[R/DEploidR.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Extract read counts from tab-delimited text files of a single sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The allele count files must be tab-delimited. The allele count files contain three columns: chromosomes, positions and allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:11:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:20:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:20:36:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L20) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                   ^
```
[R/DEploidR.R:20:37:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                    ^
```
[R/DEploidR.R:20:38:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[R/DEploidR.R:20:51:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/DEploidR.R:20:62:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                             ^
```
[R/DEploidR.R:23:12:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L23) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( data.frame( CHROM = ref[, 1],
           ^
```
[R/DEploidR.R:23:13:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L23) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( data.frame( CHROM = ref[, 1],
            ^
```
[R/DEploidR.R:23:25:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L23) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( data.frame( CHROM = ref[, 1],
                        ^
```
[R/DEploidR.R:26:45:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L26) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                         altCount = alt[, 3] )
                                            ^
```
[R/DEploidR.R:35:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The VCF file should only contain one sample. If more samples present in the VCF, it only returns coverage for of the first sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:39:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
#' @param ADFieldIndex Index of the AD field of the sample field. For example, if the format is "GT:AD:DP:GQ:PL", the AD index is 2 (by default).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:41:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:49:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:49:36:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L49) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                   ^
```
[R/DEploidR.R:49:37:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L49) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                    ^
```
[R/DEploidR.R:49:38:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                     ^~~~~~~~~~~
```
[R/DEploidR.R:49:51:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:49:67:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L49) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                                                  ^
```
[R/DEploidR.R:52:14:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
         if ( any( grepl( "gzfile connection", w) ) )
             ^
```
[R/DEploidR.R:52:19:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
         if ( any( grepl( "gzfile connection", w) ) )
                  ^
```
[R/DEploidR.R:52:26:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
         if ( any( grepl( "gzfile connection", w) ) )
                         ^
```
[R/DEploidR.R:52:50:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
         if ( any( grepl( "gzfile connection", w) ) )
                                                 ^
```
[R/DEploidR.R:52:52:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
         if ( any( grepl( "gzfile connection", w) ) )
                                                   ^
```
[R/DEploidR.R:53:24:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
         invokeRestart( "muffleWarning" )
                       ^
```
[R/DEploidR.R:53:40:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
         invokeRestart( "muffleWarning" )
                                       ^
```
[R/DEploidR.R:57:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L57) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:58:33:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    line <- withCallingHandlers( readLines(gzf, n = 1), warning = h)
                                ^
```
[R/DEploidR.R:59:12:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L59) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( length(line) > 0 ){
           ^
```
[R/DEploidR.R:59:29:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L59) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( length(line) > 0 ){
                            ^
```
[R/DEploidR.R:60:29:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L60) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if (grepl("##", line )){
                            ^
```
[R/DEploidR.R:61:13:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L61) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:65:37:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        line <- withCallingHandlers( readLines(gzf, n = 1), warning = h)
                                    ^
```
[R/DEploidR.R:69:23:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    vcf <- read.table( gzfile(vcfFileName), skip = numberOfHeaderLines,
                      ^
```
[R/DEploidR.R:73:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L73) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:79:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L79) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:81:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L81) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:82:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L82) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:84:12:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L84) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( data.frame( CHROM = vcf[, 1],
           ^
```
[R/DEploidR.R:84:13:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L84) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( data.frame( CHROM = vcf[, 1],
            ^
```
[R/DEploidR.R:84:25:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L84) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( data.frame( CHROM = vcf[, 1],
                        ^
```
[R/DEploidR.R:87:45:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L87) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                         altCount = altCount )
                                            ^
```
[R/DEploidR.R:96:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The text file must have header, and population level allele frequency recorded in the "PLAF" field.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:105:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L105) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:108:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
^~~~~~~~~~~
```
[R/DEploidR.R:108:25:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L108) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractPLAF <- function ( plafFileName ){
                        ^
```
[R/DEploidR.R:108:26:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
extractPLAF <- function ( plafFileName ){
                         ^
```
[R/DEploidR.R:108:27:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
                          ^~~~~~~~~~~~
```
[R/DEploidR.R:108:39:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
extractPLAF <- function ( plafFileName ){
                                      ^
```
[R/DEploidR.R:109:12:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L109) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( read.table(plafFileName, header = T)$PLAF )
           ^
```
[R/DEploidR.R:109:13:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L109) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( read.table(plafFileName, header = T)$PLAF )
            ^
```
