[R/aggregate-methods.R:122:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L122) *style:* **Variable or function name should be snake_case.**
```r
.aggregateFuns <- c("sum", "mean")
^~~~~~~~~~~~~~
```
[R/aggregate-methods.R:127:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L127) *style:* **Variable or function name should be snake_case.**
```r
.aggregateMessage <- function(groupings, fun) {
^~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:128:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L128) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
    assert_is_factor(groupings)
    ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:129:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L129) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
    assert_is_a_string(fun)
    ^~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:153:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L153) *warning:* **no visible global function definition for ‘assertHasValidDimnames’**
```r
        assertHasValidDimnames(object)
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:154:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L154) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
        assert_is_factor(groupings)
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:155:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L155) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(object), names(groupings))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:156:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L156) *warning:* **no visible global function definition for ‘assertAllAreValidNames’**
```r
        assertAllAreValidNames(levels(groupings))
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:158:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L158) *warning:* **no visible global function definition for ‘.aggregateMessage’**
```r
        .aggregateMessage(groupings, fun = fun)
        ^~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:220:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L220) *warning:* **no visible global function definition for ‘assertHasValidDimnames’**
```r
        assertHasValidDimnames(object)
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:221:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L221) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
        assert_is_factor(groupings)
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:222:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L222) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(object), names(groupings))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:223:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L223) *warning:* **no visible global function definition for ‘assertAllAreValidNames’**
```r
        assertAllAreValidNames(levels(groupings))
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:225:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L225) *warning:* **no visible global function definition for ‘.aggregateMessage’**
```r
        .aggregateMessage(groupings, fun = fun)
        ^~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:281:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L281) *warning:* **no visible global function definition for ‘assertHasValidDimnames’**
```r
        assertHasValidDimnames(object)
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:282:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L282) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(col)
        ^~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:286:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L286) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(col, colnames(rowData(object)))
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:286:40:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L286) *warning:* **no visible global function definition for ‘rowData’**
```r
        assert_is_subset(col, colnames(rowData(object)))
                                       ^~~~~~~
```
[R/aggregate-methods.R:287:22:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L287) *warning:* **no visible global function definition for ‘rowData’**
```r
        groupings <- rowData(object)[[col]]
                     ^~~~~~~
```
[R/aggregate-methods.R:288:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L288) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
        assert_is_factor(groupings)
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:289:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L289) *warning:* **no visible global function definition for ‘assertAllAreValidNames’**
```r
        assertAllAreValidNames(levels(groupings))
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:312:36:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L312) *warning:* **no visible global function definition for ‘emptyRanges’**
```r
            args[["rowRanges"]] <- emptyRanges(names = rownames)
                                   ^~~~~~~~~~~
```
[R/aggregate-methods.R:314:34:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L314) *warning:* **no visible global function definition for ‘DataFrame’**
```r
            args[["rowData"]] <- DataFrame(row.names = rownames)
                                 ^~~~~~~~~
```
[R/aggregate-methods.R:316:30:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L316) *warning:* **no visible binding for global variable ‘SummarizedExperiment’**
```r
        se <- do.call(what = SummarizedExperiment, args = args)
                             ^~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:337:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L337) *warning:* **no visible global function definition for ‘assertHasValidDimnames’**
```r
        assertHasValidDimnames(object)
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:338:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L338) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(col)
        ^~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:342:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L342) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(col, colnames(colData(object)))
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:342:40:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L342) *warning:* **no visible global function definition for ‘colData’**
```r
        assert_is_subset(col, colnames(colData(object)))
                                       ^~~~~~~
```
[R/aggregate-methods.R:343:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L343) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(col, colnames(sampleData(object)))
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:344:22:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L344) *warning:* **no visible global function definition for ‘colData’**
```r
        groupings <- colData(object)[[col]]
                     ^~~~~~~
```
