[R/AllClasses.R:1:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L1) *style:* **Variable or function name should be snake_case.**
```r
validateS4 <- function(...) {
^~~~~~~~~~
```
[R/AllClasses.R:66:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L66) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L70) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink <- slot(object, "lfcShrink")
        ^~~~~~~~~
```
[R/AllClasses.R:71:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:76:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L76) *style:* **Commented code should be removed.**
```r
        #         y = colnames(rowData(data))
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/AllClasses.R:79:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L79) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:107:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L107) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:163:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:166:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L166) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(results)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/AllClasses.R:167:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L167) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:171:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L171) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:173:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L173) *style:* **Variable or function name should be snake_case.**
```r
        degMatch <- removeNA(str_match(
        ^~~~~~~~
```
[R/AllClasses.R:177:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/AllClasses.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/alphaSummary-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/alphaSummary-methods.R#L45) *warning:* **no visible global function definition for ‘assert_is_numeric’**
```r
        assert_is_numeric(alpha)
        ^~~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/alphaSummary-methods.R#L46) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(contrast, c("character", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/alphaSummary-methods.R#L47) *warning:* **no visible global function definition for ‘assertIsStringOrNULL’**
```r
        assertIsStringOrNULL(name)
        ^~~~~~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:61:24:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/alphaSummary-methods.R#L61) *warning:* **no visible global function definition for ‘resultsNames’**
```r
            caption <- resultsNames(object)[[1L]]
                       ^~~~~~~~~~~~
```
[R/contrastName-methods.R:29:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/contrastName-methods.R#L29) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        contrast <- mcols(object)[2L, "description"]
                    ^~~~~
```
[R/contrastName-methods.R:30:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/contrastName-methods.R#L30) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(contrast)
        ^~~~~~~~~~~~~~~~~~~
```
[R/contrastName-methods.R:74:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/contrastName-methods.R#L74) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrastName(slot(object, name = "results"))
        ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:5:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L5) *style:* **Variable or function name should be snake_case.**
```r
.addIsDECol <- function(
^~~~~~~~~~~
```
[R/DESeq2-internal.R:7:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L7) *style:* **Variable or function name should be snake_case.**
```r
    testCol = "padj",
    ^~~~~~~
```
[R/DESeq2-internal.R:9:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L9) *style:* **Variable or function name should be snake_case.**
```r
    lfcCol = "log2FoldChange",
    ^~~~~~
```
[R/DESeq2-internal.R:10:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L10) *style:* **Variable or function name should be snake_case.**
```r
    lfcThreshold = 0L
    ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:16:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L16) *style:* **Variable or function name should be snake_case.**
```r
    isDE <- mapply(
    ^~~~
```
[R/DESeq2-internal.R:36:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L36) *style:* **Variable or function name should be snake_case.**
```r
    isDE <- as.factor(isDE)
    ^~~~
```
[R/DESeq2-internal.R:43:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L43) *style:* **Variable or function name should be snake_case.**
```r
.ddsMsg <- function() {
^~~~~~~
```
[R/DESeq2-internal.R:58:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L58) *style:* **Variable or function name should be snake_case.**
```r
    lfcThreshold = NULL,
    ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:61:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L61) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:63:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L63) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/DESeq2-internal.R:65:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L65) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
    assertIsAlpha(alpha)
    ^~~~~~~~~~~~~
```
[R/DESeq2-internal.R:67:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L67) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:67:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L67) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/DESeq2-internal.R:69:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L69) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
    assert_is_a_number(lfcThreshold)
    ^~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:70:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L70) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
    assert_all_are_non_negative(lfcThreshold)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:74:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L74) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
    padj <- sym("padj")
            ^~~
```
[R/DESeq2-internal.R:75:12:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L75) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
    lfc <- sym("log2FoldChange")
           ^~~
```
[R/DESeq2-internal.R:80:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L80) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
    assert_is_subset(cols, colnames(data))
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:81:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L81) *warning:* **no visible global function definition for ‘select’**
```r
    data <- select(data, !!!syms(cols))
            ^~~~~~
```
[R/DESeq2-internal.R:81:29:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L81) *warning:* **no visible global function definition for ‘syms’, Did you mean 'sum'?**
```r
    data <- select(data, !!!syms(cols))
                            ^~~~
```
[R/DESeq2-internal.R:101:12:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L101) *warning:* **no visible global function definition for ‘pull’, Did you mean 'poly'?**
```r
    deg <- pull(data, "rowname")
           ^~~~
```
[R/DESeq2-internal.R:108:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L108) *style:* **Variable or function name should be snake_case.**
```r
.matchResults <- function(
^~~~~~~~~~~~~
```
[R/DESeq2-internal.R:111:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    lfcShrink = FALSE
    ^~~~~~~~~
```
[R/DESeq2-internal.R:113:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L113) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqAnalysis")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:118:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L118) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
    assert_is_scalar(results)
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:119:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L119) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
    assert_is_a_bool(lfcShrink)
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:121:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L121) *style:* **Variable or function name should be snake_case.**
```r
        slotName <- "lfcShrink"
        ^~~~~~~~
```
[R/DESeq2-internal.R:123:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L123) *style:* **Variable or function name should be snake_case.**
```r
        slotName <- "results"
        ^~~~~~~~
```
[R/DESeq2-internal.R:126:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L126) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(results, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:129:35:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L129) *warning:* **no visible global function definition for ‘contrastName’**
```r
    msg <- paste("DESeqResults:", contrastName(results))
                                  ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:140:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L140) *style:* **Variable or function name should be snake_case.**
```r
.transformCountsAxisLabel <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:141:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L141) *warning:* **no visible global function definition for ‘.transformType’**
```r
    paste(.transformType(object), "counts (log2)")
          ^~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:146:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L146) *style:* **Variable or function name should be snake_case.**
```r
.transformType <- function(object) {
^~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:147:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeq2-internal.R#L147) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqTransform")
    ^~~~~~~~~~~~~~~~
```
[R/DESeqAnalysis.R:35:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqAnalysis.R#L35) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink
        ^~~~~~~~~
```
[R/DESeqAnalysis.R:48:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqAnalysis.R#L48) *style:* **Variable or function name should be snake_case.**
```r
.contrastNames <- function(object) {
^~~~~~~~~~~~~~
```
