[R/AllClasses.R:1:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L66) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:79:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L79) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:107:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L107) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:163:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:166:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L167) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:171:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L171) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:173:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/alphaSummary-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/DESeqResultsTables-methods.R#L187) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- sampleNames(data)
        ^~~~~~~~~~~
```
[R/export-methods.R:41:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L41) *style:* **Variable or function name should be snake_case.**
```r
.prepareDESeqResults <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:43:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L43) *style:* **Variable or function name should be snake_case.**
```r
    rowData = NULL,
    ^~~~~~~
```
[R/export-methods.R:45:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L45) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames = NULL
    ^~~~~~~~~~~
```
[R/export-methods.R:47:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L47) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:48:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L48) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(rowData, c("DataFrame", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:49:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L49) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(counts, c("matrix", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:50:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L50) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(sampleNames, c("character", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:58:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L58) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(rowData, "DataFrame")
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:59:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L59) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- sanitizeRowData(rowData)
        ^~~~~~~
```
[R/export-methods.R:59:20:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L59) *warning:* **no visible global function definition for ‘sanitizeRowData’**
```r
        rowData <- sanitizeRowData(rowData)
                   ^~~~~~~~~~~~~~~
```
[R/export-methods.R:60:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L60) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(rowData))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:67:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L67) *warning:* **no visible global function definition for ‘assert_is_matrix’**
```r
        assert_is_matrix(counts)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L68) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:75:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L75) *warning:* **no visible global function definition for ‘assert_has_names’**
```r
            assert_has_names(sampleNames)
            ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:76:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L76) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
            assert_are_identical(names(sampleNames), colnames(counts))
            ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L79) *warning:* **no visible global function definition for ‘assert_are_disjoint_sets’**
```r
        assert_are_disjoint_sets(colnames(data), colnames(counts))
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:93:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L93) *style:* **Variable or function name should be snake_case.**
```r
        rowData = NULL,
        ^~~~~~~
```
[R/export-methods.R:95:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L95) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames = NULL
        ^~~~~~~~~~~
```
[R/export-methods.R:104:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L104) *warning:* **no visible global function definition for ‘export’**
```r
        export(x = x, file = file, format = format)
        ^~~~~~
```
[R/export-methods.R:120:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L120) *style:* **Variable or function name should be snake_case.**
```r
.prepareResultsTablesList <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:121:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L121) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqResultsTables"))
    ^~~~~~~~~~~
```
[R/export-methods.R:125:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L125) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
    assert_is_list(deg)
    ^~~~~~~~~~~~~~
```
[R/export-methods.R:126:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L126) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
    assert_are_identical(names(deg), c("up", "down"))
    ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:134:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L134) *style:* **Variable or function name should be snake_case.**
```r
    rowData <- slot(object, "rowRanges") %>%
    ^~~~~~~
```
[R/export-methods.R:139:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L139) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames <- slot(object, "sampleNames")
    ^~~~~~~~~~~
```
[R/export-methods.R:147:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L147) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(all, "DataFrame"))
    ^~~~~~~~~~~
```
[R/export-methods.R:162:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L162) *warning:* **no visible global function definition for ‘initDir’**
```r
        dir <- initDir(dir)
               ^~~~~~~
```