[R/aggregate-methods.R:345:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L345) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
        assert_is_factor(groupings)
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:346:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L346) *warning:* **no visible global function definition for ‘assertAllAreValidNames’**
```r
        assertAllAreValidNames(levels(groupings))
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:364:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L364) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- sampleData(object)[["aggregate"]]
        ^~~~~~~~~~~
```
[R/aggregate-methods.R:365:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L365) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
        assert_is_factor(sampleNames)
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:366:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L366) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- levels(sampleNames)
        ^~~~~~~~~~~
```
[R/aggregate-methods.R:367:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L367) *style:* **Variable or function name should be snake_case.**
```r
        sampleData <- DataFrame(
        ^~~~~~~~~~
```
[R/aggregate-methods.R:378:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L378) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- setdiff(interestingGroups(object), "sampleName")
        ^~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:379:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L379) *style:* **Variable or function name should be snake_case.**
```r
        sampleData <- sampleData(object) %>%
        ^~~~~~~~~~
```
[R/aggregate-methods.R:389:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L389) *warning:* **no visible global function definition for ‘assertHasRownames’**
```r
        assertHasRownames(sampleData)
        ^~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:397:20:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L397) *warning:* **no visible global function definition for ‘rowRanges’**
```r
            args[["rowRanges"]] <- rowRanges(object)
                   ^~~~~~~~~
```
[R/aggregate-methods.R:399:20:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L399) *warning:* **no visible global function definition for ‘rowData’**
```r
            args[["rowData"]] <- rowData(object)
                   ^~~~~~~
```
[R/aggregate-methods.R:401:30:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L401) *warning:* **no visible binding for global variable ‘SummarizedExperiment’**
```r
        se <- do.call(what = SummarizedExperiment, args = args)
                             ^~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:402:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L402) *warning:* **no visible global function definition for ‘metadata’**
```r
        metadata(se)[["aggregate"]] <- TRUE
        ^~~~~~~~
```
[R/aggregate-methods.R:402:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L402) *warning:* **no visible global function definition for ‘metadata<-’**
```r
        metadata(se)[["aggregate"]] <- TRUE
        ^~~~~~~~
```
[R/aggregate-methods.R:427:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L427) *style:* **Variable or function name should be snake_case.**
```r
        colData <- colData(object)
        ^~~~~~~
```
[R/aggregate-methods.R:428:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L428) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(c("sampleID", "aggregate"), colnames(colData))
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:429:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L429) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
        assert_is_factor(colData[["aggregate"]])
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:463:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L463) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(names(groupings), colnames(object))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:464:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L464) *warning:* **no visible global function definition for ‘colData<-’, Did you mean 'colData'?**
```r
        colData(object)[["aggregate"]] <- groupings
        ^~~~~~~
```
[R/aggregate-methods.R:472:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L472) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(rse, "RangedSummarizedExperiment")
        ^~~~~~~~~~~~~~~~
```
[R/aggregate-methods.R:475:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregate-methods.R#L475) *style:* **Variable or function name should be snake_case.**
```r
        colData <- colData(rse)
        ^~~~~~~
```
[R/aggregateCellsToSamples-methods.R:28:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregateCellsToSamples-methods.R#L28) *warning:* **no visible global function definition for ‘colData’**
```r
        colData(rse)[["aggregate"]] <- cell2sample(object)
        ^~~~~~~
```
[R/aggregateCellsToSamples-methods.R:28:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregateCellsToSamples-methods.R#L28) *warning:* **no visible global function definition for ‘colData<-’**
```r
        colData(rse)[["aggregate"]] <- cell2sample(object)
        ^~~~~~~
```
[R/aggregateCellsToSamples-methods.R:28:40:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/aggregateCellsToSamples-methods.R#L28) *warning:* **no visible global function definition for ‘cell2sample’**
```r
        colData(rse)[["aggregate"]] <- cell2sample(object)
                                       ^~~~~~~~~~~
```
[R/cell2sample-methods.R:33:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/cell2sample-methods.R#L33) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset("sampleID", colnames(colData(object)))
        ^~~~~~~~~~~~~~~~
```
[R/cell2sample-methods.R:36:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/cell2sample-methods.R#L36) *style:* **Variable or function name should be snake_case.**
```r
        colData <- colData(object)
        ^~~~~~~
```
[R/cell2sample-methods.R:40:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/cell2sample-methods.R#L40) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
            assert_is_factor(sample)
            ^~~~~~~~~~~~~~~~
```
[R/combine-methods.R:80:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L80) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(class(x), class(y))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/combine-methods.R:91:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L91) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(x), rownames(y))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/combine-methods.R:94:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L94) *warning:* **no visible global function definition for ‘assert_are_disjoint_sets’**
```r
        assert_are_disjoint_sets(colnames(x), colnames(y))
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/combine-methods.R:124:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L124) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
