[R/bootstrap.R:27:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
#'  prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                                                      ^~
```
[R/bootstrap.R:35:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L35) *style:* **Trailing whitespace is superfluous.**
```r
bootstrapAUC <- function(SE_scored, annotationColName, signatureColNames,
                                                                         ^
```
[R/bootstrap.R:38:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L38) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:41:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L41) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:51:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L51) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bootstrap.R:56:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L56) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bootstrap.R:68:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L68) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bootstrap.R:73:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L73) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:80:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L80) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:86:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:88:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L88) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:90:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L90) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:93:40:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L93) *style:* **Trailing whitespace is superfluous.**
```r
#'  choose_sigs <- subset(TBsignatures,
                                       ^
```
[R/bootstrap.R:101:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L101) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/bootstrap.R:102:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L102) *style:* **Trailing whitespace is superfluous.**
```r
tableAUC <- function(SE_scored, annotationColName, signatureColNames,
                                                                     ^
```
[R/bootstrap.R:110:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L110) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:126:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L126) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:139:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L139) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:141:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L141) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:144:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L144) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:155:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L155) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~
```
[R/bootstrap.R:171:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L171) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:175:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L175) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:177:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L177) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:179:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L179) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:187:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L187) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bootstrap.R:191:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L191) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:239:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L239) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:247:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L247) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:260:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L260) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:271:36:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L271) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::scale_color_manual("",
                                   ^
```
[R/bootstrap.R:275:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L275) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:359:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L359) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:375:7:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L375) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(any(is.nan(this.conf$UpperTPR))) {
      ^
```
[R/bootstrap.R:390:84:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L390) *style:* **Trailing whitespace is superfluous.**
```r
  if (is.null(name)) name <- paste("ROC plots for Gene Signatures, ", ci.lev * 100,
                                                                                ^
```
[R/bootstrap.R:441:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/bootstrap.R#L441) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/evaluate.R:172:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/evaluate.R#L172) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:177:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/evaluate.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:183:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/evaluate.R#L183) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:192:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/evaluate.R#L192) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/plot.R:67:69:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L67) *style:* **Trailing whitespace is superfluous.**
```r
#'                                      colData = DataFrame(sample =
                                                                    ^
```
[R/plot.R:78:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L78) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~
```
[R/plot.R:82:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L82) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plot.R:88:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L88) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~~
```
[R/plot.R:91:62:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
                             colList = list(), scale = FALSE,
                                                             ^
```
[R/plot.R:161:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L161) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/plot.R:174:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L174) *style:* **Trailing whitespace is superfluous.**
```r
#' @param inputData an input data object. It should either be of the class
                                                                          ^
```
[R/plot.R:175:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L175) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{SummarizedExperiment} and contain the profiled signature data and
                                                                          ^
```
[R/plot.R:176:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L176) *style:* **Trailing whitespace is superfluous.**
```r
#' annotation data as columns in the \code{colData}, or alternatively be of the
                                                                               ^
```
[R/plot.R:177:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L177) *style:* **Trailing whitespace is superfluous.**
```r
#' classes \code{data.frame} or \code{matrix} and contain only the gene
                                                                       ^
```
[R/plot.R:179:82:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L179) *style:* **Trailing whitespace is superfluous.**
```r
#' @param annotationData a \code{data.frame} or \code{matrix} of annotation data,
                                                                                ^
```
[R/plot.R:180:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L180) *style:* **Trailing whitespace is superfluous.**
```r
#' with one column. Only required if \code{inputData} is a \code{data.frame} or
                                                                               ^
```
[R/plot.R:182:82:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L182) *style:* **Trailing whitespace is superfluous.**
```r
#' @param signatureColNames a \code{vector} of the column names in \code{colData}
                                                                                ^
```
[R/plot.R:183:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L183) *style:* **Trailing whitespace is superfluous.**
```r
#' that contain the signature data. Only required if \code{inputData} is a
                                                                          ^
```
[R/plot.R:185:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L185) *style:* **Trailing whitespace is superfluous.**
```r
#' @param annotationColName a character string naming the column name in the
                                                                            ^
```
[R/plot.R:186:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L186) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{colData} that contains the annotation data to be used in making the
                                                                            ^
```
[R/plot.R:188:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L188) *style:* **Trailing whitespace is superfluous.**
```r
#' @param name a character string giving the title of the boxplot. The default
                                                                              ^
```
[R/plot.R:190:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L190) *style:* **Trailing whitespace is superfluous.**
```r
#' @param scale logical. Setting \code{scale = TRUE} scales the signature data.
                                                                               ^
```
[R/plot.R:192:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L192) *style:* **Trailing whitespace is superfluous.**
```r
#' @param includePoints logical. If \code{TRUE}, points will be included over
                                                                             ^
```
[R/plot.R:194:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L194) *style:* **Trailing whitespace is superfluous.**
```r
#' @param notch logical. Notches are used to compare groups; if the notches of
                                                                              ^
```
[R/plot.R:195:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L195) *style:* **Trailing whitespace is superfluous.**
```r
#' two boxes do not overlap, this suggests that the medians are significantly
                                                                             ^
```
[R/plot.R:196:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L196) *style:* **Trailing whitespace is superfluous.**
```r
#' different. If \code{TRUE}, the boxplot will be notched. The default is
                                                                         ^
```
[R/plot.R:198:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L198) *style:* **Trailing whitespace is superfluous.**
```r
#' @param rotateLabels logical. If \code{TRUE}, the x-axis labels will be
                                                                         ^
```
[R/plot.R:210:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L210) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plot.R:218:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L218) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:221:67:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L221) *style:* **Trailing whitespace is superfluous.**
```r
#'                                    colData = DataFrame(sample =
                                                                  ^
```
[R/plot.R:224:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L224) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:234:69:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L234) *style:* **Trailing whitespace is superfluous.**
```r
                             annotationColName, name = "Signatures",
                                                                    ^
```
[R/plot.R:235:66:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L235) *style:* **Trailing whitespace is superfluous.**
```r
                             scale = FALSE, includePoints = TRUE,
                                                                 ^
```
[R/plot.R:236:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L236) *style:* **Trailing whitespace is superfluous.**
```r
                             notch = FALSE, rotateLabels = FALSE, nrow = NULL,
                                                                              ^
```
[R/plot.R:249:68:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L249) *style:* **Trailing whitespace is superfluous.**
```r
      SummarizedExperiment::colData(inputData)[, annotationColName,
                                                                   ^
```
[R/plot.R:252:68:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L252) *style:* **Trailing whitespace is superfluous.**
```r
      SummarizedExperiment::colData(inputData)[, signatureColNames,
                                                                   ^
```
[R/plot.R:289:60:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L289) *style:* **Trailing whitespace is superfluous.**
```r
                               variable.name = "Signature",
                                                           ^
```
[R/plot.R:291:41:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L291) *style:* **Trailing whitespace is superfluous.**
```r
  theplot <- ggplot2::ggplot(boxplotdfm,
                                        ^
```
[R/plot.R:293:53:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L293) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::facet_wrap(~Signature, scales = 'free',
                                                    ^
```
[R/plot.R:295:46:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L295) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::geom_boxplot(outlier.shape = NA,
                                             ^
```
[R/plot.R:315:57:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L315) *style:* **Trailing whitespace is superfluous.**
```r
#' and creates a heatmap based on the expression scores.