[R/DESeqAnalysis.R:49:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqAnalysis.R#L49) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqAnalysis"))
    ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:69:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L69) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResults"))
        ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L70) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(c("log2FoldChange", "padj"), colnames(object))
        ^~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:71:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L71) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:72:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L72) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:73:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L73) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:74:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L74) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:75:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L75) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L78) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/DESeqResultsTables-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        testCol <- "padj"
        ^~~~~~~
```
[R/DESeqResultsTables-methods.R:80:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L80) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        lfc <- sym(lfcCol)
               ^~~
```
[R/DESeqResultsTables-methods.R:81:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L81) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        test <- sym(testCol)
                ^~~
```
[R/DESeqResultsTables-methods.R:130:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L130) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:159:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L159) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- rowRanges(data)
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:169:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L169) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
        mcols(rowRanges) <- mcols
        ^~~~~
```
[R/DESeqResultsTables-methods.R:170:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L170) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
        assert_is_non_empty(rowRanges)
        ^~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:187:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/DESeqResultsTables-methods.R#L187) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- sampleNames(data)
        ^~~~~~~~~~~
```
[R/export-methods.R:28:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L28) *style:* **Variable or function name should be snake_case.**
```r
.prepareDESeqResults <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:30:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L30) *style:* **Variable or function name should be snake_case.**
```r
    rowData = NULL,
    ^~~~~~~
```
[R/export-methods.R:32:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L32) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames = NULL
    ^~~~~~~~~~~
```
[R/export-methods.R:34:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L34) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:35:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L35) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(rowData, c("DataFrame", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:36:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L36) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(counts, c("matrix", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:37:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L37) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(sampleNames, c("character", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L45) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(rowData, "DataFrame")
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L46) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- sanitizeRowData(rowData)
        ^~~~~~~
```
[R/export-methods.R:46:20:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L46) *warning:* **no visible global function definition for ‘sanitizeRowData’**
```r
        rowData <- sanitizeRowData(rowData)
                   ^~~~~~~~~~~~~~~
```
[R/export-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L47) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(rowData))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:54:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L54) *warning:* **no visible global function definition for ‘assert_is_matrix’**
```r
        assert_is_matrix(counts)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:55:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L55) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:62:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L62) *warning:* **no visible global function definition for ‘assert_has_names’**
```r
            assert_has_names(sampleNames)
            ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:63:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L63) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
            assert_are_identical(names(sampleNames), colnames(counts))
            ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:66:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L66) *warning:* **no visible global function definition for ‘assert_are_disjoint_sets’**
```r
        assert_are_disjoint_sets(colnames(data), colnames(counts))
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:75:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L75) *style:* **Variable or function name should be snake_case.**
```r
.prepareResultsTablesList <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:76:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L76) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqResultsTables"))
    ^~~~~~~~~~~
```
[R/export-methods.R:80:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L80) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
    assert_is_list(deg)
    ^~~~~~~~~~~~~~
```
[R/export-methods.R:81:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L81) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
    assert_are_identical(names(deg), c("up", "down"))
    ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:89:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L89) *style:* **Variable or function name should be snake_case.**
```r
    rowData <- slot(object, "rowRanges") %>%
    ^~~~~~~
```
[R/export-methods.R:94:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L94) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames <- slot(object, "sampleNames")
    ^~~~~~~~~~~
```
[R/export-methods.R:102:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L102) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(all, "DataFrame"))
    ^~~~~~~~~~~
```
[R/export-methods.R:117:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L117) *warning:* **no visible global function definition for ‘initDir’**
```r
        dir <- initDir(dir)
               ^~~~~~~
```
[R/export-methods.R:118:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L118) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(compress)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:121:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L121) *warning:* **no visible global function definition for ‘.prepareResultsTablesList’**
```r
        tables <- .prepareResultsTablesList(x)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:122:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L122) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
        assert_is_list(tables)
        ^~~~~~~~~~~~~~
```
[R/export-methods.R:129:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L129) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
        stem <- snake(contrastName(x))
                ^~~~~
```
[R/export-methods.R:129:23:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L129) *warning:* **no visible global function definition for ‘contrastName’**
```r
        stem <- snake(contrastName(x))
                      ^~~~~~~~~~~~
```
[R/export-methods.R:135:51:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L135) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
        files <- file.path(dir, paste0(stem, "_", snake(names(tables)), ext))
                                                  ^~~~~
```
[R/export-methods.R:144:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L144) *warning:* **no visible global function definition for ‘export’**
```r
                export(x = x, file = file)
                ^~~~~~
```
[R/export-methods.R:151:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/export-methods.R#L151) *warning:* **no visible global function definition for ‘assert_all_are_existing_files’**
```r
        assert_all_are_existing_files(files)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/markdown-methods.R:26:14:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L26) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        show(markdownHeader("Contrast names"))
             ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:27:14:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L27) *warning:* **no visible global function definition for ‘markdownList’**
```r
        show(markdownList(.contrastNames(object)))
             ^~~~~~~~~~~~
```
[R/markdown-methods.R:27:27:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L27) *warning:* **no visible global function definition for ‘.contrastNames’**
```r
        show(markdownList(.contrastNames(object)))
                          ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L45) *style:* **Variable or function name should be snake_case.**
```r
        headerLevel = 2L
        ^~~~~~~~~~~
```
[R/markdown-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L47) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResultsTables"))
        ^~~~~~~~~~~
```
[R/markdown-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L49) *warning:* **no visible global function definition for ‘assertIsHeaderLevel’**
```r
        assertIsHeaderLevel(headerLevel)
        ^~~~~~~~~~~~~~~~~~~
```