            assert_are_identical(rowRanges(x), rowRanges(y))
            ^~~~~~~~~~~~~~~~~~~~
```
[R/combine-methods.R:125:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L125) *style:* **Variable or function name should be snake_case.**
```r
            rowRanges <- rowRanges(x)
            ^~~~~~~~~
```
[R/combine-methods.R:126:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L126) *style:* **Variable or function name should be snake_case.**
```r
            rowData <- NULL
            ^~~~~~~
```
[R/combine-methods.R:128:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L128) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
            assert_are_identical(rowData(x), rowData(y))
            ^~~~~~~~~~~~~~~~~~~~
```
[R/combine-methods.R:129:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L129) *style:* **Variable or function name should be snake_case.**
```r
            rowData <- rowData(x)
            ^~~~~~~
```
[R/combine-methods.R:130:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L130) *style:* **Variable or function name should be snake_case.**
```r
            rowRanges <- NULL
            ^~~~~~~~~
```
[R/combine-methods.R:134:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L134) *warning:* **no visible global function definition for ‘assert_are_set_equal’**
```r
        assert_are_set_equal(colnames(colData(x)), colnames(colData(y)))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/combine-methods.R:136:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L136) *style:* **Variable or function name should be snake_case.**
```r
        colData <- rbind(
        ^~~~~~~
```
[R/combine-methods.R:155:30:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/combine-methods.R#L155) *warning:* **no visible binding for global variable ‘makeSummarizedExperiment’**
```r
        se <- do.call(what = makeSummarizedExperiment, args = args)
                             ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertGenesToSymbols-methods.R:59:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertGenesToSymbols-methods.R#L59) *warning:* **no visible global function definition for ‘assert_all_are_non_missing_nor_empty_character’**
```r
        assert_all_are_non_missing_nor_empty_character(object)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertGenesToSymbols-methods.R:60:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertGenesToSymbols-methods.R#L60) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(gene2symbol, "Gene2Symbol")
        ^~~~~~~~~~~~~~~~
```
[R/convertGenesToSymbols-methods.R:121:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertGenesToSymbols-methods.R#L121) *style:* **Variable and function names should not be longer than 30 characters.**
```r
convertGenesToSymbols.sparseMatrix <- convertGenesToSymbols.matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertGenesToSymbols-methods.R:121:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertGenesToSymbols-methods.R#L121) *style:* **Variable or function name should be snake_case.**
```r
convertGenesToSymbols.sparseMatrix <- convertGenesToSymbols.matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertGenesToSymbols-methods.R:136:16:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertGenesToSymbols-methods.R#L136) *warning:* **no visible global function definition for ‘Gene2Symbol’**
```r
        g2s <- Gene2Symbol(object)
               ^~~~~~~~~~~
```
[R/convertGenesToSymbols-methods.R:138:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertGenesToSymbols-methods.R#L138) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**
```r
        assert_has_no_duplicates(symbols)
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertGenesToSymbols-methods.R:167:16:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertGenesToSymbols-methods.R#L167) *warning:* **no visible global function definition for ‘Gene2Symbol’**
```r
        g2s <- Gene2Symbol(object)
               ^~~~~~~~~~~
```
[R/convertGenesToSymbols-methods.R:172:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertGenesToSymbols-methods.R#L172) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**
```r
        assert_has_no_duplicates(g2s[["geneID"]])
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertSampleIDsToNames-methods.R:22:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertSampleIDsToNames-methods.R#L22) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- sampleNames(object)
        ^~~~~~~~~~~
```
[R/convertSampleIDsToNames-methods.R:30:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertSampleIDsToNames-methods.R#L30) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**
```r
            assert_has_no_duplicates(colnames)
            ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertSampleIDsToNames-methods.R:32:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertSampleIDsToNames-methods.R#L32) *warning:* **no visible global function definition for ‘colData’**
```r
            colData(object)[["sampleName"]] <- NULL
            ^~~~~~~
```
[R/convertSampleIDsToNames-methods.R:32:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertSampleIDsToNames-methods.R#L32) *warning:* **no visible global function definition for ‘colData<-’**
```r
            colData(object)[["sampleName"]] <- NULL
            ^~~~~~~
```
[R/convertTranscriptsToGenes-methods.R:65:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertTranscriptsToGenes-methods.R#L65) *warning:* **no visible global function definition for ‘assert_all_are_non_missing_nor_empty_character’**
```r
        assert_all_are_non_missing_nor_empty_character(object)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertTranscriptsToGenes-methods.R:66:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertTranscriptsToGenes-methods.R#L66) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**
```r
        assert_has_no_duplicates(object)
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertTranscriptsToGenes-methods.R:67:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertTranscriptsToGenes-methods.R#L67) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(tx2gene, "Tx2Gene")
        ^~~~~~~~~~~~~~~~
```
[R/convertTranscriptsToGenes-methods.R:102:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertTranscriptsToGenes-methods.R#L102) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(aggregate)
        ^~~~~~~~~~~~~~~~
```
[R/convertTranscriptsToGenes-methods.R:111:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertTranscriptsToGenes-methods.R#L111) *warning:* **no visible global function definition for ‘aggregateRows’**
```r
            aggregateRows(object, groupings = t2g)
            ^~~~~~~~~~~~~
```
[R/convertTranscriptsToGenes-methods.R:130:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertTranscriptsToGenes-methods.R#L130) *style:* **Variable and function names should not be longer than 30 characters.**
```r