                                                        ^
```
[R/plot.R:318:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L318) *style:* **Trailing whitespace is superfluous.**
```r
#' @param inputData a \code{SummarizedExperiment} object containing the profiled
                                                                                ^
```
[R/plot.R:323:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L323) *style:* **Trailing whitespace is superfluous.**
```r
#' @param sigGenes a vector identifying the genes in the signature to use in
                                                                            ^
```
[R/plot.R:326:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L326) *style:* **Trailing whitespace is superfluous.**
```r
#' @param name a character string with the plot title of the heatmap. The
                                                                         ^
```
[R/plot.R:328:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L328) *style:* **Trailing whitespace is superfluous.**
```r
#' @param signatureColNames a vector of the column names in the \code{colData}
                                                                              ^
```
[R/plot.R:330:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L330) *style:* **Trailing whitespace is superfluous.**
```r
#' @param annotationColNames a vector of the column names in the \code{colData}
                                                                               ^
```
[R/plot.R:332:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L332) *style:* **Trailing whitespace is superfluous.**
```r
#' @param scale logical. Setting \code{scale = TRUE} scales the signature data.
                                                                               ^
```
[R/plot.R:334:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L334) *style:* **Trailing whitespace is superfluous.**
```r
#' @param showColumnNames logical. Setting \code{showColumnNames = TRUE} will
                                                                             ^
```
[R/plot.R:335:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L335) *style:* **Trailing whitespace is superfluous.**
```r
#' show the column names (i.e. sample names) on the heatmap. The default is
                                                                           ^
```
[R/plot.R:337:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L337) *style:* **Trailing whitespace is superfluous.**
```r
#' @param showRowNames logical. Setting \code{showColumnNames = TRUE} will
                                                                          ^
```
[R/plot.R:338:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L338) *style:* **Trailing whitespace is superfluous.**
```r
#' show the row names (i.e. signature names) on the heatmap. The default is
                                                                           ^
```
[R/plot.R:355:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L355) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:358:67:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L358) *style:* **Trailing whitespace is superfluous.**
```r
#'                                    colData = DataFrame(sample =
                                                                  ^
```
[R/plot.R:366:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L366) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:380:53:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L380) *style:* **Trailing whitespace is superfluous.**
```r
                                 "Dark2", "Paired"),
                                                    ^
```
[R/plot.R:381:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L381) *style:* **Trailing whitespace is superfluous.**
```r
                                 choose_color = c("red", "white", "blue"),
                                                                          ^
```
[R/plot.R:386:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L386) *style:* **Trailing whitespace is superfluous.**
```r
                                colData(inputData)[, signatureColNames,
                                                                       ^
```
[R/plot.R:391:56:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L391) *style:* **Trailing whitespace is superfluous.**
```r
      pathwaycols[[i]] <- circlize::colorRamp2(c(t1min,
                                                       ^
```
[R/plot.R:392:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L392) *style:* **Trailing whitespace is superfluous.**
```r
                                                 mean(c(t1min, t1max)),
                                                                       ^
```
[R/plot.R:394:62:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L394) *style:* **Trailing whitespace is superfluous.**
```r
                                               c("darkgreen",
                                                             ^
```
[R/plot.R:395:58:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L395) *style:* **Trailing whitespace is superfluous.**
```r
                                                 "white",
                                                         ^
```
[R/plot.R:404:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L404) *style:* **Trailing whitespace is superfluous.**
```r
                                 colData(inputData)[, annotationColNames,
                                                                         ^
```
[R/plot.R:445:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L445) *style:* **Trailing whitespace is superfluous.**
```r
                                    colData(inputData)[, annotationColNames,
                                                                            ^
```
[R/plot.R:450:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L450) *style:* **Trailing whitespace is superfluous.**
```r
                                    colData(inputData)[, annotationColNames,
                                                                            ^
```
[R/plot.R:458:61:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L458) *style:* **Trailing whitespace is superfluous.**
```r
      height = grid::unit(0.4 * length(c(annotationColNames,
                                                            ^
```
[R/plot.R:459:69:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L459) *style:* **Trailing whitespace is superfluous.**
```r
                                         signatureColNames)), "cm"),
                                                                    ^
```
[R/plot.R:460:26:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L460) *style:* **Trailing whitespace is superfluous.**
```r
      show_legend = TRUE,
                         ^
```
[R/plot.R:490:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L490) *style:* **Trailing whitespace is superfluous.**
```r
#' @param hues a vector of character strings indicating the R colors available
                                                                              ^
```
[R/plot.R:491:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L491) *style:* **Trailing whitespace is superfluous.**
```r
#' from the \code{colors()} function. These will be used as the base colors for
                                                                               ^
```
[R/plot.R:492:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L492) *style:* **Trailing whitespace is superfluous.**
```r
#' the clustering scheme. Different saturations and values (i.e. darkness)
                                                                          ^
```
[R/plot.R:493:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L493) *style:* **Trailing whitespace is superfluous.**
```r
#' will be generated for each hue. Default is \code{c("red", "cyan", "orange",
                                                                              ^
```
[R/plot.R:495:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L495) *style:* **Trailing whitespace is superfluous.**
```r
#' @param saturation.range a numeric vector of length 2 with values between 0
                                                                             ^
```
[R/plot.R:497:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L497) *style:* **Trailing whitespace is superfluous.**
```r
#' @param value.range a numeric vector of length 2 with values between 0 and 1
                                                                              ^
```
[R/plot.R:499:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L499) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plot.R:502:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L502) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plot.R:504:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L504) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plot.R:521:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L521) *style:* **Trailing whitespace is superfluous.**
```r
  ## for all hues. Likewise, high saturation with high value (i.e. low darkness)
                                                                                ^
```
[R/plot.R:522:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L522) *style:* **Trailing whitespace is superfluous.**
```r
  ## is hard to distinguish. Therefore, saturation and value are set to be
                                                                          ^
```
[R/plot.R:525:65:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/plot.R#L525) *style:* **Trailing whitespace is superfluous.**
```r
  s <- seq(from = saturation.range[1], to = saturation.range[2],
                                                                ^
```
[R/profile.R:5:73:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#' Using some subset of the signatures listed in \code{TBsignatures} and
                                                                        ^
```
[R/profile.R:6:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#' specified scoring algorithms, this function runs gene signature profiling
                                                                            ^
```
[R/profile.R:7:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#' on an input gene expression dataset. It allows for scores to be computed for
                                                                               ^
```
[R/profile.R:11:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L11) *style:* **Trailing whitespace is superfluous.**
```r
#' @param input an input data object of the class \code{SummarizedExperiment},
                                                                              ^
```
[R/profile.R:13:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L13) *style:* **Trailing whitespace is superfluous.**
```r
#' @param useAssay a character string specifying the assay to use for signature
                                                                               ^
```
[R/profile.R:14:83:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L14) *style:* **Trailing whitespace is superfluous.**
```r
#' profiling when \code{input} is a \code{SummarizedExperiment}. Required only for
                                                                                ^
```
[R/profile.R:15:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L15) *style:* **Trailing whitespace is superfluous.**
```r
#' input data of the class \code{SummarizedExperiment}. If null, the assay
                                                                          ^
```
[R/profile.R:17:85:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L17) *style:* **Trailing whitespace is superfluous.**
```r
#' @param signatures a \code{list} of signatures to run with their associated genes.