[R/markdown-methods.R:50:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:52:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:54:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L54) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(object)
                    ^~~~~~~~~~~~
```
[R/markdown-methods.R:55:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L55) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        markdownHeader(contrast, level = headerLevel, asis = TRUE)
        ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:56:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L56) *style:* **Variable or function name should be snake_case.**
```r
        headerLevel <- headerLevel + 1L
        ^~~~~~~~~~~
```
[R/markdown-methods.R:57:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:60:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:81:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~
```
[R/markdown-methods.R:82:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L82) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
            markdownHeader("File downloads", level = headerLevel, asis = TRUE)
            ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:109:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:111:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L111) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        markdownHeader("Top tables", level = headerLevel, asis = TRUE)
        ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:112:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/markdown-methods.R#L112) *warning:* **no visible global function definition for ‘topTables’**
```r
        topTables(object)
        ^~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:36:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L36) *style:* **Variable or function name should be snake_case.**
```r
        clusteringMethod = "ward.D2",
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:40:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L40) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(object, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:42:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L42) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(counts, "DESeqTransform")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:44:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L44) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(object), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:45:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L45) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotDEGHeatmap-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L46) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L47) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:47:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L47) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotDEGHeatmap-methods.R:48:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L48) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L49) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:51:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGHeatmap-methods.R#L51) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(clusteringMethod)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:37:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L37) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(object, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:39:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L39) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(counts, "DESeqTransform")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:41:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L41) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(object), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:42:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L42) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L46) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(counts) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:47:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L47) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotDEGPCA-methods.R:48:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L48) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L49) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:49:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L49) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotDEGPCA-methods.R:50:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L50) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:51:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L51) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:85:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L85) *style:* **Trailing whitespace is superfluous.**
```r
    f = "plotPCA",
                  ^
```
[R/plotDEGPCA-methods.R:108:20:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotDEGPCA-methods.R#L108) *warning:* **no visible global function definition for ‘.matchResults’**
```r
        results <- .matchResults(object = object, results = results)
                   ^~~~~~~~~~~~~
```
[R/plotGene-methods.R:32:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotGene-methods.R#L32) *style:* **Variable or function name should be snake_case.**
```r
            countsAxisLabel <- "rlog counts (log2)"
            ^~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:34:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotGene-methods.R#L34) *style:* **Variable or function name should be snake_case.**
```r
            countsAxisLabel <- "vst counts (log2)"
            ^~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:72:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L72) *style:* **Variable or function name should be snake_case.**
```r
        pointColor = "gray50",
        ^~~~~~~~~~
```
[R/plotMA-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        sigPointColor = c(upregulated = "purple", downregulated = "orange"),
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:77:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L77) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotMA-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L78) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotMA-methods.R:79:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L79) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotMA-methods.R:80:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L80) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:81:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L81) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:82:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L82) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(genes, c("character", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:83:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L83) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(gene2symbol, c("Gene2Symbol", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:85:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L85) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(ntop)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:86:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L86) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(ntop)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:90:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L90) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(pointColor)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:91:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L91) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(sigPointColor)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:93:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L93) *style:* **Variable or function name should be snake_case.**
```r
            sigPointColor <- c(
            ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:98:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L98) *warning:* **no visible global function definition for ‘assert_is_of_length’**
```r
        assert_is_of_length(sigPointColor, n = 2L)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:103:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L103) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "svalue"  # nocov
            ^~~~~~~
```
[R/plotMA-methods.R:105:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L105) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "padj"
            ^~~~~~~
```
[R/plotMA-methods.R:109:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L109) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/plotMA-methods.R:140:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L140) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) > 0L)
                                   ^~~
```
[R/plotMA-methods.R:142:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L142) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) < 0L)
                                   ^~~
```
[R/plotMA-methods.R:157:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L157) *style:* **Variable or function name should be snake_case.**
```r
        log10BaseMean <- log10(data[["baseMean"]])
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:160:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L160) *style:* **Variable or function name should be snake_case.**
```r
        xBreaks <- 10L ^ seq(from = floor, to = ceiling, by = 1L)
        ^~~~~~~
```
[R/plotMA-methods.R:240:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L240) *style:* **Variable or function name should be snake_case.**
```r
            labelData <- data %>%
            ^~~~~~~~~
```
[R/plotMA-methods.R:275:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L275) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/plotMA-methods.R:315:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L315) *style:* **Variable or function name should be snake_case.**
```r
plotMeanAverage <- function(...) {
^~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:317:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotMA-methods.R#L317) *warning:* **no visible global function definition for ‘plotMA’, Did you mean 'plot'?**
```r
    plotMA(...)