[R/export-methods.R:163:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L163) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(compress)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:166:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L166) *warning:* **no visible global function definition for ‘.prepareResultsTablesList’**
```r
        tables <- .prepareResultsTablesList(x)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:167:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L167) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
        assert_is_list(tables)
        ^~~~~~~~~~~~~~
```
[R/export-methods.R:174:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L174) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
        stem <- snake(contrastName(x))
                ^~~~~
```
[R/export-methods.R:174:23:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L174) *warning:* **no visible global function definition for ‘contrastName’**
```r
        stem <- snake(contrastName(x))
                      ^~~~~~~~~~~~
```
[R/export-methods.R:180:51:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L180) *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:189:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L189) *warning:* **no visible global function definition for ‘export’**
```r
                export(x = x, file = file)
                ^~~~~~
```
[R/export-methods.R:196:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L196) *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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:52:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:54:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:60:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:81:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~
```
[R/markdown-methods.R:82:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:111:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/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/a4900392ba527a870ecd9ef16624357577d4b2e3/R/topTables-methods.R#L128) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(contrast)


@smith my understanding of Coefficient of Restitution is that it is the ratio of the relative velocities of 2 colliding objects before and after collision. The value ranges from 0 to 1. If the type of collision is:
Elastic: Momentum and kinetic energy are conserved, then COR = 1
Inelastic:  Momentum is conserved but kinetic energy  is not, it becomes smaller after collision, COR <1
Completely Inelastic: Momentum is conserved, kinetic energy becomes smaller, objects stick together after collision, COR = 0
Super-elastic collision, momentum is conserved and kinetic energy is larger, COR >1, this might be related to explosion which is not required in our collision scenarios.
This is what I refer to as "elasticity". But then on a second thought this might not be the property of the bodies but of the collision between the bodies.
Hope I am understanding this correctly and if this is the case, then can elasticity/COR be referred to as a surface property of the bodies?
Any inputs on this?


Do not use #id as css selector


Лучше сделать это константой


Same


ok, you are right


This is clear now. Thanks. Since I declared ` address public owner;` immediately after opening the contract and outside of any function, now ` owner` is a property of the contract. Also, ` owner = msg.sender;` is now part of the constructor. With these, I guess that the assignments ` msg.sender = owner` is now correct to have them in both functions, `  changeOwner` and ` killMe`, am I right?


Fix code style: must be **spoiler {** not **spoiler{**


Copy of this build can be found at
https://www.mewbuilds.com/build/6b8970c0eff791b6190dcbf12be364aecfe3b364/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmZHtAthSbSZ8919PtEd3ZoU8dDv1H63WJVjsQctMtaXcF


Same, do not use #id as css selector


**type="text/javascript"** - remove it


@Mornix I saw the comments Dr. @JacquesCarette gave. Seems like he likes the most of the changes. Only the problems are with `Deferred` and the `rprog` renaming problem. If everything else is fine, I want to merge this back to `sentence` as soon as possible. And I had another branch `toUseRef2` which was branched off from your branch. So if changes on that branch are fine too. I want to merge everything back to `sentence` and then we can proceed to the next stage. Is this suggestion good for you @JacquesCarette ?


Added disability (ra).


It would be better to point to the license file provided by SE lawyers :)
https://github.com/EcoStruxure/OLGA/blob/master/LICENSE.TXT


Use English


a description for the purpose of the update would be great :)


Remove extra space **let el   =**


#user can log in


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/529b8ded-028b-43ad-90e6-e022e37fdc0f?env_id=ibm%3Ayp%3Aeu-de "ChatServer-Toolchain"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/437e6884-8922-46f1-8ecd-72624d25543f?env_id=ibm%3Ayp%3Aeu-de "THISISchatPIPELINE") deployed [Chat-Server](https://github.com/dmddmd/Chat-Server/releases/tag/deploy-ibm-yp-eu-de-seyma.yueksel-student.reutlingen-university.de-dev-20181120-210709 "deploy-ibm-yp-eu-de-seyma.yueksel-student.reutlingen-university.de-dev-20181120-210709") to [dev](https://console.bluemix.net/apps/18d66966-121f-46b7-a074-1ff74e33cbb4?env_id=ibm:yp:eu-de "ibm:yp:eu-de:seyma.yueksel@student.reutlingen-university.de:dev"), including this commit


You can write something like that
let name = 'product';
let el   = document.getElementById(name);


This remove a lot of null protection from the code, are you sure this is right?  I did spot that you strategically added `|| []` in some spots, but not all.


Nice explanations, Matt! The only thing I would note is that question 2 is asking about the lifecycle _events_, where you're explaining the lifecycle of the component itself. So the mounting methods are methods that are called when the component is created and inserted into the DOM, etc. Other than that, everything looks great!


Aplicando uma correção ao RatyRate

wazery/ratyrate#42


When testing with a small IP list, max_lines was getting set to 0. Should fix BinaryDefense/goatrider#2


Shouldn't it be [Slack](https://cloudfoundry.slack.com) ?


if (data && data > 1) ...


English


