thanks for it !

On Fri, Oct 26, 2018 at 11:55 PM Juran <notifications@github.com> wrote:

> Hi
> my opinion
> It's correct to change '을' to '를'
> but there is no need to change 'sales' to '판매액'
> thanks
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/MicrosoftDocs/powerbi-docs.ko-kr/commit/542f50b020e4347990ba23cd817590583975b648#commitcomment-31067357>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AqOMZyBSdoq1boXq5DuUGL3mihic5Y0Gks5uo9lJgaJpZM4X9Obi>
> .
>

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maybe remove this?


may I know what "discussion about twister2" means?


@ksooo Removed the indentation changes.


@ksooo Here you go, only en-GB, removed other language files.


Exporting FAILURES from subshells didn't work, so use { groups; instead }

Another typical output, since LDC tends to be missing:
```
vagrant@vagrant-ubuntu-trusty-64:~$ tools/test.sh
Testing LDC SAD...
LDC SAD failed because the code for LDC SAD is missing. This is normal, as we are still awaiting the official release!
Testing noisemes...
Noisemes passed the test.
Testing OpenSmile SAD...
OpenSmile SAD passed the test.
Testing ToCombo SAD...
TOCOMBO SAD passed the test.
Testing DIARTK...
DiarTK passed the test.
Testing Yunitator...
Yunitator passed the test.
Testing Dscore...
DScore passed the test.
Testing LDC evalSAD
LDC evalSAD failed because the code for LDC SAD is missing. This is normal, as we are still awaiting the official release!
Some tools did not pass the test, but you can still use others
```


Just Testing


Created multidev environment [d8-digital-stlawu#ci-340](https://dashboard.pantheon.io/sites/9f185cec-9c0b-4fcb-972f-9a5f2f6ed252#ci-340).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-340-d8-digital-stlawu.pantheonsite.io/)


[R/EggNOG.R:10:9:](https://github.com/steinbaugh/basejump.classes/blob/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/R/PANTHER.R#L32) *style:* **Variable or function name should be snake_case.**
```r
.splitTerms <- function(vec, progress = FALSE) {
^~~~~~~~~~~
```
[R/PANTHER.R:35:19:](https://github.com/steinbaugh/basejump.classes/blob/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/R/PANTHER.R#L122) *warning:* **no visible global function definition for ‘mutate’**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "FBgn\\d{7}$"))
        ^~~~~~
```
[R/PANTHER.R:122:31:](https://github.com/steinbaugh/basejump.classes/blob/ef310157abe9f843a4b3d7700bf67b1b459f85ad/R/PANTHER.R#L122) *warning:* **no visible global function definition for ‘str_extract’**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "FBgn\\d{7}$"))
                              ^~~~~~~~~~~
```
[R/PANTHER.R:122:45:](https://github.com/steinbaugh/basejump.classes/blob/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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}$"))
                                            ^~~
```
[R/PANTHER.R:129:9:](https://github.com/steinbaugh/basejump.classes/blob/ef310157abe9f843a4b3d7700bf67b1b459f85ad/R/PANTHER.R#L129) *warning:* **no visible global function definition for ‘mutate’**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "WBGene\\d{8}$"))
        ^~~~~~
```
[R/PANTHER.R:129:31:](https://github.com/steinbaugh/basejump.classes/blob/ef310157abe9f843a4b3d7700bf67b1b459f85ad/R/PANTHER.R#L129) *warning:* **no visible global function definition for ‘str_extract’**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "WBGene\\d{8}$"))
                              ^~~~~~~~~~~
```
[R/PANTHER.R:129:45:](https://github.com/steinbaugh/basejump.classes/blob/ef310157abe9f843a4b3d7700bf67b1b459f85ad/R/PANTHER.R#L129) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        mutate(data, geneID = str_extract(!!sym("keys"), "WBGene\\d{8}$"))
                                            ^~~
```
[R/PANTHER.R:142:5:](https://github.com/steinbaugh/basejump.classes/blob/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/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/ef310157abe9f843a4b3d7700bf67b1b459f85ad/R/Tx2Gene-methods.R#L76) *warning:* **no visible global function definition for ‘rowData’**
```r
        data <- rowData(object)
                ^~~~~~~
```


@cstrahan Same question as https://github.com/NixOS/nixpkgs/commit/9ce0c1cb7113#r23138805, why does `TimeoutStartSec = 0;` make sense here?