    ^~~~~~
```
[R/plotVolcano-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L78) *style:* **Variable or function name should be snake_case.**
```r
        pointColor = "gray50",
        ^~~~~~~~~~
```
[R/plotVolcano-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        sigPointColor = c(upregulated = "purple", downregulated = "orange"),
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:84:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L84) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotVolcano-methods.R:85:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L85) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:86:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L86) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotVolcano-methods.R:86:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L86) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotVolcano-methods.R:87:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L87) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:88:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L88) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(ylim)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:94:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L94) *warning:* **no visible global function definition for ‘assertIsImplicitInteger’**
```r
        assertIsImplicitInteger(ntop)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:95:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L95) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(c(lfcThreshold, ntop))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:97:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L97) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(pointColor)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:98:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L98) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(sigPointColor)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:100:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L100) *style:* **Variable or function name should be snake_case.**
```r
            sigPointColor <- c(
            ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:105:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L105) *warning:* **no visible global function definition for ‘assert_is_of_length’**
```r
        assert_is_of_length(sigPointColor, n = 2L)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:106:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L106) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(histograms)
        ^~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:111:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L111) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "svalue"  # nocov
            ^~~~~~~
```
[R/plotVolcano-methods.R:113:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L113) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "padj"
            ^~~~~~~
```
[R/plotVolcano-methods.R:117:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L117) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/plotVolcano-methods.R:118:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L118) *style:* **Variable or function name should be snake_case.**
```r
        negLogTestCol <- camel(paste("neg", "log10", testCol))
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:118:26:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L118) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**
```r
        negLogTestCol <- camel(paste("neg", "log10", testCol))
                         ^~~~~
```
[R/plotVolcano-methods.R:147:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L147) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) > 0L)
                                   ^~~
```
[R/plotVolcano-methods.R:149:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L149) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) < 0L)
                                   ^~~
```
[R/plotVolcano-methods.R:158:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L158) *style:* **Variable or function name should be snake_case.**
```r
        lfcHist <- ggplot(
        ^~~~~~~
```
[R/plotVolcano-methods.R:183:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L183) *style:* **Variable or function name should be snake_case.**
```r
        pvalueHist <- ggplot(
        ^~~~~~~~~~
```
[R/plotVolcano-methods.R:277:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L277) *style:* **Variable or function name should be snake_case.**
```r
            labelData <- data %>%
            ^~~~~~~~~
```
[R/plotVolcano-methods.R:331:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/plotVolcano-methods.R#L331) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/show-methods.R:19:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/show-methods.R#L19) *style:* **Variable or function name should be snake_case.**
```r
.showHeader <- function(object, version = NULL) {
^~~~~~~~~~~
```
[R/show-methods.R:34:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/show-methods.R#L34) *style:* **Variable or function name should be snake_case.**
```r
        contrastNames <- .contrastNames(object)
        ^~~~~~~~~~~~~
```
[R/show-methods.R:34:26:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/show-methods.R#L34) *warning:* **no visible global function definition for ‘.contrastNames’, Did you mean 'contrastNames'?**
```r
        contrastNames <- .contrastNames(object)
                         ^~~~~~~~~~~~~~
```
[R/show-methods.R:58:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/show-methods.R#L58) *warning:* **local variable ‘deg’ assigned but may not be used**
```r
        deg <- slot(object, "deg")
        ^~~
```
[R/show-methods.R:66:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/show-methods.R#L66) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(results)
                    ^~~~~~~~~~~~
```
[R/show-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/show-methods.R#L68) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(results)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/show-methods.R:85:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/show-methods.R#L85) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
            assert_is_a_string(dirname)
            ^~~~~~~~~~~~~~~~~~
```
[R/show-methods.R:89:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/show-methods.R#L89) *warning:* **no visible global function definition for ‘showSlotInfo’**
```r
        showSlotInfo(list)
        ^~~~~~~~~~~~
```
[R/topTables-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L47) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResultsTables"))
        ^~~~~~~~~~~
```
[R/topTables-methods.R:50:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L50) *warning:* **no visible global function definition for ‘assertIsImplicitInteger’**
```r
        assertIsImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:53:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L53) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(results, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L68) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(keep, colnames(data))
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:69:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L69) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(deg, rownames(data))
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- slot(object, "rowRanges")
        ^~~~~~~~~
```
[R/topTables-methods.R:76:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L76) *style:* **Variable or function name should be snake_case.**
```r
            rowData <- as(rowRanges, "DataFrame")
            ^~~~~~~
```
[R/topTables-methods.R:83:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L83) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
            assert_is_subset(rownames(data), rownames(rowData))
            ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:84:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L84) *style:* **Variable or function name should be snake_case.**
```r
            rowData <- rowData[rownames(data), keep, drop = FALSE]
            ^~~~~~~
```
[R/topTables-methods.R:126:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L126) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:127:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L127) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(object)
                    ^~~~~~~~~~~~
```
[R/topTables-methods.R:128:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L128) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(contrast)
        ^~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:131:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/e1c8e5fb6bd5224b4b6f2f402b2031a1dff5a54d/R/topTables-methods.R#L131) *warning:* **no visible global function definition for ‘.topTable’**
```r
        up <- .topTable(object, direction = "up", n = n)
              ^~~~~~~~~
```


Successfully aliased the URL <https://minimizese-jx40ls29b.now.sh> to the following aliases.

* https://www.minimize.se
* https://minimize.se


I'm glad you approve :smile: :+1:


Wrong commit title. It should be:

player: add missing variables

These variables are created only to speed-up var_Inherit from the input_thread_t or other childs.


Please do not push directly to master


I


You should explain why.


05c68ff053485e9d5089969303e73045fb6cab6c should have fixed the coq backend although I haven't actually tried running coq on the result.


Лучше функцию задать снаружи, так читаемее. Это вспомогательная функция так что, думаю, лучше ее положить в tools.py
По поводу названия: вообще большие буквы не желательно добавлять в названия функций (правда мы в файле scailing_features.py добавили, но у нас по смыслу там заглавная буква должна быть) и желательно чтобы в названии был глагол и сам оно писалось вот_так_вот, т е с маленьких букв разделенные нижним подверкиванием (это все из руководства PEP8). Ну вот, функцию можно просто назвать "отыскание порога яркости", а в комментарии к функции написать что это метод Оцу


Why are changing the intf linked list in this commit ?
If you have a good reason, this should be done in a separate commit.