[R/DEploidR.R:109:55:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L109) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( read.table(plafFileName, header = T)$PLAF )
                                                      ^
```
[R/DEploidR.R:115:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L115) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot the MCMC samples of the proportion, indexed by the MCMC chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:117:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
#' @param proportions Matrix of the MCMC proportion samples. The matrix size is number of the MCMC samples by the number of strains.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:130:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L130) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:131:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
#' panelFile = system.file("extdata", "labStrains.test.panel.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:137:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
#' plotProportions( PG0390CoverageTxt.deconv$Proportions, "PG0390-C proportions" )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:139:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L139) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function (proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:139:29:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L139) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotProportions <- function (proportions, title = "Components",
                            ^
```
[R/DEploidR.R:140:24:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                       ^~~~~~~
```
[R/DEploidR.R:140:37:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                    ^~~~~~~~
```
[R/DEploidR.R:140:51:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                  ^~~~~~~~
```
[R/DEploidR.R:140:63:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L140) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                              ^
```
[R/DEploidR.R:141:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L141) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:151:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L151) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot alternative allele count vs reference allele count at each site.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:159:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
#' @param exclude.ref Numeric array of reference allele count at sites that are not deconvoluted.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:161:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L161) *style:* **Lines should not be more than 80 characters.**
```r
#' @param exclude.alt Numeric array of alternative allele count at sites that are not deconvoluted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:183:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L183) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function ( ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:183:26:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L183) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotAltVsRef <- function ( ref, alt, title = "Alt vs Ref",
                         ^
```
[R/DEploidR.R:183:27:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L183) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
plotAltVsRef <- function ( ref, alt, title = "Alt vs Ref",
                          ^
```
[R/DEploidR.R:184:21:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L184) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:184:40:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L184) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:185:21:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                    ^~~~~~~
```
[R/DEploidR.R:185:34:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                 ^~~~~~~~
```
[R/DEploidR.R:185:48:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                               ^~~~~~~~
```
[R/DEploidR.R:185:60:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L185) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                           ^
```
[R/DEploidR.R:189:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L189) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:190:10:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L190) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    plot ( ref, alt, xlim = c(0, tmpRange), ylim = c(0, tmpRange),
         ^
```
[R/DEploidR.R:190:11:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L190) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    plot ( ref, alt, xlim = c(0, tmpRange), ylim = c(0, tmpRange),
          ^
```
[R/DEploidR.R:232:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L232) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:239:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:243:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L243) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:243:22:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L243) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                     ^
```
[R/DEploidR.R:243:23:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L243) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                      ^
```
[R/DEploidR.R:243:24:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L243) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                       ^~~~~~~
```
[R/DEploidR.R:245:17:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                ^~~~~~~
```
[R/DEploidR.R:245:30:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                             ^~~~~~~~
```
[R/DEploidR.R:245:44:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                           ^~~~~~~~
```
[R/DEploidR.R:245:56:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L245) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                       ^
```
[R/DEploidR.R:246:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:247:9:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L247) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( exclusive ){
        ^
```
[R/DEploidR.R:247:19:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L247) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( exclusive ){
                  ^
```
[R/DEploidR.R:248:9:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L248) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:248:31:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L248) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
                              ^
```
[R/DEploidR.R:248:33:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L248) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
                                ^
```
[R/DEploidR.R:248:63:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L248) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
                                                              ^
```
[R/DEploidR.R:250:12:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L250) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return (hist(obsWSAF[tmpWSAFIndex], main = title,
           ^
```
[R/DEploidR.R:263:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L263) *style:* **Lines should not be more than 80 characters.**
```r
#' @param obsWSAF Numeric array of observed altenative allele frequencies within sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:282:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:283:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:290:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L290) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:291:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L291) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:295:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:295:28:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L295) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                           ^
```