See also https://github.com/NixOS/nixpkgs/issues/49415#issuecomment-435055275


Isn't **Y**ouclick.fr better ? 🦆


Ok. Done and tested again.


Can constant it is better to make private?


closes #8


my only concern with this version of the refactor is that right here at the `default` block we don't immediately jump to the reset part of the code. The admittedly weak concern is that *if* we added some code right after the switch, then the default block does not skip over that new code. This might be a bunch of concern about nothing, but the original code and my refactor did properly handle such a case, I believe. I do like the relative simplicity of this approach here, however.


can I do the changes mentioned in the comments in my technologies?


Are we checking for the existence of the file and conditionally adding it, and then unconditionally adding the same file? This looks like an oops!


[R/convertUCSCBuildToEnsembl.R:14:1:](https://github.com/steinbaugh/basejump.annotations/blob/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/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/ccdb2a1ab5e18252daccdaefb688351e8765a482/R/package.R#L44) *style:* **Variable or function name should be snake_case.**
```r
.prototypeMetadata <- list(
^~~~~~~~~~~~~~~~~~
```


[R/coerceS4ToList.R:13:1:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/coerceS4ToList.R#L13) *style:* **Variable or function name should be snake_case.**
```r
coerceS4ToList <- function(from) {
^~~~~~~~~~~~~~
```
[R/coerceS4ToList.R:30:1:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/coerceS4ToList.R#L30) *style:* **Variable or function name should be snake_case.**
```r
flatFiles <- coerceS4ToList
^~~~~~~~~
```
[R/SummarizedExperiment-methods.R:11:13:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L11) *style:* **Variable or function name should be snake_case.**
```r
            rowMeta <- metadata(rowRanges(x))
            ^~~~~~~
```
[R/SummarizedExperiment-methods.R:11:24:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L11) *warning:* **no visible global function definition for ‘metadata’**
```r
            rowMeta <- metadata(rowRanges(x))
                       ^~~~~~~~
```
[R/SummarizedExperiment-methods.R:11:33:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L11) *warning:* **no visible global function definition for ‘rowRanges’**
```r
            rowMeta <- metadata(rowRanges(x))
                                ^~~~~~~~~
```
[R/SummarizedExperiment-methods.R:14:13:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L14) *style:* **Variable or function name should be snake_case.**
```r
            rowMeta <- metadata(rowData(x))
            ^~~~~~~
```
[R/SummarizedExperiment-methods.R:14:24:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L14) *warning:* **no visible global function definition for ‘metadata’**
```r
            rowMeta <- metadata(rowData(x))
                       ^~~~~~~~
```
[R/SummarizedExperiment-methods.R:14:33:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L14) *warning:* **no visible global function definition for ‘rowData’, Did you mean 'rowMeta'?**
```r
            rowMeta <- metadata(rowData(x))
                                ^~~~~~~
```
[R/SummarizedExperiment-methods.R:17:9:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L17) *warning:* **no visible global function definition for ‘metadata<-’**
```r
        metadata(rowData(x)) <- rowMeta
        ^~~~~~~~
```
[R/SummarizedExperiment-methods.R:17:18:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L17) *warning:* **no visible global function definition for ‘rowData’, Did you mean 'rowMeta'?**
```r
        metadata(rowData(x)) <- rowMeta
                 ^~~~~~~
```
[R/SummarizedExperiment-methods.R:17:18:](https://github.com/steinbaugh/basejump.coercion/blob/aefd4fc40194eb72331d692b7e16d7298419e2e9/R/SummarizedExperiment-methods.R#L17) *warning:* **no visible global function definition for ‘rowData<-’**
```r
        metadata(rowData(x)) <- rowMeta
                 ^~~~~~~
```


What sort of errors did you get?


aaaa!


maybe another accidental revert?


I think this is actually making the docs unavailable ...