removed and released in version `1.0.1` 👍


package com.monsanto.mbt;

import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;

public class Shipment {

	 public static List<Widget> getSampleWidgets() {
	        List<Widget> widgets = new ArrayList<Widget>();

	        widgets.add(new Widget(1, "Red", stringToDateConverter("01-01-2006")));
	        widgets.add(new Widget(2, "Blue",  stringToDateConverter("02-03-2007")));
	        widgets.add(new Widget(3, "Red",  stringToDateConverter("03-09-2006")));
	        widgets.add(new Widget(4, "Green", stringToDateConverter( "04-01-2009")));
	        widgets.add(new Widget(5, "Green",  stringToDateConverter("05-07-2011")));
	        widgets.add(new Widget(6, "Blue", stringToDateConverter( "06-02-2016")));
	        widgets.add(new Widget(7, "Green",  stringToDateConverter("07-01-2008")));
	        widgets.add(new Widget(8, "Blue",  stringToDateConverter("08-02-2009")));
	        widgets.add(new Widget(9, "Red",  stringToDateConverter("09-01-2005")));
	        widgets.add(new Widget(10, "Blue",  stringToDateConverter("01-03-2013")));
	        widgets.add(new Widget(22, "Blue",  stringToDateConverter("02-13-2007")));
	        widgets.add(new Widget(23, "Red",  stringToDateConverter("03-14-2006")));
	        widgets.add(new Widget(25, "Green",  stringToDateConverter("05-16-2011")));
	        widgets.add(new Widget(24, "Red",  stringToDateConverter("04-15-2009")));

	        return widgets;
	    }

	    public static Date stringToDateConverter(String strDate){
	        Date parsedDate = null;
	        SimpleDateFormat formatter = new SimpleDateFormat("MM-dd-yyyy");
	        try {
	            parsedDate = formatter.parse(strDate);
	        } catch (ParseException e) {
	            e.printStackTrace();
	        }
	        return parsedDate;
	    }

	public static void main(String[] args) {

		List<Widget> empArr1 = Shipment.getSampleWidgets();
		Widget[] empArr  =empArr1.toArray(new Widget[empArr1.size()]);
		 Arrays.sort(empArr);

        Arrays.sort(empArr, Widget.colorComparator);
        System.out.println("Widget list sorted by color");

        System.out.println("-----------------------------------------------------------------------------");
        System.out.printf("%10s %30s %50s", "Serial No", "Color", "Production Date");
        System.out.println();
        System.out.println("-----------------------------------------------------------------------------");
        for(Widget student: empArr){
            System.out.format("%10s %30s %50s",
                    student.getSerialNumber(), student.getColor(), student.getProductionDate());
            System.out.println();
        }
        System.out.println("-----------------------------------------------------------------------------");

        Arrays.sort(empArr, Widget.productionDateComparator);
        System.out.println("Widget list sorted by  Production Date");

        System.out.println();
        System.out.println("-----------------------------------------------------------------------------");
        System.out.printf("%10s %30s %50s","Serial No", "Color", "Production Date");
        System.out.println();
        System.out.println("-----------------------------------------------------------------------------");
        for(Widget student: empArr){
            System.out.format("%10s %30s %50s",
                    student.getSerialNumber(), student.getColor(), student.getProductionDate());
            System.out.println();
        }
        System.out.println("-----------------------------------------------------------------------------");

       }

}


why do you need this? Just for returning the `Control` property below right? If so, there's a cast for NSView -> Control already, so no need to convert to GtkWidget AFAICS


This function is racy (it had always been but now you can fix it). Indeed, aout_DevicesList, aout_DeviceGet and aout_DeviceSet should be executed withing the same lock context. You can do it now that you are in aout src.


@paales The `total-workings.gif` image seems to be missing from the repository?


Are you building a web app with ASP.NET MVC?


@AlekseyMartynov, may be use `until hg outgoing; do` ?


Смотри, я насколько понял ты тут находишь для каждого пикселя значение яркости. И ты это несколько раз в коде делаешь. Наверное удобнее сделать отдельную функцию, которая будет возвращать словарь, где ключами будут кортежи (x, y) координат пикселей, а значениями будут яркость соответствующего пикселя


You can drop the `else` and run the block directly since the `if` branch has `return` statement as the last command.


И если будет табличка для яркостей, то можно тогда заполнить гистограмму не циклом а геренатором словарей к примеру


Hi !
with MinGW-gcc8.1 I have other warnings and one error :-(
```
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp: In member function 'bool nana::dragdrop_service::dragdrop(nana::window)':
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:586:12: warning: deleting object of polymorphic class type 'nana::drop_source' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete drop_src;
            ^~~~~~~~
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:597:11: warning: deleting object of polymorphic class type 'nana::drop_source' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
    delete drop_src;
           ^~~~~~~~
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:598:11: warning: deleting object of polymorphic class type 'nana::drop_data' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
    delete drop_dat;
           ^~~~~~~~
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:593:9: warning: unused variable 'status' [-Wunused-variable]
    auto status = ::DoDragDrop(drop_dat, drop_src, DROPEFFECT_COPY, &eff);
         ^~~~~~
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp: In lambda function:
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:814:54: warning: typedef 'using basic_window = struct nana::detail::basic_window' locally defined but not used [-Wunused-local-typedefs]
     using basic_window = ::nana::detail::basic_window;
                                                      ^
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp: In lambda function:
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:824:53: warning: typedef 'using basic_window = struct nana::detail::basic_window' locally defined but not used [-Wunused-local-typedefs]
    using basic_window = ::nana::detail::basic_window;
                                                     ^
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp: In member function 'void nana::dragdrop::implementation::make_data()':
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:963:20: error: converting to execution character set: Illegal byte sequence
    files.push_back(L"D:\\ÐÂ½¨ÎÄ±¾ÎÄµµ.cpp");
                    ^~~~~~~~~~~~~~~~~~~~~~~
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp: In lambda function:
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:1029:10: warning: unused variable 'drop_wd' [-Wunused-variable]
     auto drop_wd = API::find_window(API::cursor_position());
          ^~~~~~~
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp: In instantiation of 'ULONG nana::win32com_iunknown<Interface, iid>::Release() [with Interface = IDataObject; const IID& iid = IID_IDataObject; ULONG = long unsigned int]':
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:118:24:   required from here
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:121:19: warning: deleting object of abstract class type 'nana::win32com_iunknown<IDataObject, IID_IDataObject>' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
    if (cRef == 0) delete this;
                   ^~~~~~
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp: In instantiation of 'ULONG nana::win32com_iunknown<Interface, iid>::Release() [with Interface = IDropSource; const IID& iid = IID_IDropSource; ULONG = long unsigned int]':
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:118:24:   required from here
C:\Prog\ExtLib\nana\source\gui\dragdrop.cpp:121:19: warning: deleting object of abstract class type 'nana::win32com_iunknown<IDropSource, IID_IDropSource>' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]

```


#4 THis issue has been resolved


Здесть тоже, можно будет одной строчкой sum(brightness.values())


Quick question regarding this volume_inversion change....