[R/DEploidR.R:295:29:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L295) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                            ^
```
[R/DEploidR.R:295:36:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                                   ^~~~~~~
```
[R/DEploidR.R:295:45:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                                            ^~~~~~~
```
[R/DEploidR.R:297:23:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                      ^~~~~~~
```
[R/DEploidR.R:297:36:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                   ^~~~~~~~
```
[R/DEploidR.R:297:50:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                 ^~~~~~~~
```
[R/DEploidR.R:297:62:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L297) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                             ^
```
[R/DEploidR.R:298:10:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L298) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    plot ( plaf, obsWSAF, cex = 0.5, xlim = c(0, 1), ylim = c(0, 1),
         ^
```
[R/DEploidR.R:298:11:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L298) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    plot ( plaf, obsWSAF, cex = 0.5, xlim = c(0, 1), ylim = c(0, 1),
          ^
```
[R/DEploidR.R:301:9:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L301) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( length(expWSAF) > 0 ){
        ^
```
[R/DEploidR.R:301:29:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L301) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( length(expWSAF) > 0 ){
                            ^
```
[R/DEploidR.R:302:16:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L302) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
        points ( plaf, expWSAF, cex = 0.5, col = "blue")
               ^
```
[R/DEploidR.R:302:17:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L302) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        points ( plaf, expWSAF, cex = 0.5, col = "blue")
                ^
```
[R/DEploidR.R:310:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot observed alternative allele frequency within sample against expected WSAF.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:329:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L329) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:330:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L330) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:331:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L331) *style:* **Lines should not be more than 80 characters.**
```r
#' PG0390CoverageVcf.deconv = dEploid(paste("-vcf", vcfFile, "-plaf", plafFile, "-noPanel"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:332:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L332) *style:* **Lines should not be more than 80 characters.**
```r
#' prop = PG0390CoverageVcf.deconv$Proportions[dim(PG0390CoverageVcf.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:336:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:336:28:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L336) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                           ^
```
[R/DEploidR.R:336:29:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                            ^~~~~~~
```
[R/DEploidR.R:336:38:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                                     ^~~~~~~
```
[R/DEploidR.R:338:23:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                      ^~~~~~~
```
[R/DEploidR.R:338:36:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                   ^~~~~~~~
```
[R/DEploidR.R:338:50:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                 ^~~~~~~~
```
[R/DEploidR.R:338:62:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L338) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                             ^
```
[R/DEploidR.R:350:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L350) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Compute observed allele frequency within sample from the allele counts.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:367:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L367) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:372:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L372) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:374:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L374) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function (alt, ref) {
^~~~~~~~~~~~~~
```
[R/DEploidR.R:374:28:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L374) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
computeObsWSAF <- function (alt, ref) {
                           ^
```
[R/DEploidR.R:375:12:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L375) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( alt / (ref + alt + 0.00000001) )
           ^
```
[R/DEploidR.R:375:13:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L375) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( alt / (ref + alt + 0.00000001) )
            ^
```
[R/DEploidR.R:375:44:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L375) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( alt / (ref + alt + 0.00000001) )
                                           ^
```
[R/DEploidR.R:381:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L381) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot the posterior probabilities of a haplotype given the refernece panel.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:383:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L383) *style:* **Lines should not be more than 80 characters.**
```r
#' @param posteriorProbabilities Posterior probabilities matrix with the size of number of loci by the number of reference strain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:30:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L391) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                             ^
```
[R/DEploidR.R:391:31:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                              ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:67:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:392:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/R/DEploidR.R#L392) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:7:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L7) *style:* **Variable or function name should be snake_case.**
```r
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:9:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L9) *style:* **Variable or function name should be snake_case.**
```r
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:10:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L10) *style:* **Variable or function name should be snake_case.**
```r
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:12:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L12) *style:* **Variable or function name should be snake_case.**
```r
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:15:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L15) *style:* **Variable or function name should be snake_case.**
```r
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:18:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:54:30:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L54) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    expect_null(plotAltVsRef( PG0390CoverageVcf$refCount,
                             ^
```
[tests/testthat/test-DEploid_tools.R:55:35:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-DEploid_tools.R#L55) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        PG0390CoverageVcf$altCount ))
                                  ^
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-dEploid.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-dEploid.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/dee3f1bb14d40faa7089967b854c803acc6699ed/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