You should close off the fallback function for the time being because it does no accounting.


My bad I forgot to change the name.


That's right, however, in the rules, we specified that the action should be between 0 and 1. So unfortunately either solution is wrong: clipping is unfair to those who trained without, while not clipping is unfair to those who tried to follow the rules. We decided to implement the latter solution.

We will try to acknowledge the best solution without clipping separately (not yet decided how). We also got extra Google Cloud Credits ($400 for top 50 participants of Round 1), which hopefully will help to retrain the models at least partly.


Here you sent to only 1 person, only half of the value that was sent in this transaction. The splitter splits in 2 and sends half to each recipient. There are 2 recipients.


> а как он для строки работать будет?

Кто как будет работать для строки? Ни новый, ни старый варианты для строки не подходят.

> и у нас есть вариант отсечения цвета у строки

Ну и что? Вопрос в том, попадает ли цвет в буфер. Он туда может попасть только если цвет находился внутри имени.

Но, как я говорил, если оно так - то новый вариант тоже не должен работать. Т. к., по сути, делает то же самое, что и старый. Всё, что изменилось - теперь капитализируется первая буква имени, которое ставится в начало строки. Это не верно чисто по идеологически. По факту же выполняется то же самое, что и было. А значит либо тест был не верен, либо ошибка где-то много глубже.


FWIW, I like this approach as I think its a reasonable compromise between your thoughts and @gmriggs' desire to not pre-load unnecessary landblocks.


v


Perfect, thanks a lot!


fix checkbox indicator display (#3113)

Previews: documentation | landing | table


Here speaks the piss vinaigre: "Too many repetitions"  ;-)


i just checked on docker centos6 with python 2.6.6
print() works just fine without any "from future import print statement" statement.
but maybe a lower version of 2.6 could be problematic.


what feature is it | what's the feature


I think this is right:

```
if (required file not there)
    throw and die

Add needed file to args

if (optional file exists)
   Add optional file
```


I have renamed the `openjfx` plugin to `javafx`. If you're still using JavaFX components you need to keep it as a dependency to be compatible with Java 11.


See https://josm.openstreetmap.de/ticket/16912 for details


OK. I think I understand.

Adding basic behavior for a trigger mode should be easy. The simple way would be to use an input pin for the trigger (pulse). The state of the pin would be recorded on startup. Each time the pin goes from that state (high or low) to the other state, it would restart the oscillators. To ignore that pin, just connect it to ground.

Does that sound like it would work for your application?

Bob

> On Nov 1, 2018, at 10:03 AM, gabrielcichero <notifications@github.com> wrote:
>
> We may have the oscilators working freely, wich is nice use of them too.. but if i plug a pulse on the "sync", then, it restarts from cero for each incoming pulse..
>
> This is an idea that had in mind meanwhile i was working in your proyect, makes sense to you?
>
> I think that the technical name is "Clock Reset".
>
> Regards!
> Gabriel
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub <https://github.com/robertgallup/ArduinoDualLFO/commit/4ae520e46e658195dc59629cbdd20850d2ef74af#commitcomment-31137714>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AARqX3CIExNbzyhaLYPG_2Ms0-_oNgmSks5uqylYgaJpZM4YGhM1>.
>


A


Created multidev environment [rescue-x#oct-18](https://dashboard.pantheon.io/sites/c8430b75-4272-4aca-bfcd-206b12279315#oct-18).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://oct-18-rescue-x.pantheonsite.io/)


i borked it.  -____- in web browser it works but in  game not so much


testando


all good :)


ok


FALSE FLAG, FALSE FLAG!


this fix is not working for me... now any number just doesn't produce any output.


This is the initial comment for Activity 2


I was trying not to leave any gaps in the version history.  I was thinking about the public and not the folks around here who have been pulling from the master.


second comment


У нас в задании было задать размер изображения 200x200
или это нужно было его через фотошоп редактировать?

> 1 нояб. 2018 г., в 11:28, Maryia Kabash <notifications@github.com> написал(а):
>
> Картинки отображаются неправильно (сжатыми).
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or mute the thread.


hero