If in my script I used to do:
`# Inversion tasks
execute_entity_task(tasks.prepare_for_inversion, gdirs, add_debug_var=True)

execute_entity_task(tasks.volume_inversion, gdirs, glen_a=cfg.A, fs=cfg.FS)`

now I should just do:
`execute_entity_task(tasks.mass_conservation_inversion, gdirs, glen_a=cfg.PARAMS['inversion_glen_a'],
fs=cfg.PARAMS['inversion_fs'])`

Sorry for the silly question I am new with this oggm version :)


Looks good @miina 👍


The error gets omitted silently here. It's better to return both endpoint resolved and error.


In the back end i finish creating the tables for the three doctors plus their update


The `current` value must be changed between `vlc_playlist_state_Save()` and `vlc_playlist_state_NotifyChanges()`.


Few months ago, @tguillem said that we received the callback only when the media has changed *automatically*.

So @tguillem, I have a patch:
```diff
diff --git a/src/playlist/player.c b/src/playlist/player.c
index d34addf01f..bbdc39ba0e 100644
--- a/src/playlist/player.c
+++ b/src/playlist/player.c
@@ -31,8 +31,6 @@
 #include "playlist.h"
 #include "preparse.h"

-/* called when the current media has changed _automatically_ (not on
- * SetCurrentItem) */
 static void
 player_on_current_media_changed(vlc_player_t *player, input_item_t *new_media,
                                 void *userdata)
```

:wink:

@Psilokos So to avoid the problem with state notification, I suggest to reset the current media on the player first instead:

```diff
diff --git a/src/playlist/content.c b/src/playlist/content.c
index 86de05ccf9..7c8fca044c 100644
--- a/src/playlist/content.c
+++ b/src/playlist/content.c
@@ -204,10 +204,10 @@ vlc_playlist_Clear(vlc_playlist_t *playlist)
 {
     vlc_playlist_AssertLocked(playlist);

-    vlc_playlist_ClearItems(playlist);
     int ret = vlc_player_SetCurrentMedia(playlist->player, NULL);
     VLC_UNUSED(ret); /* what could we do? */

+    vlc_playlist_ClearItems(playlist);
     vlc_playlist_ItemsReset(playlist);
 }
```


@sandy081 Not really sure why I did this. :thinking:


A community with strong social interaction, such as pedigree information, geographical information, genetic similarity information, is presented with block chain technology to create a multi-dimensional, in-depth and strong application of block chain as a platform for social ecology.

一个通过将谱系信息、地域信息、基因相似信息等强社会互动关系社区以区块链技术呈现，打造多元化、深度化、强应用化的区块链先导社交生态的平台。


**NOTE**: There may be something in this, _or the previous_, commit that has degraded the scoring ability by 10-20% of so.  Try to get a script written to handle automated trials and percentage of win calculation after 'x' number of games.


이미지 파일은 깃허브에 못올려요?


Even overlegd met Pieter, het commentaar bij vierde punt moet zijn:
1.18: Begin geldigheid T487200000012531 aangepast naar 01-07-1980

Dit staat in de referentieset goed, alleen de commit message week iets af.


시벌 왜 지우냐


Don't use `static` function, getting error in gcc 4.9,  it should be like this:
`void put_inst_helper(struct kref *kref)`

Error log:
`../drivers/media/platform/msm/vidc_3x/msm_vidc_common.c:745:13: error: static declaration of 'put_inst' follows non-static declaration
 static void put_inst(struct msm_vidc_inst *inst)
             ^
In file included from ../drivers/media/platform/msm/vidc_3x/msm_vidc_common.c:22:0:
../drivers/media/platform/msm/vidc_3x/msm_vidc_common.h:102:6: note: previous declaration of 'put_inst' was here
 void put_inst(struct msm_vidc_inst *inst);
      ^
`


신기 엿머겅 ㅗㅗㅗㅗㅗㅗㅗㅗㅗㅗㅗㅗ


@kpodemski Sorry, I know realize this was a jerk move of me. I changed it back to your name. At the end I made my own facebook chat module with a bit more options. If you want, I add it and do a PR to your repo. Again sorry.


Don't think we set host now, but we could probably do that. The idea with devbox is that it's supposed to provide a [12factor](https://12factor.net/)-style environment for development.


페이스북 로그인 기능(미완성), Recaptcha(미완성)


u suck


@Chocobozzz I just checked this on a test server, `docker-compose pull && docker-compose up -d` works perfectly fine. There is no need to run `docker-compose down`.


csokiscsiga jöhet nekem is


Hi Bea, yes.

Although you can avoid to specify the params yourself. If you look at the code (https://github.com/OGGM/oggm/blob/8d52e49120fee164e1ff15adf49ade5bb6379974/oggm/core/inversion.py#L166) these are the default


максимальную и минимальную яркость можно будет найти функциями min и max


Changed Jenkins plugin to enhance the ecosystem support and scan enabled support to the bayesian analytics call.

The .hpi file was built from fabric8-analytics/fabric8-analytics-jenkins-plugin#19

Tag: https://github.com/fabric8-analytics/fabric8-analytics-jenkins-plugin/releases/tag/0.3.2
Resolves: openshiftio/openshift.io#4344


### Lipsum Really?

So we __really__ were not able to find better filter text?


PropertyPad expects a Gtk control, we have to do the same like we did with the Toolbox


Or you wanna stay inline with the origin patch, just replace this line with this:
`static void put_inst(struct msm_vidc_inst *inst)`


Successfully aliased the URL <https://packagephobia-chcxawknfl.now.sh> to the following alias.