Если все предыдущие сообщение в двойных кавычках, то надо придерживаться этого стиля.


Опечатка.


A typo here ? No leading brace for `jetty.base` variable.


Dudes, this generates a random number from 10 to 14...


دنیای بامقافات


Okay. That's is the case right now. I'll update my documentation to warn users off of calling this outside of its intended use case.


repetido


I think colon is more correct, and I think teat scripts should use json


Yup, good catch, thanks!


Farhadhp


(Y)


this should probably go first since it's decisive for the rest of the condition


You are indeed right, author provides that paths, sorry I didn't check it beforehand.

But you must provide too the path I suggested, because that is the canonical path in most Linux distros and it will not work otherwise.

```
equery f openblas
 * Searching for openblas ...
 * Contents of sci-libs/openblas-0.2.19:
/etc
/etc/env.d
/etc/env.d/alternatives
/etc/env.d/alternatives/blas
/etc/env.d/alternatives/blas/openblas-openmp
/etc/env.d/alternatives/blas/openblas-openmp/_importance
/etc/env.d/alternatives/blas/openblas-openmp/usr
/etc/env.d/alternatives/blas/openblas-openmp/usr/lib64
/etc/env.d/alternatives/blas/openblas-openmp/usr/lib64/pkgconfig
/etc/env.d/alternatives/blas/openblas-openmp/usr/lib64/pkgconfig/blas.pc -> ../../../../../../../../usr/lib64/pkgconfig/openblas-openmp.pc
/etc/env.d/alternatives/cblas
/etc/env.d/alternatives/cblas/openblas-openmp
/etc/env.d/alternatives/cblas/openblas-openmp/_importance
/etc/env.d/alternatives/cblas/openblas-openmp/usr
/etc/env.d/alternatives/cblas/openblas-openmp/usr/lib64
/etc/env.d/alternatives/cblas/openblas-openmp/usr/lib64/pkgconfig
/etc/env.d/alternatives/cblas/openblas-openmp/usr/lib64/pkgconfig/cblas.pc -> ../../../../../../../../usr/lib64/pkgconfig/openblas-openmp.pc
/usr
/usr/bin
/usr/include
/usr/include/openblas
/usr/include/openblas/cblas.h
/usr/include/openblas/f77blas.h
/usr/include/openblas/openblas_config.h
/usr/lib64
/usr/lib64/cmake
/usr/lib64/cmake/openblas
/usr/lib64/cmake/openblas/OpenBLASConfig.cmake
/usr/lib64/cmake/openblas/OpenBLASConfigVersion.cmake
/usr/lib64/libopenblas_openmp.so -> libopenblas_openmp_haswellp-r0.2.19.so
/usr/lib64/libopenblas_openmp.so.0 -> libopenblas_openmp_haswellp-r0.2.19.so
/usr/lib64/libopenblas_openmp_haswellp-r0.2.19.so
/usr/lib64/pkgconfig
/usr/lib64/pkgconfig/openblas-openmp.pc
/usr/share
/usr/share/doc
/usr/share/doc/openblas-0.2.19
/usr/share/doc/openblas-0.2.19/BACKERS.md.bz2
/usr/share/doc/openblas-0.2.19/CONTRIBUTORS.md.bz2
/usr/share/doc/openblas-0.2.19/Changelog.txt.bz2
/usr/share/doc/openblas-0.2.19/GotoBLAS_01Readme.txt.bz2
/usr/share/doc/openblas-0.2.19/GotoBLAS_03FAQ.txt.bz2
/usr/share/doc/openblas-0.2.19/GotoBLAS_04FAQ.txt.bz2
/usr/share/doc/openblas-0.2.19/GotoBLAS_05LargePage.txt.bz2
/usr/share/doc/openblas-0.2.19/GotoBLAS_06WeirdPerformance.txt.bz2
/usr/share/doc/openblas-0.2.19/README.md.bz2
/usr/share/doc/openblas-0.2.19/USAGE.md.bz2
```


Worth investigating refactoring for hokomokos new attachment system? Not sure how well it plays with isfireplatform


Instead of a script tag for every comment, you should use a for loop in the latter script tag selecting all torrent comment.