                                                                                ^
```
[R/profile.R:18:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L18) *style:* **Trailing whitespace is superfluous.**
```r
#' This list should be in the same format as \code{TBsignatures}, included in
                                                                             ^
```
[R/profile.R:19:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L19) *style:* **Trailing whitespace is superfluous.**
```r
#' the TBSignatureProfiler package. If \code{signatures = NULL}, the default set
                                                                                ^
```
[R/profile.R:20:68:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L20) *style:* **Trailing whitespace is superfluous.**
```r
#' of signatures \code{TBsignatures} list is used. For details, run
                                                                   ^
```
[R/profile.R:22:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
#' @param algorithm a vector of algorithms to run, or character string if only
                                                                              ^
```
[R/profile.R:25:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L25) *style:* **Trailing whitespace is superfluous.**
```r
#' @param combineSigAndAlgorithm logical, not supported if \code{input} is a
                                                                            ^
```
[R/profile.R:26:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L26) *style:* **Trailing whitespace is superfluous.**
```r
#' SummarizedExperiment object (in which case, the default is \code{TRUE}).
                                                                           ^
```
[R/profile.R:27:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
#' For a matrix or data frame, if \code{TRUE}, the row names will be in the form
                                                                                ^
```
[R/profile.R:33:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L33) *style:* **Trailing whitespace is superfluous.**
```r
#' ASSIGN results if \code{algorithm} specifies \code{"ASSIGN"}. The default is
                                                                               ^
```
[R/profile.R:35:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L35) *style:* **Trailing whitespace is superfluous.**
```r
#' @param outputFormat a character string specifying the output data format.
                                                                            ^
```
[R/profile.R:36:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L36) *style:* **Trailing whitespace is superfluous.**
```r
#' Possible values are \code{"SummarizedExperiment"}, \code{"matrix"}, or
                                                                         ^
```
[R/profile.R:37:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L37) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{"data.frame"}. The default is to return the same type as the
                                                                     ^
```
[R/profile.R:39:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L39) *style:* **Trailing whitespace is superfluous.**
```r
#' @param parallel.sz an integer identifying the number of processors to use
                                                                            ^
```
[R/profile.R:40:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L40) *style:* **Trailing whitespace is superfluous.**
```r
#' when running the calculations in parallel for the GSVA and ssGSEA algorithms.
                                                                                ^
```
[R/profile.R:42:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L42) *style:* **Trailing whitespace is superfluous.**
```r
#' @param ASSIGNiter an integer indicating the number of iterations to use in
                                                                             ^
```
[R/profile.R:44:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L44) *style:* **Trailing whitespace is superfluous.**
```r
#' @param ASSIGNburnin an integer indicating the number of burn-in iterations
                                                                             ^
```
[R/profile.R:45:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L45) *style:* **Trailing whitespace is superfluous.**
```r
#' to use in the MCMC for the ASSIGN algorithm. These iterations are discarded
                                                                              ^
```
[R/profile.R:46:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L46) *style:* **Trailing whitespace is superfluous.**
```r
#' when computing the posterior means of the model parameters. The default is
                                                                             ^
```
[R/profile.R:49:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L49) *style:* **Trailing whitespace is superfluous.**
```r
#' @return A \code{SummarizedExperiment} object, \code{data.frame}, or
                                                                      ^
```
[R/profile.R:50:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L50) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{matrix} of signature profiling results. The returned object will be
                                                                            ^
```
[R/profile.R:51:51:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L51) *style:* **Trailing whitespace is superfluous.**
```r
#' of the format specified in \code{outputFormat}.
                                                  ^
```
[R/profile.R:52:56:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L52) *style:* **Trailing whitespace is superfluous.**
```r
#' If \code{input} is a \code{SummarizedExperiment} and
                                                       ^
```
[R/profile.R:53:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L53) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{outputFormat = "SummarizedExperiment"}, then the output will retain
                                                                            ^
```
[R/profile.R:54:69:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L54) *style:* **Trailing whitespace is superfluous.**
```r
#' any input information stored in the input colData. In general, if
                                                                    ^
```
[R/profile.R:55:83:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L55) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{outputFormat = "SummarizedExperiment"} then columns in the \code{colData}
                                                                                ^
```
[R/profile.R:56:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L56) *style:* **Trailing whitespace is superfluous.**
```r
#' will include the scores for each desired signature with samples on the rows.
                                                                               ^
```
[R/profile.R:57:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L57) *style:* **Trailing whitespace is superfluous.**
```r
#' If \code{input} is a \code{data.frame} or \code{matrix}, then the returned
                                                                             ^
```
[R/profile.R:58:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L58) *style:* **Trailing whitespace is superfluous.**
```r
#' object will have signatures on the rows and samples on the columns.
                                                                      ^
```
[R/profile.R:59:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:60:15:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L60) *style:* **Trailing whitespace is superfluous.**
```r
#' @references
              ^
```
[R/profile.R:61:96:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L61) *style:* **Trailing whitespace is superfluous.**
```r
#' Barbie,  D.A., Tamayo, P., Boehm, J.S., Kim, S.Y., Moody,	 S.E., Dunn, I.F., Schinzel, A.C.,
                                                                                ^
```
[R/profile.R:62:90:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L62) *style:* **Trailing whitespace is superfluous.**
```r
#' Sandy, P., Meylan, E., Scholl, C., et al. (2009).  Systematic RNA interference reveals
                                                                                ^
```
[R/profile.R:65:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L65) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:66:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L66) *style:* **Trailing whitespace is superfluous.**
```r
#' Foroutan, M. et al. (2018). Single sample scoring of molecular phenotypes.