* https://packagephobia.now.sh


TDD 기반: 작성 수준이 일부 지나치게 자세함.


I am not familiar with this part of the code but airing a few concerns _just in case_.

Are you sure it should be *out* and not `out` from the `@bindings` above? Most likely they are the same, but who knows.

Output from java side is not going through `*out*`, right? So to completely solve the issues one would need to move cider-nrepl/out middleware logic here.

There is also `*err*` which should be taken care.

Can it be that two subsequent `evaluate` bind different `*out*`? If so, then you will still be loosing output from previous evals. In any case, it seems to me that we should refrain from resetting `*out*` root-var or `setOut`  on every evaluate. Just doesn't feel right.

Finally, setting thread local value of *out* instead of the root value would be achieving the same goal, no?


Still under development


My mistake, thanks for pointing this out.


### Lipsum Really?

So we __really__ were not able to find better filler text?


for부터 print문까지: recipe 내부 함수화.


Вот тут если в гистограмме будут значения яркости, для которых нашлось 0 пикселей, то это будет ненужный цикл. Вот почему можно сделать гистограмму не списком, а словарем, где ключи будут только для значений яркости, для которых нашлись пиксели на картинке. И тогда можно пробегать только по таким значениям (histogram.keys())


yeah, I think the code is relying on very modern cmake. it works for me locally but not on travis (for example: https://travis-ci.org/libical/libical/jobs/456426827)

If I recall,  the problem was due to _scangobj_prefix . try commenting that set(_scangobj_prefix...) line

Hard for me to test without installing an older cmake.


Test resource가 필요합니다.


Ah, push force 🙄


This patch is the original patch https://github.com/solid/node-solid-server/pull/857/commits/834aebedfd6a4299e520bd490d6db520196e7c4a for https://github.com/solid/node-solid-server/pull/857 recreated on top of release/v5.0.0 with a prior merge conflict resolved.


server pass


@rsantos88 can we delete this branch? The code fix targeted here was reverted at https://github.com/roboticslab-uc3m/teo-configuration-files/commit/ed94eaecbea1bee7af357d660f0b17e3a91ca889.


Simple example sketch.


Всё понятно, но не помешали бы комментарии в классах SettingsController и Method.


Its not hard code dont "save" it in comments. And fix tabs in raws below.


ok thanks!


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ℹ [API Diff (from PR only)](http://xamarin-storage/jenkins/xamarin-macios/maccore-issue-1118-v2/b0621e18270288b611d885c9614adbaa005fe370/1/jenkins-results/apicomparison/index.html) (please review changes)
✅ [Generator Diff](http://xamarin-storage/jenkins/xamarin-macios/maccore-issue-1118-v2/b0621e18270288b611d885c9614adbaa005fe370/1/jenkins-results/generator-diff/index.html) (no change)
🔥 [Test run failed](http://xamarin-storage/jenkins/xamarin-macios/maccore-issue-1118-v2/b0621e18270288b611d885c9614adbaa005fe370/1/jenkins-results/tests/index.html) 🔥

# Test results

# Test run in progress: NotStarted: 284, Ignored: 1657


ical master fails for me with 3.12.0 (include problems when the linker tries to link the gtk doc).
The problem is even worse with CMake imported targets. I'm testing a fix and I'll submit my changes after that.

I really think this gtkdoc module shall be split in smaller functions instead of this macro-blob, it would help detecting issues.


Implements #56


![](https://github.trello.services/images/mini-trello-icon.png) [Fix glossary.world/app/ route](https://trello.com/c/3MuYvWdn/44-fix-glossaryworld-app-route)


@rohitwaghchaure https://github.com/frappe/erpnext/pull/15842/commits/36ad72e148f5c50601550750df855d2ea0a4ac13


helvetica


В репозитории должен быть файл .gitignore, который не доает попасть файлам сборки в репозиторий


Isn't it really overkill to do that?
You know load all results before selecting the one you want.

I think it will be really slow.


@ppaulweber  do you know why the clang and gcc tests here are failing?


আচ্ছা ভাইয়া
> টেবিল গুলো মুছে ফেলে
বলতে আমি বুঝতেসি যে সব টেবিল ড্রপ করে আবার রেক্রিয়েট করা। এই ডেফিনিশন অনুযায়ী `refresh` কমান্ড টা আসলে ঠিক না। ঠিক হতো `fresh` কমান্ড টা। একটু docs পরে দেখবেন আমি ঠিক বলছি কিনা।


Also update the comments to be consistent?


The same here about omitting the error.


(we discussed it IRL)

autostart is only used once on start, so it should not be in the playlist at all.


Did you mean to release this? (crates.io still only has 0.0.1)


Можем сделать как ul > li > a ?


you have my blessing to do whatever you think is best.
any fix needs to go into the 3.0 branch as well.

let me know if you need my help testing


Зачем явно вызывать обработчик прерывания?


Rule of beatiful code says - if u use some part of code more then twise - extract it into function.


![](https://github.trello.services/images/mini-trello-icon.png) [#9 Daily Scrum](https://trello.com/c/BZjJxHPq/53-9-daily-scrum)


Second time same code


Third


а почему не first_class_prob * second_class_prob * mean_delta**2 ?


no need class


Incorrect Error message - points to missing receipient address in observables even thought in case of `case` the code inspects tags not artifacts.


I count six.


to remove margin-bottom of the jumbotron


Если хочешь чтобы переменная называлась image а не img, лучше, наверное, изменить название аргумента у функции


А зачем явно вызывается обработчик прерывания?


for a best repartition on the page


onur git


https://oss.sonatype.org/content/repositories/snapshots/org/junit/jupiter/junit-jupiter-api/5.3.2-SNAPSHOT/

Nice! 👍


Нужно поправить отсутпы здесь и далее.


