~~~~~~~~~
```
[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’**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "FBgn\\d{7}$"))
        ^~~~~~
```
[R/PANTHER.R:122:31:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L122) *warning:* **no visible global function definition for ‘str_extract’**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "FBgn\\d{7}$"))
                              ^~~~~~~~~~~
```
[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'?**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "FBgn\\d{7}$"))
                                            ^~~
```
[R/PANTHER.R:129:9:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L129) *warning:* **no visible global function definition for ‘mutate’**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "WBGene\\d{8}$"))
        ^~~~~~
```
[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’**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "WBGene\\d{8}$"))
                              ^~~~~~~~~~~
```
[R/PANTHER.R:129:45:](https://github.com/steinbaugh/basejump.classes/blob/678288b91f7abffff71bba7511e4dad7b603c6a2/R/PANTHER.R#L129) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "WBGene\\d{8}$"))
                                            ^~~
```
[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’**
```r
    assert_that(has_internet())
    ^~~~~~~~~~~
```
[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’**
```r
    assert_that(has_internet())
                ^~~~~~~~~~~~
```
[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.**
```r
    pantherName <-  .pantherMappings[[organism]]
    ^~~~~~~~~~~
```
[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’**
```r
    pantherName <-  .pantherMappings[[organism]]
                    ^~~~~~~~~~~~~~~~
```
[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’**
```r
    assert_is_a_string(pantherName)
    ^~~~~~~~~~~~~~~~~~
```
[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’**
```r
    assert_is_a_string(release)
    ^~~~~~~~~~~~~~~~~~
```
[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’**
```r
    assert_is_a_bool(progress)
    ^~~~~~~~~~~~~~~~
```
[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’**
```r
    assert_is_a_string(file)
    ^~~~~~~~~~~~~~~~~~
```
[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'?**
```r
    fun <- get(paste("", "PANTHER", camel(organism), sep = "."))
                                    ^~~~~
```
[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’**
```r
    assert_is_function(fun)
    ^~~~~~~~~~~~~~~~~~
```
[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’**
```r
    assert_has_rows(data)
    ^~~~~~~~~~~~~~~
```
[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’**
```r
    assert_has_no_duplicates(data[["geneID"]])
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[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<-’**
```r
    metadata(data) <- .prototypeMetadata
    ^~~~~~~~
```
[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’**
```r
    metadata(data) <- .prototypeMetadata
                      ^~~~~~~~~~~~~~~~~~
```
[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’**
```r
    metadata(data)[["organism"]] <- organism
    ^~~~~~~~
```
[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<-’**
```r
    metadata(data)[["organism"]] <- organism
    ^~~~~~~~
```
[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’**
```r
    metadata(data)[["release"]] <- release
    ^~~~~~~~
```
[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<-’**
```r
    metadata(data)[["release"]] <- release
    ^~~~~~~~
```
[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.**
```r
.showHeader <- function(object) {
^~~~~~~~~~~
```
[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’**
```r
    cat(paste(class(object), metadata(object)[["version"]]), sep = "\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’**
```r
        .showHeader(object)
        ^~~~~~~~~~~
```
[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’**
```r
        .showHeader(object)
        ^~~~~~~~~~~
```
[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’**
```r
        show.DataFrame(object)
        ^~~~~~~~~~~~~~
```
[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’**
```r
        .showHeader(object)
        ^~~~~~~~~~~
```
[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’**
```r
        show.DataFrame(object)
        ^~~~~~~~~~~~~~
```
[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’**
```r
        assert_has_rows(object)
        ^~~~~~~~~~~~~~~
```
[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<-’**
```r
        metadata(data) <- .genomeMetadata(object)
        ^~~~~~~~
```
[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’**
```r
        metadata(data) <- .genomeMetadata(object)
                          ^~~~~~~~~~~~~~~
```
[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<-’**
```r
        metadata(data) <- metadata(object)
        ^~~~~~~~
```
[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’**
```r
        metadata(data) <- metadata(object)
        ^~~~~~~~
```
[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’**
```r
        object <- as.SummarizedExperiment(object)
                  ^~~~~~~~~~~~~~~~~~~~~~~
```
[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’**
```r
        data <- rowData(object)
                ^~~~~~~
```


Yes.  :-)


This commit makes a lot of unnecessary changes to `lex.yy.c`, including replacing `yy_size_t` with `int`. Maybe regenerate it with a newer toolchain?


Move the string here


addEventListener api 사용하는걸로 바꿔볼까요.


Now could not deploy this pull request since the `now.json` file explicitly sets `dotenv` to true.
However, there's no `.env` file in the repo.

Commit a `.env` file or unset the `dotenv` flag.
For secret environment variables, check out [Now Secrets](https://zeit.co/docs/getting-started/secrets).


Use std::regex instead of boost. All our platforms support it.


Files in uploaded segments don't contains provided headers like X-Delete-After, so objects aren't removed. This commit repairs.


@Mint-Choco-Love ㅋㅋㅋㅋㅋ 블로그 다시 시작해보려구요


current_player ? true : false


var ivArray = new Array();
var ivArray = [];
차이가 뭘까요


Why the non-capturing lookahead? We don't use groups at all. I'd probably just let the groups capture for terseness, or you label them all non-capturing. I'd prbably use `?:` for that, tho that's mostly style.


Это и выше 2 метода логика игры


꼭 배열을 사용해야되는지도 다시 생각해보세요 ㅋㅋ


gets.chomp =~ /^[Yy]$/ ? ... : ...
/^[Yy]$/  можно еще в константу


Looks fine.


That won't work. It needs to catch and raise the error. But the sleep will still happen down at L276 ish.
```python
    while len(CE_to_SE_mapping) != maps_size:
        time.sleep(0.1)
```


console.log는 개발하고 디버깅할때만 쓰고 실제 제품 코드에 들어있으면 안되요.


We use jenkins for monthly builds instead of travis CI.


1.
Login options
- students login for test
- tutors login for questions
- mentor login for guidance
Tutor login
-will create a test batteries
-add Questions / options/answer
-edit also
- compile new battery from existing qns


Lets look this information up in a dict. So we don't end up with big old if statement.


> Simon and I agreed

But it is not up to you two, is it?


canteen for eatable items


Created multidev environment [visualizing-faculty-research#ci-142](https://dashboard.pantheon.io/sites/3f330315-1192-4ce1-93ac-1446fdb4b97a#ci-142).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-142-visualizing-faculty-research.pantheonsite.io/)


scroll 생기게 하는게 목적이면 명시적으로 scroll 값을 주는게 낫겠죠?


Beaucoup de choses sont so-2000. :-) J'essaie de mettre un peu à jour la base de code pour préparer un transfert vers Azure, et en profite pour éliminer toutes les fonctions qui me semblent inutiles aujourd'hui.


Point [conceded](https://github.com/felixrieseberg/ember-electron/pull/371#issuecomment-434018941)


Make `explicit`. Also, `std::function` may allocate. I'd use a template here. I don't think we need to be fancy and use SFINE to constrain `callback` to be a callable. There are no other single parameter constructors this competes with and the compile error should be understandable without it.


There's an addition "if .. then" needed :/

if the setup is CRI-O+flannel and the user wants to use kata:
https://github.com/clearlinux/clr-bundles/issues/81


Для класса Card добавь простую валидацию, чтобы нельзя было создать карту не из набора


Из этого класса нужно перенести константы в класс Card, а здесь обращайся:
`Card::SUITS`