                                                                             ^
```
[R/profile.R:67:46:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L67) *style:* **Trailing whitespace is superfluous.**
```r
#' \emph{BMC Bioinformatics}, \bold{19}. doi:
                                             ^
```
[R/profile.R:70:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L70) *style:* **Trailing whitespace is superfluous.**
```r
#' Lee, E. et al. (2008). Inferring pathway activity toward precise disease
                                                                           ^
```
[R/profile.R:71:63:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L71) *style:* **Trailing whitespace is superfluous.**
```r
#' classification. \emph{PLoS Comp Biol}, 4(11):e1000217. doi:
                                                              ^
```
[R/profile.R:74:73:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L74) *style:* **Trailing whitespace is superfluous.**
```r
#' Shen, Y. et al. (2015). ASSIGN: context-specific genomic profiling of
                                                                        ^
```
[R/profile.R:76:19:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L76) *style:* **Trailing whitespace is superfluous.**
```r
#' 1745-1753. doi:
                  ^
```
[R/profile.R:78:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L78) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:79:82:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L79) *style:* **Trailing whitespace is superfluous.**
```r
#' Subramanian, A. et al. (2005). Gene set enrichment analysis: A knowledge-based
                                                                                ^
```
[R/profile.R:83:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L83) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:84:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L84) *style:* **Trailing whitespace is superfluous.**
```r
#' Tomfohr, J. et al. (2005). Pathway level analysis of gene expression using
                                                                             ^
```
[R/profile.R:88:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L88) *style:* **Trailing whitespace is superfluous.**
```r
#' @source Profiling for the Z-Score, PLAGE, GSVA, ssGSEA algorithms are all
                                                                            ^
```
[R/profile.R:97:83:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L97) *style:* **Trailing whitespace is superfluous.**
```r
#'  # Create some toy data to test Zak_RISK_16 signature, using 5 samples with low
                                                                                ^
```
[R/profile.R:106:54:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L106) *style:* **Trailing whitespace is superfluous.**
```r
#'                         signatures = TBsignatures,
                                                     ^
```
[R/profile.R:107:60:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L107) *style:* **Trailing whitespace is superfluous.**
```r
#'                         algorithm = c("GSVA", "ssGSEA"),
                                                           ^
```
[R/profile.R:111:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L111) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:121:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L121) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/profile.R:124:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L124) *style:* **Trailing whitespace is superfluous.**
```r
                             algorithm = c("GSVA", "ssGSEA", "ASSIGN",
                                                                      ^
```
[R/profile.R:138:4:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L138) *style:* **Trailing whitespace is superfluous.**
```r
  }
   ^
```
[R/profile.R:158:56:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L158) *style:* **Trailing whitespace is superfluous.**
```r
  if (!all(algorithm %in% c("GSVA", "ssGSEA", "ASSIGN",
                                                       ^
```
[R/profile.R:160:68:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L160) *style:* **Trailing whitespace is superfluous.**
```r
    stop("Invalid algorithm. Supported algorithms are GSVA, ssGSEA,
                                                                   ^
```
[R/profile.R:189:52:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L189) *style:* **Trailing whitespace is superfluous.**
```r
    singscore_res <- matrix(ncol = ncol(runindata),
                                                   ^
```
[R/profile.R:195:25:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L195) *style:* **Commas should always have a space after.**
```r
      singscore_res[sig,] <- suppressWarnings(singscore::simpleScore(
                        ^
```
[R/profile.R:196:28:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L196) *style:* **Trailing whitespace is superfluous.**
```r
        rankData = rankDat,
                           ^
```
[R/profile.R:217:56:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L217) *style:* **Trailing whitespace is superfluous.**
```r
        message("Not enough signature genes in ", i, ",
                                                       ^
```
[R/profile.R:261:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L261) *style:* **Trailing whitespace is superfluous.**
```r
    # if combineSigAndAlgorithm TRUE, we can just concatenate the name to the
                                                                             ^
```
[R/profile.R:290:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L290) *style:* **Trailing whitespace is superfluous.**
```r
        rownames(gsvaRes_PLAGE) <- paste("PLAGE", rownames(gsvaRes_PLAGE),
                                                                          ^
```
[R/profile.R:299:68:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L299) *style:* **Trailing whitespace is superfluous.**
```r
        rownames(gsvaRes_Z) <- paste("Zscore", rownames(gsvaRes_Z),
                                                                   ^
```
[R/profile.R:308:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L308) *style:* **Trailing whitespace is superfluous.**
```r
        rownames(singscore_res) <- paste("singscore", rownames(singscore_res),
                                                                              ^
```
[R/profile.R:411:65:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L411) *style:* **Trailing whitespace is superfluous.**
```r
    absent <- subset(names(signatures), !(names(signatures) %in%
                                                                ^
```
[R/profile.R:413:7:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L413) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(algorithm) == 1) {
      ^
```
[R/profile.R:415:83:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L415) *style:* **Trailing whitespace is superfluous.**
```r
        paste("No identifiers in the gene sets could be matched to the identifiers
                                                                                ^
```
[R/profile.R:416:66:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L416) *style:* **Trailing whitespace is superfluous.**
```r
          in the expression data for the following signatures: ",
                                                                 ^
```
[R/profile.R:454:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L454) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:457:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L457) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{compareSigs} function allows the input of a data object and conducts
                                                                             ^
```
[R/profile.R:458:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L458) *style:* **Trailing whitespace is superfluous.**
```r
#' profiling on each signature desired, and outputting a heatmap for each
                                                                         ^
```
[R/profile.R:464:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L464) *style:* **Trailing whitespace is superfluous.**
```r
#' from the profiling should be suppressed (including progress bar output).