Interpolation https://developer.mozilla.org/ru/docs/Web/JavaScript/Reference/template_strings


Same


I don't understand this, if we have no user we should return an error on password reset like a 400, no an object full of `null`s


https://travis-ci.org/darktable-org/darktable/jobs/457564906
```c
/build/darktable/src/imageio/storage/piwigo.c:240:8: error: logical not is only applied to the left hand side of this comparison [-Werror,-Wlogical-not-parentheses]
    if(!json_node_get_node_type(root) == JSON_NODE_OBJECT) goto cleanup;
       ^                              ~~
/build/darktable/src/imageio/storage/piwigo.c:240:8: note: add parentheses after the '!' to evaluate the comparison first
    if(!json_node_get_node_type(root) == JSON_NODE_OBJECT) goto cleanup;
       ^
        (                                                )
/build/darktable/src/imageio/storage/piwigo.c:240:8: note: add parentheses around left hand side expression to silence this warning
    if(!json_node_get_node_type(root) == JSON_NODE_OBJECT) goto cleanup;
       ^
       (                             )
```


Hi


remove **console.log(this.products)**


I wonder, should add_to_serializer just handle this automatically? On the :person_fencing: here but it seems less error prone.


**} else {**


![](https://github.trello.services/images/mini-trello-icon.png) [#8 Daily Scrum](https://trello.com/c/6mM6cmRe/52-8-daily-scrum)


This would have been amazing for speedrunning! :P
Like the HL2 bunny hop :)


10/10

The gender icon is interesting! I like it.


This is not right. If the topic is not found we should return an error with failed json, not eat it.


**(i + 1)**


![](https://github.trello.services/images/mini-trello-icon.png) [Создать API для взаимодействия между контроллером и моделью](https://trello.com/c/qCL5MG5e/2-%D1%81%D0%BE%D0%B7%D0%B4%D0%B0%D1%82%D1%8C-api-%D0%B4%D0%BB%D1%8F-%D0%B2%D0%B7%D0%B0%D0%B8%D0%BC%D0%BE%D0%B4%D0%B5%D0%B9%D1%81%D1%82%D0%B2%D0%B8%D1%8F-%D0%BC%D0%B5%D0%B6%D0%B4%D1%83-%D0%BA%D0%BE%D0%BD%D1%82%D1%80%D0%BE%D0%BB%D0%BB%D0%B5%D1%80%D0%BE%D0%BC-%D0%B8-%D0%BC%D0%BE%D0%B4%D0%B5%D0%BB%D1%8C%D1%8E)


Haaaaaah. OK. Fair enough. I accept your rationale. It's a good rationale.


this.products.length - move to separate variable, for example **const ln = this.products.length**


10/10
Nice!


'element' a pretty vague variable name, using something like 'tab' could make it the code clearer.


Why you can not use ES6 Classes?


Yes, since `degree` is not used. I removed `degree` from `si_units'. The `nw degree` I added is for the everything ChunkDB. But the actual units printed out are pulled out from si_units. So now, this should be the right.


10/10
Awesome!


This is what breaks demo-app, can't directly import from `kepler.gl/utils/utils`, `generateHashId` is already exported from utils, you can import it from `kepler.gl/utils/utils`


# Autenticação vs Autorização
Autenticar é logar o usuário no sistema.
Autorizar é dar permissões sobre o que o usuário pode ou não fazer no sistema.

## Uso
* gem ‘pundit’
* include Pundit (Application Controller)
* rails g pundit:install (app/policies)

## Gerenciamento de errors
Manages Pundit Errors
`rescue_from Pundit::NotAuthorizedError, with: :user_not_authorized`
```
def user_not_authorized
    flash[:alert] = "Você não está autorizado a executar essa ação."
    redirect_to(request.referrer || root_path)
end
```

### Dúvidas
https://github.com/varvet/pundit
https://github.com/varvet/pundit#rescuing-a-denied-authorization-in-rails
https://github.com/elabs/pundit#policies
https://github.com/varvet/pundit#customize-pun


**new function()** ???


Nice


Successfully aliased the URL <https://pfblog-kxlya3afm.now.sh> to the following alias.

* https://www.christopherpfaff.com


OK. My basic principle was that a numeric value should generally be initialized to 0, not None.


move to constants


While this is fine in this scenario due to the contents of the data provided with this project, a better key would be something guaranteed to be unique.


add unsubscribes


Did you wrote JS code by yourself?

What is a strange commit message **asd** ? What does it mean?


Disregard, found it in the readme: https://autohotkey.com/boards/viewtopic.php?t=34890


does this want to be called on Init? or just on user request?


See https://github.com/FriendsOfTYPO3/extension_builder/issues/181 - tests will most likely fail until being adjusted


7/10

Viewing all students functionality?


Don't we have [the Config object](https://doc.wikimedia.org/mediawiki-core/master/php/interfaceConfig.html) for that?


Successfully aliased the URL <https://pfblog-o5hi8lfg4.now.sh> to the following alias.

* https://www.christopherpfaff.com


Переменные всегда с малой буквы


Successfully aliased the URL <https://simon-kjellberg-iwleoazodz.now.sh> to the following aliases.

* https://simonkjellberg.com
* https://www.simonkjellberg.com
* https://simonkjellberg.se
* https://www.simonkjellberg.se


good


Нужно добавлять **класс**


I submitted it at 4, but I forgot to add the .deal to it so I updated it


10/10 Nice!


add get groups() to predictor. this should return predictor.valueNames


Capitalization problem seems not like a small job. Do I take care of this problem? If do, I guess I need more time to think of it. @JacquesCarette


![](https://github.trello.services/images/mini-trello-icon.png) [Добавил футер, хэдер, табы, СТА-секцию для всех разрешений](https://trello.com/c/ycfpQxa6/11-%D0%B4%D0%BE%D0%B1%D0%B0%D0%B2%D0%B8%D0%BB-%D1%84%D1%83%D1%82%D0%B5%D1%80-%D1%85%D1%8D%D0%B4%D0%B5%D1%80-%D1%82%D0%B0%D0%B1%D1%8B-%D1%81%D1%82%D0%B0-%D1%81%D0%B5%D0%BA%D1%86%D0%B8%D1%8E-%D0%B4%D0%BB%D1%8F-%D0%B2%D1%81%D0%B5%D1%85-%D1%80%D0%B0%D0%B7%D1%80%D0%B5%D1%88%D0%B5%D0%BD%D0%B8%D0%B9)


![](https://github.trello.services/images/mini-trello-icon.png) [Добавил коммит с добавленной странице мастеров на все версии.](https://trello.com/c/anko7NBL/10-%D0%B4%D0%BE%D0%B1%D0%B0%D0%B2%D0%B8%D0%BB-%D0%BA%D0%BE%D0%BC%D0%BC%D0%B8%D1%82-%D1%81-%D0%B4%D0%BE%D0%B1%D0%B0%D0%B2%D0%BB%D0%B5%D0%BD%D0%BD%D0%BE%D0%B9-%D1%81%D1%82%D1%80%D0%B0%D0%BD%D0%B8%D1%86%D0%B5-%D0%BC%D0%B0%D1%81%D1%82%D0%B5%D1%80%D0%BE%D0%B2-%D0%BD%D0%B0-%D0%B2%D1%81%D0%B5-%D0%B2%D0%B5%D1%80%D1%81%D0%B8%D0%B8)


Hm... tests did not fail... "great"