convertTranscriptsToGenes.sparseMatrix <- convertTranscriptsToGenes.matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertTranscriptsToGenes-methods.R:130:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertTranscriptsToGenes-methods.R#L130) *style:* **Variable or function name should be snake_case.**
```r
convertTranscriptsToGenes.sparseMatrix <- convertTranscriptsToGenes.matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertTranscriptsToGenes-methods.R:147:16:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/convertTranscriptsToGenes-methods.R#L147) *warning:* **no visible global function definition for ‘Tx2Gene’**
```r
        t2g <- Tx2Gene(object)
               ^~~~~~~
```
[R/counts-methods.R:38:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/counts-methods.R#L38) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset("counts", assayNames(object))
        ^~~~~~~~~~~~~~~~
```
[R/counts-methods.R:38:36:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/counts-methods.R#L38) *warning:* **no visible global function definition for ‘assayNames’**
```r
        assert_is_subset("counts", assayNames(object))
                                   ^~~~~~~~~~
```
[R/counts-methods.R:39:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/counts-methods.R#L39) *warning:* **no visible global function definition for ‘assays’**
```r
        assays(object)[["counts"]]
        ^~~~~~
```
[R/counts-methods.R:58:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/counts-methods.R#L58) *warning:* **no visible global function definition for ‘assays’**
```r
        assays(object)[["counts"]] <- value
        ^~~~~~
```
[R/counts-methods.R:58:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/counts-methods.R#L58) *warning:* **no visible global function definition for ‘assays<-’**
```r
        assays(object)[["counts"]] <- value
        ^~~~~~
```
[R/detectLanes.R:13:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectLanes.R#L13) *style:* **Variable or function name should be snake_case.**
```r
detectLanes <- function(
^~~~~~~~~~~
```
[R/detectLanes.R:17:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectLanes.R#L17) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(object)
    ^~~~~~~~~~~~~~~~~~~
```
[R/detectLanes.R:18:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectLanes.R#L18) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
    assert_is_a_string(lanePattern)
    ^~~~~~~~~~~~~~~~~~
```
[R/detectLanes.R:18:24:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectLanes.R#L18) *warning:* **no visible binding for global variable ‘lanePattern’**
```r
    assert_is_a_string(lanePattern)
                       ^~~~~~~~~~~
```
[R/detectLanes.R:21:20:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectLanes.R#L21) *warning:* **no visible global function definition for ‘str_match’**
```r
        as.integer(str_match(object, pattern)[, 2L])
                   ^~~~~~~~~
```
[R/detectOrganism.R:51:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectOrganism.R#L51) *style:* **Variable or function name should be snake_case.**
```r
detectOrganism <- function(object) {
^~~~~~~~~~~~~~
```
[R/detectOrganism.R:52:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectOrganism.R#L52) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(object)
    ^~~~~~~~~~~~~~~~~~~
```
[R/detectOrganism.R:60:14:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectOrganism.R#L60) *warning:* **no visible global function definition for ‘.detectOrganism.string’**
```r
        x <- .detectOrganism.string(object[[i]])
             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/detectOrganism.R:74:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectOrganism.R#L74) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(object)
        ^~~~~~~~~~~~~~~~~~
```
[R/detectOrganism.R:82:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/detectOrganism.R#L82) *warning:* **no visible global function definition for ‘assert_is_tbl_df’**
```r
        assert_is_tbl_df(data)
        ^~~~~~~~~~~~~~~~
```
[R/geometricMean-methods.R:50:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/geometricMean-methods.R#L50) *style:* **Variable or function name should be snake_case.**
```r
        removeNA = TRUE,
        ^~~~~~~~
```
[R/geometricMean-methods.R:51:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/geometricMean-methods.R#L51) *style:* **Variable or function name should be snake_case.**
```r
        zeroPropagate = FALSE
        ^~~~~~~~~~~~~
```
[R/geometricMean-methods.R:53:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/geometricMean-methods.R#L53) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(removeNA)
        ^~~~~~~~~~~~~~~~
```
[R/geometricMean-methods.R:54:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/geometricMean-methods.R#L54) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(zeroPropagate)
        ^~~~~~~~~~~~~~~~
```
[R/geometricMean-methods.R:113:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/geometricMean-methods.R#L113) *style:* **Variable or function name should be snake_case.**
```r
geometricMean.sparseMatrix <- geometricMean.matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/logRatio-methods.R:34:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/logRatio-methods.R#L34) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(base)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/logRatio-methods.R:36:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/logRatio-methods.R#L36) *warning:* **no visible global function definition for ‘assert_all_are_positive’**
```r
        assert_all_are_positive(base)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/logRatio-methods.R:57:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/logRatio-methods.R#L57) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(base)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/logRatio-methods.R:59:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/logRatio-methods.R#L59) *warning:* **no visible global function definition for ‘assert_all_are_positive’**
```r
        assert_all_are_positive(base)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeSingleCellExperiment.R:25:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSingleCellExperiment.R#L25) *style:* **Variable or function name should be snake_case.**
```r
makeSingleCellExperiment <- function(
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeSingleCellExperiment.R:27:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSingleCellExperiment.R#L27) *style:* **Variable or function name should be snake_case.**
```r
    rowRanges,
    ^~~~~~~~~
```
[R/makeSingleCellExperiment.R:28:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSingleCellExperiment.R#L28) *style:* **Variable or function name should be snake_case.**
```r
    colData,
    ^~~~~~~
```
[R/makeSingleCellExperiment.R:30:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSingleCellExperiment.R#L30) *style:* **Variable or function name should be snake_case.**