ProportionalDCVEnhancements (lgu1234) - x86_64-Linux-Ubuntu-14.04-gcc-4.8-UnitTestsCoverage-Debug: OK (1298 of 1298 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-37.69%25-green.png)


یاعلی


There were the following issues with your Pull Request

  * A "License" and a "Signed-off-by" trailers are required. See [the guidelines about this](https://github.com/ipfs/community/blob/master/contribution-guidelines.md#a-license-and-a-signed-off-by-trailers-are-required)

We ask for a few features in the commit message for Open Source licensing hygiene and commit message clarity.
`git commit --amend` can often help you quickly improve the commit message.
[Guidelines](https://github.com/ipfs/community/blob/master/contribution-guidelines.md#commit-messages) and [a script](https://github.com/ipfs/community/blob/master/dev/hooks/setup_commit_msg_hook.sh) are available to help in the long run.
Your feedback on GitCop is welcome on [this issue](https://github.com/ipfs/infrastructure/issues/23).

---
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Armour markings test?


I think it's very important to keep the support tab here. If the customer can't activate the license, it's very easy way to contact us.


I think so. A good solution might be to have architecture detection plus
unit testing of blasfeo with at least Sandy-Bridge and generic target.

On May 22, 2017 5:58 PM, "Robin Verschueren" <notifications@github.com>
wrote:

> Is there no way of automatically detecting which architecture we have at
> configure/build time?
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/acados/acados/commit/0aff790d4a58487488175dc8331d38ad06582d0e#commitcomment-22232219>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AQCkfd4_lu9sfo2XWj1i-WkYkkkCJwbQks5r8bCygaJpZM4NiXqV>
> .
>


Bluemix [toolchain](https://console.stage1.bluemix.net/devops/toolchains/060ca494-ec60-4012-a540-554c803148dc "ATest-KEEP-Toolchain"): [Delivery Pipeline](https://console.stage1.bluemix.net/devops/pipelines/cc94f48f-bd63-4023-b7e0-b53bd9161b0c "ATest-KEEP-Toolchain") deployed [ATest-KEEP-Toolchain](https://github.com/TinaLindhqvist/ATest-KEEP-Toolchain/releases/tag/deploy-ibm-ys1-us-south-tinalindhqvist64-gmail.com-dev-20170522-171500 "deploy-ibm-ys1-us-south-tinalindhqvist64-gmail.com-dev-20170522-171500") to [dev](https://console.stage1.bluemix.net/apps/690dbeb2-f3a9-4b2a-bc68-7319b9ce9d60?env_id=ibm:ys1:us-south "ibm:ys1:us-south:tinalindhqvist64@gmail.com:dev"), including this commit


Could you please create a PR to my repo?


hello


Hey, where went my Twitter link?


> Also includes some compatibility improvements for older versions of libsodium.

Until this commit, the extension was fb-only (it's only been around a few weeks), and required our internal version of libsodium. As well as moving to public, this contains modifications that should support Ubuntu 16.04.

We've also tested this with libsodium 1.0.7 on centos7, though centos7's standard package is 1.0.5, and not compatible.


added some detail


Great, i do it, but in this case i have a doubt, what if i have to import all of the package classes?


Mybot


oh right... sorry about that. basic html.


I think we're meant to use '(Jpn)' not '(Jap)'


Prebid 1.0 requirement?


Isn't that a C++ thing? Anyways, it works under Open Watcom.


WOUAOU c'est vraiment ingénieux !


Great, is a better way to make this method more reusable.


Thanks! BitHub has sent payment of  $134.10USD for this commit.