                                                                           ^
```
[R/profile.R:466:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L466) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:469:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L469) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:471:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L471) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:472:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L472) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/profile.R:473:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L473) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/profile.R:480:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L480) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~
```
[R/profile.R:483:41:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L483) *style:* **Trailing whitespace is superfluous.**
```r
                         annotationData,
                                        ^
```
[R/profile.R:484:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L484) *style:* **Trailing whitespace is superfluous.**
```r
                         algorithm = c("GSVA", "ssGSEA", "ASSIGN", "PLAGE",
                                                                           ^
```
[R/profile.R:486:49:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L486) *style:* **Trailing whitespace is superfluous.**
```r
                         showColumnNames = TRUE,
                                                ^
```
[R/profile.R:488:46:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L488) *style:* **Trailing whitespace is superfluous.**
```r
                         useAssay = "counts",
                                             ^
```
[R/profile.R:489:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L489) *style:* **Trailing whitespace is superfluous.**
```r
                         colorSets = c("Set1", "Set2", "Set3", "Pastel1",
                                                                         ^
```
[R/profile.R:490:69:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L490) *style:* **Trailing whitespace is superfluous.**
```r
                                       "Pastel2", "Accent", "Dark2",
                                                                    ^
```
[R/profile.R:494:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L494) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/profile.R:504:4:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L504) *style:* **Trailing whitespace is superfluous.**
```r
  }
   ^
```
[R/profile.R:518:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L518) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/profile.R:521:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L521) *style:* **Trailing whitespace is superfluous.**
```r
      col.names <- subset(names(SummarizedExperiment::colData(scored)),
                                                                       ^
```
[R/profile.R:522:73:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L522) *style:* **Trailing whitespace is superfluous.**
```r
                          !(names(SummarizedExperiment::colData(scored))
                                                                        ^
```
[R/profile.R:525:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L525) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/profile.R:526:36:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/93959533102e11e03d6cdc821316dfe233bfa298/R/profile.R#L526) *style:* **Trailing whitespace is superfluous.**
```r
    return(signatureHeatmap(scored,
                                   ^
```


Successfully aliased the URL <https://cdb-q1gv0pr3t.now.sh> to the following aliases:

* https://cdb.cdebotton.now.sh
* https://cdb-git-master.cdebotton.now.sh


Successfully aliased the URL <https://ref-backend-jmmli7h3n.now.sh> to the following aliases:

* https://ref-backend.ziongit.now.sh
* https://ref-backend-git-master.ziongit.now.sh


Legal, dessa maneira funciona, mas você se obriga a criar vários alunos para cursos diferente.
Nesse seu caso o mesmo aluno não pode fazer dois cursos ao mesmo tempo e se ocorrer tal caso você seria obrigado a realizar o mesmo cadastro de aluno mas com curso diferente, o que acaba gerando duplicidade de dados.

O correto seria ter uma terceira tabela onde existiriam apenas as PKs das duas tabelas como FKs nessa tabela de relacionamento.

Seria algo como

Create table aluno_curso (
  aluno_id integer,
  curso_id integer,
  matriculado integer,
  constraint fk_aluno_id foreign key (aluno_id) references alunos(id)
  constraint fk_curso_id foreign key (curso_id) references cursos(id)
)

Daí nessa tabela é onde você iria armazenar os alunos e em quais curso eles estão matriculados.


Successfully aliased the URL <https://next-learn-pgjhzzjgc.now.sh> to the following aliases:

* https://next-learn.pquinteros.now.sh
* https://next-learn-git-master.pquinteros.now.sh


![](https://github.trello.services/images/mini-trello-icon.png) [Removing the selected game from a playlist does not deselect it](https://trello.com/c/nhUZyWUN/52-removing-the-selected-game-from-a-playlist-does-not-deselect-it)


Successfully aliased the URL <https://next-learn-ka26ut4ie.now.sh> to the following aliases:

* https://next-learn.pquinteros.now.sh
* https://next-learn-git-master.pquinteros.now.sh


Successfully aliased the URL <https://ref-backend-4snh1t7w0.now.sh> to the following aliases:

* https://ref-backend.ziongit.now.sh
* https://ref-backend-git-master.ziongit.now.sh


Successfully aliased the URL <https://next-learn-4vxdhc2cp.now.sh> to the following aliases:

* https://next-learn.pquinteros.now.sh
* https://next-learn-git-master.pquinteros.now.sh


朝日新闻要这东西干啥？还是大庆70周年敏感节点．你们朝日有啥想法．

------------------ 原始邮件 ------------------
发件人: "Crystal-wow"<notifications@github.com>;
发送时间: 2019年7月25日(星期四) 上午10:13
收件人: "996icu/996.ICU"<996.ICU@noreply.github.com>;
抄送: "Subscribed"<subscribed@noreply.github.com>;
主题: Re: [996icu/996.ICU] 增加黑名单 (d7e34ac)

您好，

 这次报道主要是用在建国70周年这样一个专题报道中，想了解996程序员们日常的工作生活状态，包括今后的一些打算，建国100周年的时候对自己的憧憬，都是比较简单的采访，听听他们的想法。
 另外，所有涉及到隐私的地方我们都会征求本人同意来谨慎处理，这个完全不需要担心。
 最好是北京或者沈阳的程序员。

 ---------------------------------------------------------------------
 朝日新闻 中国总局 杨莹 YANG YING
 Tel :  (+86) 10-6523-2804
 Fax :  (+86) 10-6523-2704
 Mobile: 150-4116-8070
 E-mail：asahi.economic@outlook.com
 〒100600 北京市朝阳区建国门外秀水街一号院 外交公寓1-3-91

 > 在 2019年7月25日，00:00，liukean <notifications@github.com> 写道：
 >
 > 你好！想知道你主要是对那一块感兴趣
 >
 > —
 > You are receiving this because you commented.
 > Reply to this email directly, view it on GitHub, or mute the thread.
 >

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub, or mute the thread.


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Why are you removing these dependencies??


@LodanZark @dinkc64
https://mega.nz/#!exBxRQBT!Rtbs2FEM5H-Mu59L7NMGpqqpP6pIHzvDPMUwiXGw_wU
I will remove the link when you get it.


Can you be more noob


Should be `contributor`. Please fix continuous integration, or it will be a constant struggle with trivial and detectable issues.


> Warning: Can’t call setState (or forceUpdate) on an unmounted component. This is a no-op, but it indicates a memory leak in your application. To fix, cancel all subscriptions and asynchronous tasks in the componentWillUnmount method.


Oh, I forgot to make a pull request for the fix. I'll make it now


ffefefw


Hello git


PlantMassFlowRatesChangeForTankSourceSide (yzhou601) - Win64-Windows-10-VisualStudio-16: OK (2453 of 2453 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


regreso


www.996action.com/index.php/889799  这个网址怎么没法进去了，要搭梯子了吗


MAnda esses requires pro topo da página por questão de legibilidade


Aqui também


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lets just link it to the theme folder so that we dont need to update the readme everytime

or omit it ?


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Muda o nome dessa function


this is the second app


闪米特


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Aquik esse objeto não é utilizado. Pode remover ele.


merge into master from my-branch (2)


I think this is indeed a problem with TivaWare, the problem has been solved, thank you!


r


I have no idea why, but everything after this commit makes zsh unable to execute any of the aliases in my `.zshrc`. `type` finds them, `autocomp` find them, but I get a `command not found`.