```r
    transgeneNames = NULL,
    ^~~~~~~~~~~~~~
```
[R/makeSingleCellExperiment.R:31:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSingleCellExperiment.R#L31) *style:* **Variable or function name should be snake_case.**
```r
    spikeNames = NULL
    ^~~~~~~~~~
```
[R/makeSingleCellExperiment.R:56:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSingleCellExperiment.R#L56) *warning:* **no visible global function definition for ‘isSpike<-’**
```r
            isSpike(sce, spikeNames[[i]]) <- spikeNames[[i]]
            ^~~~~~~
```
[R/makeSummarizedExperiment.R:104:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L104) *style:* **Variable or function name should be snake_case.**
```r
makeSummarizedExperiment <- function(
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:106:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L106) *style:* **Variable or function name should be snake_case.**
```r
    rowRanges = NULL,  # recommended
    ^~~~~~~~~
```
[R/makeSummarizedExperiment.R:107:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L107) *style:* **Variable or function name should be snake_case.**
```r
    rowData = NULL,    # not recommended
    ^~~~~~~
```
[R/makeSummarizedExperiment.R:108:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L108) *style:* **Variable or function name should be snake_case.**
```r
    colData = NULL,
    ^~~~~~~
```
[R/makeSummarizedExperiment.R:110:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L110) *style:* **Variable or function name should be snake_case.**
```r
    transgeneNames = NULL,
    ^~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:111:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    spikeNames = NULL
    ^~~~~~~~~~
```
[R/makeSummarizedExperiment.R:118:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L118) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(rowRanges, classes = c("GRanges", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:119:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L119) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(rowData, classes = c("DataFrame", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:122:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L122) *warning:* **no visible global function definition for ‘assert_is_null’**
```r
        assert_is_null(rowData)
        ^~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:124:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L124) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(colData, classes = c("DataFrame", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:125:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L125) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(metadata, classes = c("list", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:126:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L126) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(transgeneNames, classes = c("character", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:127:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L127) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(spikeNames, classes = c("character", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:136:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L136) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
    assert_are_identical(names(assays)[[1L]], "counts")
    ^~~~~~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:141:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L141) *warning:* **no visible global function definition for ‘assertHasValidDimnames’**
```r
    assertHasValidDimnames(assay)
    ^~~~~~~~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:148:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L148) *style:* **Variable or function name should be snake_case.**
```r
    mcolsNames <- NULL
    ^~~~~~~~~~
```
[R/makeSummarizedExperiment.R:155:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L155) *warning:* **no visible global function definition for ‘assert_are_intersecting_sets’**
```r
        assert_are_intersecting_sets(rownames(assay), names(rowRanges))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:156:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L156) *style:* **Variable or function name should be snake_case.**
```r
        mcolsNames <- names(mcols(rowRanges))
        ^~~~~~~~~~
```
[R/makeSummarizedExperiment.R:156:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L156) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        mcolsNames <- names(mcols(rowRanges))
        ^~~~~
```
[R/makeSummarizedExperiment.R:160:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L160) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
            assert_is_subset(transgeneNames, setdiff)
            ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:161:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L161) *style:* **Variable or function name should be snake_case.**
```r
            transgeneRanges <- emptyRanges(
            ^~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:166:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L166) *style:* **Variable or function name should be snake_case.**
```r
            rowRanges <- suppressWarnings(c(transgeneRanges, rowRanges))
            ^~~~~~~~~
```
[R/makeSummarizedExperiment.R:171:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L171) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
            assert_is_subset(spikeNames, setdiff)
            ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:172:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L172) *style:* **Variable or function name should be snake_case.**
```r
            spikeRanges <- emptyRanges(
            ^~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:177:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L177) *style:* **Variable or function name should be snake_case.**
```r
            rowRanges <- suppressWarnings(c(spikeRanges, rowRanges))
            ^~~~~~~~~
```
[R/makeSummarizedExperiment.R:181:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L181) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(rownames(assay), rownames(rowData))
        ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:182:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L182) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- rowData[rownames(assay), , drop = FALSE]
        ^~~~~~~
```
[R/makeSummarizedExperiment.R:185:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L185) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- emptyRanges(names = rownames(assay))
        ^~~~~~~~~
```
[R/makeSummarizedExperiment.R:185:22:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L185) *warning:* **no visible global function definition for ‘emptyRanges’**
```r
        rowRanges <- emptyRanges(names = rownames(assay))