Эта переменная тут больше не нужна.


Added file to load.


you forgot to delete pawnpush bonus?


LOL!


>Изменения в форматировании и комментариях легко отключаются в нормальных diff'ах. Например:

Я знаю, можно даже на гитхабе это сделать, добавив ?w=1 к URL-у. Но это не спасает от нескольких десятков добавленных фигурных скобок...


No, you shouldn't have to convert to Gtk.Widget.


This is just a quick patch, will submit a full PR upstream


Я понял почему gray, только эта штука это рисовалка, не совем подходит название.
Кстати, ты здесь везде используешь PIL.ImageDraw.Draw() только чтобы изменить значение одного пикселя, это можно делать через image.load() (который у тебя сейчас pix)


Необязательно заводить две разные структуры, достаточно одной, но каждый раз после ипользования нужно либо делать `memset(&GPIO_InitStructure, 0, sizeof(GPIO_InitStructure)`,  либо вызывать специальную функцию для обнуления из SPL: `void GPIO_StructInit(GPIO_InitTypeDef *)`


then, we have to do the same with the Toolbox?


Should not be public.


How the "client" can react to this signal, if no info is provided?


Private


revisi


Thanks, gotcha. Already running root, because I need keyboard macros, everthing works perfectly so far, thanks for the great work!

The only thing I'm fighting right now is how to use `CapsLock` with a keyboard layout where you only can unlock it again by pressing `Shift`. But I'm not sure a comment in a commit log is the right place to ask such a common support question, going to create a issue with this question. ;)


[R/create_bd_tree.R:70:18:](https://github.com/richelbilderbeek/razzo/blob/0aeb053ed006e01cc541730712551064fc049f54/R/create_bd_tree.R#L70) *warning:* **no visible global function definition for ‘bd_phylo_2_l_table’**
```r
  bd_l_matrix <- bd_phylo_2_l_table(bd_tree)
                 ^~~~~~~~~~~~~~~~~~
```
[R/utils.R:65:10:](https://github.com/richelbilderbeek/razzo/blob/0aeb053ed006e01cc541730712551064fc049f54/R/utils.R#L65) *warning:* **no visible global function definition for ‘convert_tree2brts’**
```r
  brt <- convert_tree2brts(phylo)
         ^~~~~~~~~~~~~~~~~
```


Yes, it is the responsibility of the shell to embed whatever type of control the pad provides.


Redone the struct of the requests, respond codes


Looks like there is a problem with the cirrus-ci windows integration, the Linux-based and Darwin-based tests are running successful, so I would say no worries for now :smiley:


fgvfd


## New string
- `APPLICATION_STORE_FILTER_TYPE_ON_SALE: "On sale now"`


Successfully aliased the URL <https://synadia-website-c657ekaz9.now.sh> to the following aliases.

* https://synadia.com
* https://www.synadia.com


Эта переменная нигде не используется


Added:
{tags, owner, photos, price} to ServiceView
{tags, price } to MyServiceView


This is a part of the project Laravel/ framework.
Code Gorilla / week 7.


but then how we can include some logic/handlers in the Gtk widget?


Здесть нет нужны в тернарном опрераторе. Можно использовать
``` c
        GREEN_FLAG = !!(GREEN_FLAG != 1)
```


测试


вот тут pix[i, j] = (Y, Y, Y)


This code had a fall through condition in tests, see:

```
if ( defined( 'DOING_GRAVITYVIEW_TESTS' ) && ! empty( $GLOBALS['GravityView_API_field_label_override'] ) ) {
     /** Allow to fall through for back compatibility testing purposes. */
```

We use the code to verify that our new label API is consistent with the legacy one. The test is currently failing `GVFuture_Test::test_field_label_compat`

Options:

1. Revert this commit.
2. Consider the new API call stable enough that legacy consistency tests for this case are no longer needed.

Thoughts @zackkatz?


Кстати, это же тоже отдельная операция, сделать изображение черно-белым. Может для нее тоже сделать функцию в tools.py


Messed up and pushed straight to `master`. Finishes #2463


Можно не использовать разные структуры здесь, достаточно обнулить структуру после использования либо используя memset, либо используя `GPIO_InitStruct(GPIO_InitTypeDef *)`


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:astonished:


Label sounds very different from monitored metric, some mistake?


This sentence doesn't sound right


Hello, I was looking how to contact you to ask, why is this project going to be deprecated ?
I have an ongoing vertx project on aws ecs fargate looking for a hazelcast way to cluster de different verticles


I was asking because this: https://github.com/xamarin/Xamarin.PropertyEditing/issues/437


@Nutomic can you do a PR to correct it?


Maybe just "Active backends".  I'm assuming active means that it's executing.


На данном этапе все хорошо, но неплохо бы избавиться от повторяющегося кода в ImageWindow и добавить пробелы между функциями.


==> Number of backends executing a query


#12 jpeg変換


Better name would probably be `connection.idleInTransaction.count` or something similar. `activity` part doesn't bring any info. I saw the same in many other places, so I will not repeat.


Successfully aliased the URL <https://synadia-website-nwoblk99r.now.sh> to the following aliases.

* https://synadia.com
* https://www.synadia.com


`sys->plidx_added` may be "invalid" (out of range) for the playlist when this callback is called. I'm not sure why you listen this callback on the player (the playlist already handle it, and updates its current/prev/next automatically).


Вот тут не очень понял что происходит. kernel это маска?


После прошлого цикла у нас же на картинке остались только белые и черные пиксели?


Successfully aliased the URL <https://transferwise-components-docs-wprsurehez.now.sh> to the following alias.

* https://transferwise-components-docs.now.sh