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GSHP_desuperheater (yzhou601) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1128 of 1128 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-42.44%25-green.png)


Logs out users if time is outside of 12pm to 6pm


dont use


Change the mechanics so that it scales based on percentage of puzzles completed as opposed to points collected


PlantMassFlowRatesChangeForTankSourceSide (yzhou601) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (667 of 667 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.45%25-green.png)


I couldn't run the client on my computer because system-hook doesnt support linux. jNativeHook also works better in general


To me it's a bit odd that glitch-soc even allows h1-h6 in the first place, since it's bad for accessibility: https://github.com/tootsuite/mastodon/pull/10787#issuecomment-495940871

However for compat reasons I'm happy to accommodate glitch-soc :)


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Bad choice of words in the commit message, the buffered data is not dropped but obviously flushed by `fflush()`


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Fixes https://github.com/Megaf/707/issues/3


Reverting this one


@rodfersou sabe afirmar se existe alguma forma de evitar conflito desse nome genérico de datepicker caso o portal instale outros componentes que também usem esse namespace? Sabe se é possível alterar o código do brasil.gov.agenda permitindo isso?


Deployment failed with the following error:

~~~
The property `config` is not allowed in now.json when using Now 2.0 – please remove it.
~~~


Nit: you can remove one level of indentation by changing the containing if block to
```jl
if info.name === nothing
...
elseif info.name ∉ names
...
else
...
end
```


merci


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Migration notes:
* To create all leads with the RD station integration to all users in elos, we need to run two tasks:
  * `rake rdstation:create_leads`
  * `rake rdstation:update_leads`
* We need to run update_leads a few hours latter after create_leads to prevent inconsistencies in the database.


🔥 Device tests completed (Failed) on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2882440)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/expose-execute-proxy-auto-configuration-script/3d9cb6edd8a8df3d5d0de73b7f9898627ec44651/2882440/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>1 tests failed, 112 tests passed.</summary>

## Failed tests

 * [NUnit] Mono BCL tests group 2/tvOS - device/Release: Failed (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7f9c775cd0c0): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
</details>


I don't understand. You can do that on line 284? Also, I still dont understand why 292 is `1 +` even though this one isn't. Is the FAQ correct?


That file doesn't do anything


@yangxi Hey, I notice that whatever the release process we're doing is it seems to be missing one instance of replacing "5.3.0-SNAPSHOT" with just "5.3.0" in the docker-compose, specifically the `kafka-streams-examples-5.3.0-SNAPSHOT-standalone.jar` on line 91.

We can just update it on this branch for now but it seems like it's been happening for every release/branch cut. Can we try to fix this going forward?


зачем `else` если у вас и так будут выполняться следующие инструкции????
т.е. вы указали `continue` в случае не коректности, и вам `else` вообще не нужно


@danmar The Travis build on Precise fails. This message is shown: "This job ran on our Precise environment, which is in the process of being decommissioned. Please update to a newer Ubuntu version by specifying dist: xenial in your .travis.yml."


Just out of interest. What's the benefit of having the Jython and JRuby dependencies in scope provided? And what's the benefit of having all <Lang>Support classesl implemented using reflection?


4291-ZoneAirSysSensHeatCoolEnergyRateDocIssue (RKStrand) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (667 of 667 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.45%25-green.png)


Hey @kaste,

this is the thing we talked about to disable linting on load when there already are errors. Is it safe for a linter to access the `persist` and `util` modules?

I will probably also add a setting to disable this behavior because I'm not sure how it turns out in practice.

Ref: https://github.com/SublimeLinter/SublimeLinter/pull/1624


This might be not the right place for this function but couldn't find a better place to add this.


а вывести  вместо захардкоженых строк константы
```
std::cout << "Please, enter first argument of the equation in range [" <<
                     LOW_RANGE_VALUE                                                   <<
                     "..."
                     HIGH_RANGE_VALUE                                                  <<
                      "]"                                                                                <<
                      std::endl;
```


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зачем эту константу держать в этой области видимости, если она вам нужна только в области видимости
```
if (DISCRIMINANT > 0) {
```


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/1180) complete for merge to master.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/branch/master/index.html).

19 tests passed, 0 tests failed and 0 tests skipped in 13237 seconds

Tests produced 794 warnings. 794 were for lower-than-expected alignment scores


done


might messed up format on line 185


not tested with Redis


Go Devan!


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uf50d888821632d32461e37153ac775c0": true


@radex What does this version do? You just published 2.5.5 a couple of days ago.


New commit detected - CodeBuild : GitBot-Demo-1-PullRequest:61608526-ad3f-4400-b9a5-ae6d214421de - Status : IN_PROGRESS


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-2-emman-d8-composer-project.pantheonsite.io/)

Created multidev environment [pr-2](https://dashboard.pantheon.io/sites/3a534601-5934-471d-acfa-d06a790fc053#pr-2) for emman-d8-composer-project.


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Data Analysis


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Referencing #4
When I look at the code here I see is as `} else if (stringr::str_detect(timeframe, stringr::regex("M|mins?|minutes?"))) {` on a single line - which works fine in the source editor. I think the strange formatting I'm getting is an artifact of opening the code via the read-only definition viewer in R (clicking F2 with the cursor on the function name). It shows the ending bracket and the else on separate lines which creates an error when running from source:
```

> if (stringr::str_detect(timeframe, stringr::regex("D\|d\|days?",  +     ignore_case = T))) { +     timeframe <- "1D" +   } >   else if (stringr::str_detect(timeframe, stringr::regex("M\|mins?\|minutes?"))) {
> Error: unexpected 'else' in "  else"
>     timeframe <- paste0(stringr::str_extract(timeframe,  +       "^\\d+"), "Min")
>   } Error: unexpected '}' in "  }"

```


Deployment failed with the following error:

~~~
Ambiguous deployment (`package.json` and `Dockerfile` found). Please supply `--npm` or `--docker` to disambiguate.
~~~


ok


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Looks good.


`app` should be `redis` or `shared-session`, otherwise service will be unable to find out pods (created by deployment) which satisfy the requirement. https://medium.com/@zwhitchcox/matchlabels-labels-and-selectors-explained-in-detail-for-beginners-d421bdd05362 for more explanation.


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@bwetherfield, what is the purpose of this?

I think we may actually want to `open` this back up, as this change _reduces_ the public API (making it source-breaking).


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As well.