                     ^~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:194:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L194) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(data, "DataFrame"))
    ^~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:213:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L213) *warning:* **no visible global function definition for ‘assert_has_names’**
```r
        assert_has_names(rowRanges)
        ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:214:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L214) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(rownames(assay), names(rowRanges))
        ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:215:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L215) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- rowRanges[rownames(assay)]
        ^~~~~~~~~
```
[R/makeSummarizedExperiment.R:217:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L217) *warning:* **no visible global function definition for ‘assertHasRownames’**
```r
        assertHasRownames(rowData)
        ^~~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:218:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L218) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(rownames(assay), rownames(rowData))
        ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:219:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L219) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- rowData[rownames(assay), , drop = FALSE]
        ^~~~~~~
```
[R/makeSummarizedExperiment.R:224:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L224) *style:* **Variable or function name should be snake_case.**
```r
        colData <- DataFrame(row.names = colnames(assay))
        ^~~~~~~
```
[R/makeSummarizedExperiment.R:224:20:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L224) *warning:* **no visible global function definition for ‘DataFrame’**
```r
        colData <- DataFrame(row.names = colnames(assay))
                   ^~~~~~~~~
```
[R/makeSummarizedExperiment.R:226:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L226) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
    assert_is_subset(colnames(assay), rownames(colData))
    ^~~~~~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:227:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L227) *style:* **Variable or function name should be snake_case.**
```r
    colData <- colData[colnames(assay), , drop = FALSE]
    ^~~~~~~
```
[R/makeSummarizedExperiment.R:232:25:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L232) *warning:* **no visible global function definition for ‘realpath’**
```r
    metadata[["wd"]] <- realpath(".")
                        ^~~~~~~~
```
[R/makeSummarizedExperiment.R:233:34:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L233) *warning:* **no visible global function definition for ‘session_info’, Did you mean 'sessionInfo'?**
```r
    metadata[["sessionInfo"]] <- session_info(include_base = TRUE)
                                 ^~~~~~~~~~~~
```
[R/makeSummarizedExperiment.R:247:26:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/makeSummarizedExperiment.R#L247) *warning:* **no visible binding for global variable ‘SummarizedExperiment’**
```r
    se <- do.call(what = SummarizedExperiment, args = args)
                         ^~~~~~~~~~~~~~~~~~~~
```
[R/mapCellsToSamples.R:24:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapCellsToSamples.R#L24) *style:* **Variable or function name should be snake_case.**
```r
mapCellsToSamples <- function(cells, samples) {
^~~~~~~~~~~~~~~~~
```
[R/mapCellsToSamples.R:25:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapCellsToSamples.R#L25) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(cells)
    ^~~~~~~~~~~~~~~~~~~
```
[R/mapCellsToSamples.R:26:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapCellsToSamples.R#L26) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**
```r
    assert_has_no_duplicates(cells)
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mapCellsToSamples.R:27:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapCellsToSamples.R#L27) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(samples, c("character", "factor"))
    ^~~~~~~~~~~~~~~~
```
[R/mapCellsToSamples.R:39:41:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapCellsToSamples.R#L39) *warning:* **no visible binding for global variable ‘barcodePattern’**
```r
        pattern <- paste0("^(", sample, barcodePattern)
                                        ^~~~~~~~~~~~~~
```
[R/mapCellsToSamples.R:57:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapCellsToSamples.R#L57) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
    assert_are_identical(length(cells), length(cell2sample))
    ^~~~~~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:69:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L69) *style:* **Variable or function name should be snake_case.**
```r
.mapGenes <- function(object, genes, strict = TRUE) {
^~~~~~~~~
```
[R/mapGenes-methods.R:70:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L70) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "Gene2Symbol")
    ^~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:72:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L72) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(genes)
    ^~~~~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:73:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L73) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
    assert_is_non_empty(genes)
    ^~~~~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:74:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L74) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
    assert_is_a_bool(strict)
    ^~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:80:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L80) *warning:* **no visible global function definition for ‘assertAllAreUniqueGeneNames’**
```r
        assertAllAreUniqueGeneNames(object, genes)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:109:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L109) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
    assert_is_non_empty(mapped)
    ^~~~~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:150:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L150) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(g2s), rownames(object))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:209:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L209) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(g2s), rownames(object))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/mapGenes-methods.R:268:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/mapGenes-methods.R#L268) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(g2s), rownames(object))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/matchInterestingGroups.R:18:1:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/matchInterestingGroups.R#L18) *style:* **Variable or function name should be snake_case.**