```
[INFO] Results:
[INFO]
[INFO] Tests run: 290, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
```
:+1:


Shouldn't these be using `global.sdk_road_shields` instead of explicit true/false values? Otherwise the `visible: true` lines will turn on shields even if they are off at the global level.


That's a useful find and must be the original reason for `SWIG_Py_None`.

If there is a problem with Py_None, there would also be problems with the other similarly declared functions:

```c
// object.h:
PyAPI_DATA(PyObject) _Py_NoneStruct; /* Don't use this directly */
#define Py_None (&_Py_NoneStruct)

PyAPI_DATA(PyObject) _Py_NotImplementedStruct; /* Don't use this directly */
#define Py_NotImplemented (&_Py_NotImplementedStruct)

// sliceobject.h:
PyAPI_DATA(PyObject) _Py_EllipsisObject; /* Don't use this directly */
#define Py_Ellipsis (&_Py_EllipsisObject)
```
The preprocessed output from Visual C++ is:
```c
extern __declspec(dllimport) PyObject _Py_NoneStruct;
extern __declspec(dllimport) PyObject _Py_NotImplementedStruct;
extern __declspec(dllimport) PyObject _Py_EllipsisObject;
```
but there are many other functions declared like this:
```c
extern __declspec(dllimport) PyTypeObject PyList_Type;
```
Anyway, another solution might be to use the inc/dec ref functons from object.h instead:
```c
/*
These are provided as conveniences to Python runtime embedders, so that
they can have object code that is not dependent on Python compilation flags.
*/
PyAPI_FUNC(void) Py_IncRef(PyObject *);
PyAPI_FUNC(void) Py_DecRef(PyObject *);
```

To test your theory that modern mingw will be better, I fixed the mingw testing on Appveyor in a few commits
c7363fd95ee97144147aebc7e1cd858c17c78687..902f3f0ac58faaacbb4f53f73449b8da42486bb1 which tests the native Windows 2.7 and 3.7 Python distributions (Visual C++ built) and the test-suite passes with mingw's gcc. So in summary I think this problem is now mute and I'm going to leave the change in. No doubt if there is a problem we've missed it will be reported and we can revisit this decision.


See comment on `global.sdk_road_shields` above.


Я так и не понял зачем тебе асинхронщина понадобилась в иницилизации. Я просто не понимаю решений, которые ты принимаешь


That's just for building the sources, so I preferred using the simple version :)


I don't like it as it's not scientific, but we could have it temporarily if the demo shots from ML forum still look accurate (the ones that people used to demostrate MLV App inaccuracy in the past).


Successfully aliased the URL <https://pfblog-pk6pjeht3.now.sh> to the following alias.

* https://www.christopherpfaff.com


Or @bouncyball-git could you try on your shot with the red goggles?


Shouldn't these be using `global.sdk_road_shields` instead of explicit `true`? Otherwise it will turn on shields even if they are off at the global level.


This closes #22


Note: made some comments that I realized were incorrect re: `global.sdk_road_shields`, then deleted and replaced with correct comments :)


Copy of this build can be found at
https://www.mewbuilds.com/build/4485c88e19632b18e441937889f59e40a7c5fa7b/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmRad1e7aY6LB4j4rDbmf5pWndrkxLe8sjkfow2c36iwVp


Dunno. Reported to GitHub.


Optimization/simplification (can be for next patch/release): I think we can replace all the uses of `visible: global.sdk_road_shields` with a filter at the layer level -- if the shields global is off, *none* of these should be visible anyway. We save a lot of parsing/processing with all these rules in that case.


Thanks for the heads-up Roman, should be fixed.


ok now this is epic


Ah of course, makes sense ^^


This just broke the oss tool again because it is a schema change that needs to be adopted also in the tooling.


Will do, my bad :smile:


I think the Travis build failed for unrelated reasons. I put it back to the newest version (https://github.com/bonej-org/BoneJ2/commit/621afe10013f324ad169553c5ffe3722d355315b) and the Travis build [passed this time](https://travis-ci.org/bonej-org/BoneJ2/builds/457659873).


Pls, refactor it with accordance to other dependencies


The term elasticity often refers to the relationship between stress and strain in deformable bodies.  What you say is correct because the coefficient of restitution is including deformation, but we don't actually track the deformation.  We should probably stay away from using the term elastic, unless we are characterizing the coefficient of restitution.

You have a good point that COR is a property of the pair of objects in a collision.  I think you can consider COR a property of a given set of objects.  The COR is the same between all of them.  Making this variable between pairs of objects could be a likely change for the future.

Yes, when kinetic energy is conserved COR = 1.  If it isn't there already, you can have a constraint that COR is between 0 and 1.  Your super-elastic collisions is a neat idea, but we don't need to consider this case.


Not scientific, you are right, only a temporary solution. It looks fairly similar to what is out now but with the benefit of not coruupting blue highlights. A few tests:

Mlv App colorspace
![screenshot 2018-11-20 at 22 33 26 png_500px](https://user-images.githubusercontent.com/22038358/48804412-d09ed880-ed14-11e8-8f11-87ddd93a80d2.jpg)

Tweaked:
![screenshot 2018-11-20 at 22 33 14 png_500px](https://user-images.githubusercontent.com/22038358/48804432-e2807b80-ed14-11e8-80d9-322a07281d8f.jpg)

Official build(blue issues):
![screenshot 2018-11-20 at 22 12 57 png_500px](https://user-images.githubusercontent.com/22038358/48804462-f75d0f00-ed14-11e8-9874-22084fb9ed3b.jpg)

Tweaked:
![screenshot 2018-11-20 at 22 12 12 png_500px](https://user-images.githubusercontent.com/22038358/48804471-fe841d00-ed14-11e8-9829-32f5cb1b6cdb.jpg)

Tweaked:
![screenshot 2018-11-20 at 22 28 21 png_500px](https://user-images.githubusercontent.com/22038358/48804489-0a6fdf00-ed15-11e8-8060-c934ae5b8daf.jpg)


Are You sure that session always contains this attribute ?


Ok.


Great answers, they really reflect a great understanding of the subject matter.


this cannot use `base::Unretained` because the fetch may finish after RewardsServiceImpl has been destroyed


You should be able to do this by adding a function filter like:

```
                    all:
                        - function() { return global.sdk_road_shields; }
                        - network: ['AM:AM', ...]
                        - shield_text: true
```


Když chceš mít perfektně kulatý rámeček, tak můžeš použít `border-radius: 50%` - to zablení pak bude přesně do půlky prvku, nezávisle na jeho velikosti.


test crutique


Я не знаю, что такое "наложение чар", но предварительно предлагаю назвать enchanter_feat (типа способный делать enchant - зачароване).
После case не нужно добавлять фигурные скобки - сам case хорошо выделяет. В C нужно было иногда, чтобы объявить локальную переменную. В C++ и это не нужно. Недостаток - код уезжает вправо, его сложнее обозревать.


[quote="sam, post:2, topic:55"]
Is this hiding some transifex quirk ?
[/quote]

Yes and no. :slight_smile:

I recommend to always use the `%{count}` variable, even in the `one` category. A lot of languages use the `one` category for more than just the number 1. As we recently noticed, French is one of them. :wink:

https://meta.discourse.org/t/always-use-count-variable-when-translating-pluralized-strings/83969

This fixes two issues with Transifex:

1. Transifex uses the English text from the `one` category as suggestion for translations in the `one` category. When it contains the `%{count}` variable, we can force translators to use it and the Transifex editor actually makes that very easy. If it doesn't exist translators might forget or don't even know that they need to replace the `1` with `%{count}`.

   > Wow. I thought “`0`” was using the “`other`” category.

2. Transifex allows us to force translators to use all interpolation keys that exist in the original text in the translated text. I had to change it from "error" (which disables save) to "warn", because unfortunately it doesn't allow adding a variable, that doesn't exist in English.


Note that webcam code is currently only edits to the Sahil classes.


A little bit strange logic : Why every file uploading lead to error view ?


You should start naming your member variables with prefixes so you don't have to use this->. But it could be a matter of preference.


closes #5


Any chance I could get you to PR this back upstream? :)


Když používáš font z Google fonts, tak musíš v Customize zaškrnout sadu "Latin Extended", jinak ten font nebude umět české znaky.
![tmp](https://user-images.githubusercontent.com/932001/48727786-7c6ff780-ec33-11e8-8e3a-be3edff8c6b1.png)


You run the command to install it again.


Why english, we are developing foreign product?


Copy of this build can be found at
https://www.mewbuilds.com/build/28acc203f4a646dbf9f385b2c1c227c9ca42fbd2/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmaFntJy93WJuWHmDpgDwdSvAYBuudZGf5dbcBDwFHBFB9


Выполнила третье задание


@queuefive Thank you so much for the very useful repository on how to use kivy and sqlite3, would you please make it entirely in python (without kv file) ?


Aliasing failed with the following error:

~~~
Error! The alias primer-components.now.sh is a deployment URL or it's in use by a different team.
~~~


`margin`y jsou řešení, trochu vhodnější alternativou v tohle případě by bylo relativní či absolutní pozicování.


Pár poznámek, ale to jsou jen drobnosti. Jinak super :+1: :1st_place_medal:


There will be one hashing function, named `hashThat`. In pseudo-code, you will have `puzzle = hashThat(password1, password2)`.


@normanmaurer sorry only just saw your comments here, bit behind on email! I think they are all now addressed in the new PR though.


With the offence class this is not needed any more here.


Prefer to use emplace_back for elements that are move insertable (i.e. https://en.cppreference.com/w/cpp/named_req/MoveInsertable)


WTF ??? Why class located in enum package ? If it enum then make it enum. If it finally - make it final. Now it is smth fucking-stupid


И содержательные изменения пожалуйста отдельно от обширных бессодержательных изменений в коде типа форматирования, комментариев и т.д. Содержательные правки требуют внимательного review, но они тонут и теряются в спаме.


105: @cp -frv ../README.md **../doc/*.pdf** ../deb/data/usr/share/doc/geoeasy

$make deb
...
cp: failed to execute stat for "**../doc/*.pdf**": No such file or directory
make: *** [deb] Error 1


Is it necessary use model for single string ?


this could easily be just return answer == mAnswers[questionID];


Hello Fred!
Some weeks ago, I had begun to search sounds but wasn't very convinced by my findings.
I you have ideas, you're welcome.
If you want to convert the Sound unit to another library (as you had proposed), you're also welcome.
Regards.
Roland


Убрали скрипт из html во внешний файл и подключили его


It's temporary decision. Some kind of stub


Look, `owner` is an `address` type. Then you declared `mapping (bytes32 => NewRemittance) public remittanceBoxes;` so with `bytes32` as the key type to access the values. So when you do `remittanceBoxes[something]`, this `something` has to be a `bytes32`. So `owner` will not do.
What would be a judiciously chosen `something` key here?


:+1: :1st_place_medal:


This will just update it at the beginning of the periodic celery task (so, once every 5 minutes): https://github.com/dimagi/commcare-hq/pull/22470/commits/867f9e93506365ae34fd704e3d840975fc3d4e01


If this is the case then consider making your class final, i.e. class TriviaFactory final {};


This needs the ``"it,test"`` stuff specified, otherwise it adds junit as a compile/runtime dependency to all projects instead of just a test dependency . This was the reason i suggested making ``lazy val junit`` not a Seq. That way you can add the ``"it,test"`` part for ``lazy val test`` so it's just a test dependency to all the projects, but can also be added as a compile dependency for the tdml project.


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

InterpreterError at template.tasks[2].payload.artifacts["public/task-graph.json"].expires: unknown context value expires_in

</details>


This is wrong, you should call np.tile *only* in the case ret_val is of size 1 along the 3rd dimension. And the second point is that exp_str is assumed to contain `t` as a single independent variable, so that you need to assign the values of `t_vec` to `t`
```
t = t_vec
```
before calling `eval`. But I'm not sure at all that this will work even after this fix. Python and Matlab are different, and you should think how to implement this so that it is possible to use this method.

Suppose exp_str represents some string expression, for example, it may be like the following one:
```
exp_str='[[sin(t),cos(t)],[-cos(t),sin(t)]]'
```
Then to be able to call eval you should first be sure that `sin(t)`, `cos(t)` and so on are calculable. Then you need to call the following command before you launch `eval`:
```
from numpy import *
```
This allows you to call numpy functions without any prefix (`sin(t)` instead of `np.sin(t)`). But you obtain in this case not the desired np.ndarray, but list of lists of 1D numpy arrays, for the above example they are like the following ones (when `t_vec = np.linspace(0, 2*np.pi, 10)`):
```
ret_val[0][0]=array([ 0.00000000e+00,  6.42787610e-01,  9.84807753e-01,  8.66025404e-01,
        3.42020143e-01, -3.42020143e-01, -8.66025404e-01, -9.84807753e-01,
       -6.42787610e-01, -2.44929360e-16])
ret_val[0][1]=array([ 1.        ,  0.76604444,  0.17364818, -0.5       , -0.93969262,
       -0.93969262, -0.5       ,  0.17364818,  0.76604444,  1.        ])
ret_val[1][0]=array([-1.        , -0.76604444, -0.17364818,  0.5       ,  0.93969262,
        0.93969262,  0.5       , -0.17364818, -0.76604444, -1.        ])
ret_val[1][1]=array([ 0.00000000e+00,  6.42787610e-01,  9.84807753e-01,  8.66025404e-01,
        3.42020143e-01, -3.42020143e-01, -8.66025404e-01, -9.84807753e-01,
       -6.42787610e-01, -2.44929360e-16])
```
And you need to transform this list of lists to a 3D numpy array.

That is exactly what is to be done in this method.


No, it is not correct to have `msg.sender = owner`. Yes, it is an assignment, not a test, and no it will not compile anyway because `msg.sender` is read-only.
What you want when you want to make sure it is only accessible by the owner is a test.
Did you mean `msg.sender == owner`?


Pushed a fix to the oss tool. Pls adopt such changes in that tool as well.


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

* https://mdxjs.com
* https://www.mdxjs.com


Awesome Alex!


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Client ID project/taskcluster/tc-github/production does not have sufficient scopes and are missing the following scopes:

```
{
  "AllOf": [
    "queue:create-task:highest:aws-provisioner-v1/gecko-focus",
    "queue:create-task:highest:scriptworker-prov-v1/mobile-beetmover-v1",
    "queue:create-task:highest:aws-provisioner-v1/gecko-focus"
  ]
}
```

You have the scopes:

```
[
  "assume:project:taskcluster:mozilla-github-repository",
  "assume:repo:github.com/mozilla/application-services:tag:v-scriptworker",
  "docker-worker:cache:application-services-*",
  "docker-worker:relengapi-proxy:tooltool.download.internal",
  "docker-worker:taskcluster-proxy:tooltool.download.internal",
  "notify:email:*",
  "notify:irc-channel:*",
  "notify:irc-user:*",
  "queue:create-task:aws-provisioner-v1/github-worker",
  "queue:create-task:aws-provisioner-v1/github-worker-windows",
  "queue:create-task:aws-provisioner-v1/win2012r2",
  "queue:create-task:high:aws-provisioner-v1/application-services-r",
  "queue:create-task:highest:aws-provisioner-v1/application-services-r",
  "queue:create-task:low:aws-provisioner-v1/application-services-r",
  "queue:create-task:lowest:aws-provisioner-v1/application-services-r",
  "queue:create-task:medium:aws-provisioner-v1/application-services-r",
  "queue:create-task:very-high:aws-provisioner-v1/application-services-r",
  "queue:create-task:very-low:aws-provisioner-v1/application-services-r",
  "queue:route:garbage.*",
  "queue:route:index.garbage.*",
  "queue:route:index.project.application-services.*",
  "queue:route:index.project.fxaclient.builds.*",
  "queue:route:notify.email.*",
  "queue:route:notify.irc-channel.*",
  "queue:route:notify.irc-user.*",
  "queue:scheduler-id:taskcluster-github",
  "secrets:get:garbage/*",
  "secrets:get:project/application-services/publish",
  "secrets:set:garbage/*"
]
```

This request requires you to satisfy this scope expression:

```
{
  "AllOf": [
    "queue:scheduler-id:taskcluster-github",
    "queue:create-task:highest:aws-provisioner-v1/gecko-focus",
    "queue:create-task:highest:scriptworker-prov-v1/mobile-beetmover-v1",
    "queue:route:index.project.application-services.*",
    "docker-worker:cache:application-services-*",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/gecko-focus"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2018-11-20T21:55:15.091Z

</details>


@daveshah1 Is this a placeholder value, or is the setup time really 100ps?


Skvělý! :+1: :1st_place_medal:


Když používáš font z Google fonts, tak musíš v Customize zaškrnout sadu "Latin Extended", jinak ten font nebude umět české znaky.
![tmp](https://user-images.githubusercontent.com/932001/48727786-7c6ff780-ec33-11e8-8e3a-be3edff8c6b1.png)


One thing to be aware of with the hid guardian bit is that you have to run Gremlin as root (required to modify the registry entries) and that once you block / unblock a device you will have to unplug and then replug the device before those changes take effect.


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

* https://mdxjs.com
* https://www.mdxjs.com


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

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


I added it in here:
https://github.com/dimagi/commcare-hq/pull/22470/commits/8d0d45e3c58cdeeeec1ca8288175ef40a3f66508

Looks like the time interval is hardcoded at 1 minute: https://github.com/dimagi/commcare-hq/blob/master/corehq/motech/repeaters/const.py#L8


![](https://github.trello.services/images/mini-trello-icon.png) [André Carvalho](https://trello.com/c/MlnhnEGo/13-andr%C3%A9-carvalho)


What will happen if CDN falls down ?