[tests/testthat/test-mbd_matrices.R:74:19:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_matrices.R#L74) *style:* **Trailing whitespace is superfluous.**
```r
      entry_m_n <-
                  ^
```
[tests/testthat/test-mbd_matrices.R:78:22:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_matrices.R#L78) *style:* **Trailing whitespace is superfluous.**
```r
        q ^ (m - n) *
                     ^
```
[tests/testthat/test-mbd_matrices.R:193:19:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_matrices.R#L193) *style:* **Trailing whitespace is superfluous.**
```r
      entry_m_n <-
                  ^
```
[tests/testthat/test-mbd_matrices.R:198:16:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_matrices.R#L198) *style:* **Trailing whitespace is superfluous.**
```r
        q ^ a *
               ^
```
[tests/testthat/test-mbd_ml.R:12:7:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_ml.R#L12) *style:* **Commented code should be removed.**
```r
  #   skip("This is long")
      ^~~~~~~~~~~~~~~~~~~~
```


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7384-MaterialInfraredTransparentIssue (RKStrand) - x86_64-MacOS-10.13-clang: OK (2453 of 2453 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


[docs-app] create "Design Principles" section, mention CSS API contract (#3678)

Previews: documentation | landing | table


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Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


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Let me try again:

The `0 +` is essentially meaningless, it's just there so it can be changed to `1 +` if I ever want to change it later.


What is the change you have on this? I see new lines added??


fyi @eed3si9n


7384-MaterialInfraredTransparentIssue (RKStrand) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


TeamCity Bvcms / Build [Build 1568](https://builds.tpsdb.com/viewLog.html?buildId=7429&buildTypeId=Bvcms_Build) is now running


Good point, I'll replace it with `sys.getrecursionlimit()`


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TeamCity Gribble ORM :: Deploy [Build 1.6.196.0](http://build.mikeobrien.net/viewLog.html?buildId=4057&buildTypeId=gribble&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 501, ignored: 2 Build time: 00:01:29


ghghjghjghjghjghjghjghj


I like this version


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7384-MaterialInfraredTransparentIssue (RKStrand) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (9 of 9 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


fuck off


It does, the comment is from when I didn't believe that was the case! Will fix.


Oh dear... sorry for the huge commit. Got into things and realized at the end of the day I hadn't committed changes.


I see an error in the error console for this line because function needs parentheses -- `function()`. After that, Zutilo loads for me.


OK, I mean, I think thats a questionable reason, but w/e.

What you still haven't answered is whether the FAQ is correct or not - it seems like conditions 2 and 3 should not be symmetrical if theyre not symmetrical in the code?


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ouch! ok we have to do it. But well I wonder if we can somehow test gcc 4.6 from now on.


"bracketed" might be confusing for Americans (brackets = square brackets). How about "enclosed in parentheses"? It's deducible from context though I guess.


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4291-ZoneAirSysSensHeatCoolEnergyRateDocIssue (RKStrand) - Win64-Windows-10-VisualStudio-16: OK (2453 of 2453 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


looks good


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nuevo por php


I needed some time to look it up. Yes, the FAQ is correct as written. The `0+` vs `1+` correspond to the different thresholds (1400 vs 1500).


edit:  to allow the bot to auth before joinin chans set to +r**  'registered users'


I thought you suggested atomic herr


@commenthol Hey, committed this PR directly to the repo vs doing a pull request. Should I revert? Sorry about that. My folders got messed up.


will check and answer tomorrow.
good night ;-)


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I removed the job. Its purpose was to test gcc 4.6 compilation.


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This won't compile :-(


it's for another feature cancel builds by commit message,
still in work


### Adding***


1.0.10 released


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F... forgot it


Should this be something different in high contrast mode?


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* https://tinyfactories.tiny-factories.now.sh
* https://tinyfactories-git-master.tiny-factories.now.sh


TeamCity Bvcms / Build [Build 1568](https://builds.tpsdb.com/viewLog.html?buildId=7429&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 47 Build time: 00:13:14


Successfully aliased the URL <https://infernojs-6xtq292if.now.sh> to the following aliases:

* https://infernojs.infernojs1.now.sh
* https://infernojs-git-master.infernojs1.now.sh


7384-MaterialInfraredTransparentIssue (RKStrand) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2493 of 2493 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


@refactormyself Was this file auto-generated or copied over from STP? Which licence does apply here?


:+1: Definitely. Thanks!


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* https://video-list-api.ljavierrodriguez.now.sh
* https://video-list-api-git-master.ljavierrodriguez.now.sh


Successfully aliased the URL <https://php-7-5ytpd8m95.now.sh> to the following aliases:

* https://php-7.danielfedatto.now.sh
* https://php-7-git-master.danielfedatto.now.sh


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/1181) complete for branch giraffe-mapq.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/commit/1175952558b07879330e3219e31f7cf6d177cbf5/index.html).

19 tests passed, 0 tests failed and 0 tests skipped in 13311 seconds

Tests produced 791 warnings. 791 were for lower-than-expected alignment scores


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* https://video-list-api.ljavierrodriguez.now.sh
* https://video-list-api-git-master.ljavierrodriguez.now.sh


Why do we need this class? Was it auto-generated?


Wow, nice updates!


@refactormyself  Why do we need this class? Was it auto-generated?


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* https://components-git-master.undataforum.now.sh


[tests/testthat/test-mbd_matrices.R:74:19:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_matrices.R#L74) *style:* **Trailing whitespace is superfluous.**
```r
      entry_m_n <-
                  ^
```
[tests/testthat/test-mbd_matrices.R:78:22:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_matrices.R#L78) *style:* **Trailing whitespace is superfluous.**
```r
        q ^ (m - n) *
                     ^
```
[tests/testthat/test-mbd_matrices.R:193:19:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_matrices.R#L193) *style:* **Trailing whitespace is superfluous.**
```r
      entry_m_n <-
                  ^
```
[tests/testthat/test-mbd_matrices.R:198:16:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_matrices.R#L198) *style:* **Trailing whitespace is superfluous.**
```r
        q ^ a *
               ^
```
[tests/testthat/test-mbd_ml.R:12:7:](https://github.com/Giappo/mbd/blob/c85177aee180c559715ddaf3af4239a36a4ffcd0/tests/testthat/test-mbd_ml.R#L12) *style:* **Commented code should be removed.**
```r
  #   skip("This is long")
      ^~~~~~~~~~~~~~~~~~~~
```


invite me pls abhilashboss135@gmail.com


Separating these tests from other (slower) test is good, I like it 😄
The name is good, the more I think about it and the more they make sense to me.