You can simply this because there's only one filter keyword to match
`m_crateFilterMatcher = QRegExp(QString("^-?*(crate):(.*)$")`


The apiOperation Null validation is in the main method, but i just changed this method to receive only the requestBody.


I've added two domains (conditions) to the search it could work with some specific fields, like suppliers or customers in the required times


It is part of the 1.0 adapter requirement.


@a-frobot docs-v0.5.0


How did this even happen -- looks like @syl20bnr was the only one to touch this..


There's only one possibility for this ("crate"), so you don't need to get it from the regex.


I don't know.  I am not really a C programmer. Some of the previous battery attempts may help for when the rooks are on the same file or rank.  If rooks are not on the same file or rank, there are only 2 potential intersections of their lines of force.  The 2 squares and the rook locations make a rectangle. There is a simple formula for determining these squares.  You just reorder the ranks and files in the names of the rook locations.  If there are no obstructions, they are hitting those squares. But I am probably making this far too complicated.


texte 1


Done!


Nice look! I love the color choice.

As for functionality, you're on the way but not quite there yet.
First, you've got to link the jQuery CDN or file to use jQuery.
You can always check to make sure your jQuery is linked properly by typing $ and enter into the console - if you get this error:

Uncaught ReferenceError: $ is not defined
    at jquery.js:1

You know it hasn't loaded.

This is also not doing what I think you've intended:

 $('#cel-input').val(celOutput);

This says - hey, jquery - grab the thing with the id of cel-input. Give me it's value. But really the value of the variable celOutput.

You'd want to use a write operation here; not value. Great thought on the parseInt.


Kek


Use the same code as for text filters below here:
```
                 if (negate) {
                     pNode = std::make_unique<NotNode>(std::move(pNode));
                 }
                 pQuery->addNode(std::move(pNode));
```


Use 422 (Unprocessable Entity). Usually validation errors return 400 or 422. 5xx errors are sent when there is problem with the server.


OK, I wasn't  aware. abbrev was used in documentation comments, so not important anyway.


Forge Blockstates are a given since we're on Forge, we're not using CTM yet. It just helps me have less clutter in the models dir. :P

I was trying to find out why the item model was busted. Still busted


I'm a tech writer. Ping me if you need anything moving forward!


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/4690c6fd-390d-4462-b8f0-ec195a39465a "demoing_helloworld_toolchain_rajn"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/63a0da7d-d9fb-4512-9140-edf39ceb94dc "demoing_helloworld_toolchain_rajn") deployed [demoing_helloworld_toolchain_rajn](https://github.com/rajunarayankar123/demoing_helloworld_toolchain_rajn/releases/tag/deploy-ibm-yp-us-south-shikha.arora-daimler.com-poc-20170522-173041 "deploy-ibm-yp-us-south-shikha.arora-daimler.com-poc-20170522-173041") to [poc](https://console.ng.bluemix.net/apps/9df822f2-141f-47e5-929c-9a1646a9dbc2?env_id=ibm:yp:us-south "ibm:yp:us-south:shikha.arora@daimler.com:poc"), including this commit


Alternatively you could add "crate" as an option for m_specialFilterMatcher


Finally! 😃


Hey.
Im tried to find some "masters" for servers like yours.
But the thing is i want to exec. the "Server.java" file and it doesnt work.
Im really new to Java (I dont really know what to do) and i must find a
Private cr for our PrivateGames project.

Thanks
Omrtha


There should not be a need to keep "parsing state". The returned types should be stateless.


I thought that's what you might say but I don't see in the documentation where it's clear that field correlates to the actual class and not just the entity short hand and that might be valuable information.  Also, I just wonder about the strength of this routine if it's not going to throw an error.


Deleted, i'm not using this method yet.