```r
matchInterestingGroups <- function(object, interestingGroups = NULL) {
^~~~~~~~~~~~~~~~~~~~~~
```
[R/matchInterestingGroups.R:18:44:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/matchInterestingGroups.R#L18) *style:* **Variable or function name should be snake_case.**
```r
matchInterestingGroups <- function(object, interestingGroups = NULL) {
                                           ^~~~~~~~~~~~~~~~~
```
[R/matchInterestingGroups.R:20:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/matchInterestingGroups.R#L20) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- interestingGroups(object, check = FALSE)
        ^~~~~~~~~~~~~~~~~
```
[R/matchInterestingGroups.R:25:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/matchInterestingGroups.R#L25) *style:* **Variable or function name should be snake_case.**
```r
            interestingGroups <- "sampleName"
            ^~~~~~~~~~~~~~~~~
```
[R/matchInterestingGroups.R:28:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/matchInterestingGroups.R#L28) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(object) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/matchInterestingGroups.R:30:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/matchInterestingGroups.R#L30) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(interestingGroups)
    ^~~~~~~~~~~~~~~~~~~
```
[R/matchInterestingGroups.R:31:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/matchInterestingGroups.R#L31) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
    assert_is_non_empty(interestingGroups)
    ^~~~~~~~~~~~~~~~~~~
```
[R/meltCounts-methods.R:32:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/meltCounts-methods.R#L32) *style:* **Variable or function name should be snake_case.**
```r
        nonzeroGenes = FALSE,
        ^~~~~~~~~~~~
```
[R/meltCounts-methods.R:36:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/meltCounts-methods.R#L36) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/meltCounts-methods.R:37:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/meltCounts-methods.R#L37) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(nonzeroGenes)
        ^~~~~~~~~~~~~~~~
```
[R/meltCounts-methods.R:41:19:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/meltCounts-methods.R#L41) *warning:* **no visible global function definition for ‘assays’, Did you mean 'assay'?**
```r
        counts <- assays(object)[[assay]]
                  ^~~~~~
```
[R/meltCounts-methods.R:42:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/meltCounts-methods.R#L42) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
        assert_is_non_empty(counts)
        ^~~~~~~~~~~~~~~~~~~
```
[R/meltCounts-methods.R:61:13:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/meltCounts-methods.R#L61) *warning:* **no visible global function definition for ‘assert_is_function’**
```r
            assert_is_function(fun)
            ^~~~~~~~~~~~~~~~~~
```
[R/meltCounts-methods.R:66:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/meltCounts-methods.R#L66) *style:* **Variable or function name should be snake_case.**
```r
        sampleData <- sampleData(object) %>%
        ^~~~~~~~~~
```
[R/metrics-methods.R:81:17:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/metrics-methods.R#L81) *warning:* **no visible global function definition for ‘colData’**
```r
        data <- colData(object)
                ^~~~~~~
```
[R/metrics-methods.R:127:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/metrics-methods.R#L127) *warning:* **no visible global function definition for ‘assert_is_function’**
```r
        assert_is_function(FUN)
        ^~~~~~~~~~~~~~~~~~
```
[R/metrics-methods.R:129:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/metrics-methods.R#L129) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(metrics, "grouped_df")
        ^~~~~~~~~~~~~~~~
```
[R/metrics-methods.R:139:21:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/metrics-methods.R#L139) *warning:* **no visible global function definition for ‘select’**
```r
            data <- select(metrics, matches(pattern))
                    ^~~~~~
```
[R/metrics-methods.R:139:37:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/metrics-methods.R#L139) *warning:* **no visible global function definition for ‘matches’, Did you mean 'match'?**
```r
            data <- select(metrics, matches(pattern))
                                    ^~~~~~~
```
[R/metrics-methods.R:142:21:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/metrics-methods.R#L142) *warning:* **no visible global function definition for ‘select_if’**
```r
            data <- select_if(metrics, is.numeric)
                    ^~~~~~~~~
```
[R/metrics-methods.R:144:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/metrics-methods.R#L144) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
        assert_is_non_empty(data)
        ^~~~~~~~~~~~~~~~~~~
```
[R/metrics-methods.R:145:9:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/metrics-methods.R#L145) *style:* **Variable or function name should be snake_case.**
```r
        sampleData <- sampleData(object) %>%
        ^~~~~~~~~~
```
[R/microplate.R:31:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/microplate.R#L31) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
    assertIsAnImplicitInteger(plates)
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/microplate.R:33:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/microplate.R#L33) *warning:* **no visible global function definition for ‘assert_all_are_positive’**
```r
    assert_all_are_positive(plates)
    ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/microplate.R:35:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/microplate.R#L35) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
    assertIsAnImplicitInteger(wells)
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/microplate.R:37:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/microplate.R#L37) *warning:* **no visible global function definition for ‘assert_all_are_positive’**
```r
    assert_all_are_positive(wells)
    ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/microplate.R:38:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/microplate.R#L38) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
    assert_is_subset(wells, c(96L, 384L))
    ^~~~~~~~~~~~~~~~
```
[R/microplate.R:40:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/microplate.R#L40) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
    assertIsAnImplicitInteger(controls)
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/microplate.R:42:5:](https://github.com/steinbaugh/basejump.experiment/blob/1f82906d1062565cb1568f31a2ac4f643ecda4dc/R/microplate.R#L42) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
    assert_all_are_non_negative(controls)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Ben Commit