Leave them there, we will have for sure a chance in the future to talk again about the topic: at that point, we will check if the name continues to work for both of us 😉


Successfully aliased the URL <https://videolistapi-znwf9ms1z.now.sh> to the following aliases:

* https://video-list-api.ljavierrodriguez.now.sh
* https://video-list-api-git-master.ljavierrodriguez.now.sh


@commenthol Decided to revert as the changes weren’t peer reviewed. Will submit a proper PR. Again sorry about that.


Successfully aliased the URL <https://arpanlahacom-7slifqi8w.now.sh> to the following aliases:

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Successfully aliased the URL <https://dye-fyt9d3mry.now.sh> to the following aliases:

* https://dye.now.sh
* https://test.pacocoursey.com
* https://dye.pacocoursey.now.sh
* https://dye-git-master.pacocoursey.now.sh


Yeah... that was an error -_-'


I was trying to make my commits verified again after I lost my previous GPG key.


This commit reduces 1 use of substring. Other cases of .ToString() are unavoidable unless there is a very involved update to expander.


Successfully aliased the URL <https://cssstats-28iyfan0w.now.sh> to the following aliases:

* https://cssstats.com
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* https://cssstats-git-master.css-stats.now.sh


- Play it on a 25x25 emulator screen.
- Use 'z', 'q', 's' and 'w' keys to move the snake up, right, left and down respectively.
- These letters must be lowercase.
- You win when your snake's length hits 10.
- It's quite slow so please be patient while playing.
- if you have any comment to leave, feel free to do so.


Successfully aliased the URL <https://suddjian-blog-cvgx0ha97.now.sh> to the following aliases:

* https://blog.suddjian.com
* https://suddjian-blog.suddjian.now.sh
* https://suddjian-blog-git-master.suddjian.now.sh


Det her er sandsynligvis verdens sjoveste commit.


Can we change the line 3 of the code ?
If we,  then what ?


Maybe something similar to upgrading gcc works also with downgrading:
https://docs.travis-ci.com/user/languages/cpp/#gcc-on-linux
Adding package g++-4.6 and setting CC and CXX accordingly.


Agree, I used: str(p.relative_to(root).as_posix()))


I think this was supposed to be `beta`, not `beta1`? (this has generated urls with `beta11` on https://qa.php.net/, which 404)


Attached is the traceback I am receiving when I start-up armory in RC2.  This happens only with the RC2 and a background HDR.  The background shows up fine using the 2-20 blender 2.8 which was merged with Armory.  The traceback with RC2 and the armsdk (no errors loading) seems to point to e1cc308 and write_probes.py .  I am using a MacBook Pro (fully loaded).
<img width="1680" alt="Screen Shot 2019-07-24 at 7 23 38 PM" src="https://user-images.githubusercontent.com/10551699/61907631-78e3ed00-aef3-11e9-81a4-2a8d084d2649.png">
I read in a post somewhere that there were problems introduced by Norton banning write_probes.py - is there any known fix yet?


- New action types: `SHOW_ACTION_SHEET`, `HIDE_ACTION_SHEET`


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* https://cssstats.com
* https://www.cssstats.com
* https://cssstats.css-stats.now.sh
* https://cssstats-git-master.css-stats.now.sh


@refactormyself I also like to add such lines in unexplained and also new code. However, please do not commit such lines. Do you know how to use a debugger?


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* https://mknepprath-next-git-master.mknepprath.now.sh


reverted with 354c4e6d70a5fee1894efe909820b1f94882114b


Thanks, I talked with Patrick, they agree with you


What error do you get?

If you're using the latest version of BeEF, and you're receiving an error, please create a [new issue](https://github.com/beefproject/beef/issues/new).


@Croydon do you know if `2.10.14` works with boost `1.70.0`?


This paragraph is normative text. So it should use the normative keywords. For example, "The application however must: still synchronize ...".


Now could not deploy this pull request since it contains the following references to invalid secrets in the `env` sections of the `now.json` file:

* `wordpress_db_name` (in env: `DB_NAME)`
* `wordpress_db_user` (in env: `DB_USER)`
* `wordpress_db_password` (in env: `DB_PASSWORD)`
* `wordpress_db_host` (in env: `DB_HOST)`

Add those secrets or remove them from the `env` maps in the `now.json` file.


Successfully aliased the URL <https://suddjian-blog-2ubwrqu2p.now.sh> to the following aliases:

* https://blog.suddjian.com
* https://suddjian-blog.suddjian.now.sh
* https://suddjian-blog-git-master.suddjian.now.sh


Se modifico:
MbdCategorias
MbdEquipos
agregarCategoriaDo.jsp
agregarCategoriaForm.jsp
categorias.jsp
modificarCategoriaDo.jsp
modificarCategoriaForm.jsp


Successfully aliased the URL <https://dye-c60e73co4.now.sh> to the following aliases:

* https://dye.now.sh
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* https://dye.pacocoursey.now.sh
* https://dye-git-master.pacocoursey.now.sh


Successfully aliased the URL <https://spongebob-bot-gy23lsivf.now.sh> to the following aliases:

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* https://spongebob-bot-git-master.kp2zf.now.sh


Successfully aliased the URL <https://redfish-server-12i7elj8v.now.sh> to the following aliases:

* https://redfish-server.guandjoy.now.sh
* https://redfish-server-git-master.guandjoy.now.sh


Дифф доступен здесь: https://github.com/Sasha-Sorokin/ru-i18n-issues/commit/5e72f85e59451abfee6f1ba56cb3d0c9a79509bb (#4)


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-30-usittorg.pantheonsite.io/)

Created multidev environment [pr-30](https://dashboard.pantheon.io/sites/bd8bab1d-9fc1-4ed9-8ccf-9224a11e02d8#pr-30) for usittorg.


Successfully aliased the URL <https://cssstats-m5fhcq8vp.now.sh> to the following aliases:

* https://cssstats.com
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* https://cssstats-git-master.css-stats.now.sh


@ddworken do not pull these inline function out of the connect, you're losing all typing by doing this


Дифф доступен здесь: https://github.com/Sasha-Sorokin/ru-i18n-issues/commit/0ad2e5feb849f7ddeb74d0c546d323c56c34c439 (#4)


It was just to bypass the canvas issue of pvw for Windows. I'll have to see if I even use those protocols and trim them down...


@axxel With this, RSS14Reader is no longer thread-safe (which is a premise), isn't it?


Successfully aliased the URL <https://arpanlahacom-lrt9l2r4y.now.sh> to the following aliases:

* https://arpanlaha.com
* https://arpanlahacom.arpanlaha.now.sh
* https://arpanlahacom-git-master.arpanlaha.now.sh