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/4690c6fd-390d-4462-b8f0-ec195a39465a "demoing_helloworld_toolchain_rajn"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/63a0da7d-d9fb-4512-9140-edf39ceb94dc "demoing_helloworld_toolchain_rajn") deployed [demoing_helloworld_toolchain_rajn](https://github.com/rajunarayankar123/demoing_helloworld_toolchain_rajn/releases/tag/deploy-ibm-yp-us-south-ranaraya-us.ibm.com-dev-20170522-173244 "deploy-ibm-yp-us-south-ranaraya-us.ibm.com-dev-20170522-173244") to [dev](https://console.ng.bluemix.net/apps/e40afd62-d856-4c19-b714-fad2959b8d24?env_id=ibm:yp:us-south "ibm:yp:us-south:ranaraya@us.ibm.com:dev"), including this commit


Hi @nyalldawson

>> b) 2.18.7
>>
>> rendering time:
>> real    0m25.341s
>> user    0m19.684s
>> sys     0m1.120s
>>
>> table
>> in 9:30 minutes it loadaed about half of ~758k records (the I aborted)
>
> Please test https://github.com/qgis/QGIS/commit/b97a980b99a32f7cbbb8cc32ac6a781246df1171
> - I think this should fix it.
>

with your patch

2.18.8

rendering time:
real    0m38.663s
user    0m33.572s
sys     0m1.244s

so... quite slower in rendering my test 758k ploygon layer.

table:
it took 27 seconds to open the whole table, which is 10 seconds slower
than on 2.14.4

cheers!


Deleted, i'm not using this method.


Here in `config.js` we should put parameters that are meant or can be changed between executions of the server, which is not the case of the PBKDF2 parameters. If we change them, we stop being able to validate existing passwords. For this reason, I believe these parameters should be in `crypto.js`.

The idea of extracting them to constants is to avoid "magic numbers" in the code. By naming them, code becomes more readable.


Deleted i'm not using this method yet.


My bad, I modified the comment (to remind me of the two different syntaxes
I tried) before I pushed, so it wasn't missing it when I was actually
testing it.

That makes sense about gitignoring the JS files.

Thanks!!

On Mon, May 22, 2017 at 9:46 AM, Tommy Sullivan <notifications@github.com>
wrote:

> i see the commented out code has a missing quote mark could that have been
> part of the problem?
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
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> <https://github.com/notifications/unsubscribe-auth/ADhQRnuA2HkHScmffTgKWcXUiJLXAO4Zks5r8bv2gaJpZM4NinEV>
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>


int main


I have trouble understanding this change, or why it leaks so much in other components. I think good approach would be to put the converter function from `parser.Result` to `[]Buildstage` and all the new types for commands to a different package to make sure that this is a parse step and not supposed to leak to execution logic at all.


That's why there's a validation before do that.


Great job!


Turned out I was calling this.handleLoggedInState from render(), which is constantly called (it's supposed to). This caused the app to constantly request the accesstoken from localstorage. Whoops


Done. I'm not receiving an apiOperation now.


Well, keep in mind that someone else may need to re-use or review you code, so, it would be good to let them know where the classes come from, i mean, github does not offer those track tool like the ide's.


Trabalho realizado por Nuno Mendes nº 79172


So I believe this means belt feed should work now?! Thanks so much! I haven't gotten to properly try them out yet, so am loving that I now have that option!


Got it. That's a good idea.


The commands should not define their dispatch methods. Command is created form parser, is stateless and doesn't know how it is executed. They don't know that there is anything called `*Builder` or that commit message is used for build cache.


teste 2


The method operation.setTags receive a List, instead of a Set. What can i do in this case?


yup, I do. I just forgot to fix this one 😉


Може, все-таки і не краще але на рівні. Гарного перегляду)


this isn't pushed to a branch?


This was not needed, because it was overwritten anyway in the Python implementation :)


As an example of this being stateless: you should be able to take the typed stage information, marshal to disk, unmarshal back and start a build from that definition.


nnn


@robbyoconnor Even he was young and.... We all was :roll_eyes:
but actually (most likely)  the history was lost when the file was moved.


@ : 창고지기
# : 벽
$ : 박스(금)
(영어) O : 보관장소
map : 맵 시작
end : 맵 끝


Odd... it should be. It's possible I missed something in my updates to the tag. Retagging now...