Тобто? А як тоді ввести число?


Good discussion! The only mistake I see is that field labels should not contain spaces, and I'm doing my part to fix annotators, I mean tools (sorry, used to every tool being an 'annotator' from other projects!) - so that the labels contain single words, if necessary using underscore or dash to make this be true.

Cheers!


Lesson 2


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @mcs07 was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)


I understand... thank you!


@margar00 I added one more method.


cool 👍


Could we add a description to this method, please.


Lade till userCategory


Need to take care about FieldOutput operation mode. In this mode fields are processed by encoder separately (one task per field if I remember correctly). Current logic will lead to situation when only 1st field will have correct DTS.


Organise imports


Works fine for me... Are you sure that your login and password for the tracker are set correctly in Logimgr plugin?...


Consider checking whether elementA is already within `<code>`-tags as there is no need to apply them multiple times. `elementA.tagName`


@korli for whatever reason this doesn't seem to work: https://build.haiku-os.org/buildmaster/master/x86_gcc2/?buildrunDir=&viewMode=expanded


Done. In the future I would like to automatically upload tagged releases to pypi using the Jenkinsfile


Please, dont commit these console logs. If you have already commited and pushed them, promptly delete them in the following commits.


Second change


Refer to commit 'template' that broke everything


/**
 * Course:      Data Structures and Algorithms for CL III - WS1819
 * Assignment:  (lab 0, exercise 1.1)
 * Author:      (Yisa Salawu)
 */

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;

public class Assignment0 {

	public static void main(String[] args) {
		// used Strings to store information
		String lastName = "";
		String firstName = "";
		String id = "";
		String email = "";

		// input reader // bufferedReader to read in input

        BufferedReader br = new BufferedReader(new InputStreamReader(System.in));

		// ask for information and safe it in the strings
		System.out.println("Last name");
		try{
            lastName = br.readLine(); // Read from user's input
            }
		 catch(Exception e){
	            System.out.println("Wrong input");
	            e.printStackTrace();
	        }

		System.out.println("First name(s)");
		try{
            firstName = br.readLine(); // Read from user's input
            }
		 catch(Exception e){
	            System.out.println("Wrong input");
	            e.printStackTrace();
	        }

		System.out.println("Student ID (Matrikelnr.)");
		try{
            id = br.readLine(); // Read from user's input
            }
		 catch(Exception e){
	            System.out.println("Wrong input");
	            e.printStackTrace();
	        }
		System.out.println("Email address");
		try{
            email = br.readLine(); // Read from user's input
            }
		 catch(Exception e){
	            System.out.println("Wrong input");
	            e.printStackTrace();
	        }

		// close the scanner
		try {
			br.close();
		} catch (IOException e) {
			System.out.println("Error while closing the BufferedReader");
		}

		// output on screen
		System.out.println(lastName);
		System.out.println(firstName);
		System.out.println(id);
		System.out.println(email);

	}

}


Hi Yasmin,

Please open GitHub Desktop and select Pull from the Repository menu, then check what the folder for the King's College Cambridge files is called on your computer. If it begins with "KI" rather than "Ki" then rename it so that the i is lowercase.

This is a problem caused by Apple Macs being case-insensitive with regard to filenames (including folders) whereas GitHub runs on Linux which is case-sensitive.

Andrew.


It's true... C *does* provide all the rope to hang yourself!


Are you OK, bro? 😟


@Tk-Glitch
Well I was actually thinking to reduce the complexity. Keep separate patches per file altered. Most of the churn just in 2 files: **wined3d_private.h** and **buffer.c**. In the current wine-pba patchset (original 10 files) the wined3d **buffer.c** file is re-altered 5 times! A total nightmare for rebasing work! So I was just thinking about avoiding this. git diff can easily automate all of this (since it can compare revisions of individual files).

Obviously @acomminos has obviously pushed the patchset as far he feels he can. Most folks have moved on to DXVK anyway I guess...

The wine-pba patchset is too invasive to go into mainline, without major refactoring ( according to @zfigura ). I am sure Henri would give one of his thoughtful frowns - if anyone suggested this to him! :-)


Well written code. It worked fine for me.


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/c494835f-df5d-48e5-9264-1d09d32f77c2?env_id=ibm%3Ayp%3Aeu-gb "watsonwork-pipeline-bot"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/6a68fc6a-d059-4a0e-8702-f98f3c5fd5d5?env_id=ibm%3Ayp%3Aeu-gb "watsonwork-pipeline-bot") deployed [watsonwork-pipeline-bot](https://github.com/WilliamHolmes/watsonwork-pipeline-bot/releases/tag/deploy-ibm-yp-eu-gb-holmesw-ie.ibm.com-dev-20181031-142651 "deploy-ibm-yp-eu-gb-holmesw-ie.ibm.com-dev-20181031-142651") to [dev](https://console.bluemix.net/apps/f3173b48-637f-4fc1-b742-8468b99643a4?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:holmesw@ie.ibm.com:dev"), including this commit


This must be merged after https://github.com/cross-solution/YAWIK/pull/495

Otherwise Travis will fail

https://i.imgur.com/P5diiF4.png