The same


Successfully aliased the URL <https://clickable-box-pmsntiqv7.now.sh> to the following alias.

* https://clickable-box.now.sh


Ah, yeah I realized this last night. I think I will just use Python for this and template it in.


You are conflating 2 concepts:

* the contract state
* what happens during one transaction call to `transferEther`

Those are entirely different things.
The contract state is carried over from transaction to transaction.
Yes, a transaction call to `transferEther` will change the contract state, but it is not because I made 1 transaction call that the state is zeroed out and only has left what the transaction changed or touched.
That was my whole point of making you write the `pendingWithdrawals[alice] = ??`. On each call only 2 of them changed because there are only 2 recipients per call. But after the 2 second call there were 3 interesting values. Remember how you mistakenly believed and zeroed out one "because it was not mentioned in the transaction"

The answer to my question of how to write the `assert` for that balance invariant is that you cannot. It would need to loop through all the non-zero values in the mapping, and there is no such thing. Moreover, looping an unbounded number of times would consume so much gas that sooner or later it would be bigger than the block gas limit, and so would fail.


I responzivní :open_mouth: ! Dobře Míšo! :+1: :1st_place_medal: :1st_place_medal:


Is it necessary to include this even before page header ?


Já si myslím, že tenhle `</div >` je tu navíc :-)


@DHubernatorova w 4 pracy domowej dane są źle wczytane. Na osi OY widać że zmienna nie jest ciągłą ale jest factorem


Here, we provided the xml file our product list view and refactor our code in the DATASERVICE so that it can populate the list of item for a category when that category is selected.


This makes @rupansh happy as well


Successfully aliased the URL <https://clickable-box-log9kpona.now.sh> to the following alias.

* https://clickable-box.now.sh


Please change all this button names to more meaningful.


If we want to use the sqm_${verbosity} functions here we will need to source both functions.sh and defaults.sh:
before we call these. That in turn will make the defaults.sh version of the following variables:
    SQM_DEBUG, SQM_VERBOSITY_MAX, SQM_VERBOSITY_MIN
override the versions defined in the GUI.

. ${SQM_LIB_DIR}/defaults.sh
. ${SQM_LIB_DIR}/functions.sh


q2 simulink file


If plain `echo >>plug.py` works, that would be fine -- it works on UNIX.


Error if hashmap is empty? WOW.
In python, it just will pint "{}"


Yes, i have tried to include it in the end but it wasnt worked


DONT USE "obj" AS VAR NAME


OK!


NICE


Of course, it just template titles


The [enqueued time](https://docs.microsoft.com/en-us/azure/service-bus-messaging/service-bus-amqp-protocol-guide#message-annotations) needs to be UTC. Also the .microsecond is just the micro second part of the datetime object, its orders of magnitude too small for filtering messages from 'now'. You will likely see older messages being received (up to whatever the retention period is of the event hub) outside of the running test bounds.

What needs to happen to see messages from 'now' is to calculate milliseconds since the unix epoch. There is a [nested helper method](https://github.com/Azure/azure-iot-cli-extension/blob/dev/azext_iot/operations/hub.py#L1136) in monitor events that does this. You can extract that and put it somewhere more usable like common.utility then reference it from the test.


testing 456


Successfully aliased the URL <https://next-train-monorepo-orrnaptzx.now.sh> to the following alias.

* https://next-train.now.sh


These changes look good to me, and feel free to create a PR to MaterialX master.


Když chceš zobrazit text velkými písmeny, použij na to CSS vlastnost `text-transform`. Když to takhle napíšeš velkýma v textu, tak třeba hlasové čtečky budou na uživatele zbytečně kříčet :-)


Ok. I guess I get this.

Starting to understand the issues with sbt and with Domain-specific-languages / DSLs generally.


nazwy [SurrogateKey] jest jasna, ale raczej tak się nie robi, standardowo raczej ludzie używają konwencji TabelaId, TabelaKey:

1. [PracownikId], [PracownikKey]
2. [StanowiskoId], [StanowiskoKey]
3. ...

TabelaKey - identity, PK
TabelaId - UNIQUE, not null

a jak Pan robi tabelki, to kolumnę TabelaKey jako pierwsza, teoretycznie żadna to różnica, ale wygodniej się czyta i wszyscy są przyzwyczajeni, że przy SELECT * kolumna z PK będzie pierwsza


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

* https://jsheroes.io


Pseudotřída `:hover` existuje u všech prvků, nejen u odkazů, takže pokud chceš u nějakého prvku mít efekt při najetí myší, můžeš přidat `:hover` rovnou k němu (třeba `.velikosti li:hover`), nemusíš přidávat áčka :)