How about `BaseMarkDto`


no, it was made so no Enterprise update was necessary. Please make sure the new module is correctly installed


Refactor this.isLanding to become EnumLaunchPhase.LANDING

Also fix the following issues:
1.  model illumination above y=256
2.  landing rocket always "jumps" the final 0.8-1 block when landing on a landing pad (pad was docking it before the rocket wanted to land)
3.  sometimes no explosion when a rocket runs out of fuel and crash lands on a landing pad (same cause as 2)
4.  no sound for landing rockets
5.  landing rockets in same dimension were not spawning directly above their landing pad
6. glitchy y position for landing rockets due to server-client sync
7. Tier 3 rocket flame trail wrongly positioned if rocket tilted
8. Glitchy text in landing HUD due to number of significant figures changing
9. Incorrect 'Press SPACE to slow down' message for landing rocket


Description PDF


Not quite.

This is what your code is saying:

Hey, jquery - grab this thing with the id of submit. When you click it, run this function:

Grab the thing with the id of Fheit, do something we're calling .var with the string #Fheit and some math

You need to set up some variables to store information, and run the formulas on the values you've stored from the inputs. So, it wouldn't be .var - it would be .val() like the last homework. You'd need to run that formula on a stored variable instead of a string.

Also - you want your class and ID names to be lowercase or camelCase; not Upperlower.


#### Message: `Remove this logging statement.`

#### Occurred on:
+ **Commit**:  74a75dcbe778e99e8a0aea8b1200e35dc73387b4
+ **File**:    [WindowsFormsApp1/Form1.cs](https://github.com/trepte-ml/cSharp-Test/blob/74a75dcbe778e99e8a0aea8b1200e35dc73387b4/WindowsFormsApp1/Form1.cs)
+ **LineNum**: [50](https://github.com/trepte-ml/cSharp-Test/blob/74a75dcbe778e99e8a0aea8b1200e35dc73387b4/WindowsFormsApp1/Form1.cs#L50)
+ **Code**:    `Console.WriteLine("Time: " + time.ToString());`

#### Currently on:
+ **Commit**:  d771005da1107e869a215fcd289a85990cad5520
+ **File**:    [WindowsFormsApp1/Form1.cs](https://github.com/trepte-ml/cSharp-Test/blob/d771005da1107e869a215fcd289a85990cad5520/WindowsFormsApp1/Form1.cs)
+ **LineNum**: [52](https://github.com/trepte-ml/cSharp-Test/blob/d771005da1107e869a215fcd289a85990cad5520/WindowsFormsApp1/Form1.cs#L52)


What about tag 0x119, "Lens Geometry"?


can u add some examples here, to demonstrate access specifiers and midifiers


Thanks for catching these @rashmi815. I remember fixing all of these but maybe I haven't included the latest commit in the squash. Will fix them right away.


compatibility to 6.23+
and cast fixed digit


Thanks once again for the advice. I did get this working finally, using this:

```
artifacts {
  subProjectDistContents(installDist.destinationDir) {
    builtBy installDist
  }
}
```

But I still need to have two configurations, one on the producer side (which I use in the `artifacts` block to publish the artifact) and one on the consumer side (which I use in the `dependencies` block to fetch the artifact). This entails more than a little duplication. Is there any way around this, or is this simply a necessity when decoupling projects?

Either way, thanks a lot for the help!


it's not the tag that's the issue, it's the fact that this commit only exists as the tag. master is still at 41ef773b5a066f9fbea56654cc9656e0e9a29859


Se adicionado una nueva linea


Great job. I'm not sure why the API thought you were in Poland; it thinks I'm in Bayonne and that's pretty close to Staten Island.


fixes #1


test comments


Ik vroeg me al af of hier nog iets gebeurde ;)


@dingjingpisces2015 I am concerned about this. Not removing this for users who decided to check in their `Pods/` directory means that there could be files there that do not get cleaned up in a long timespan.

The xcode project won't point at them but we do leave files there that are not used anywhere.


From commit : https://github.com/Cosmic-OS/platform_frameworks_base/commit/ac26827f09e235d66a10fd463b82f2b28edcbe6a
Huge thanks to Thecrazyskull


agreed


I connected my Canon MP210 printer to a PC with both Haiku and Ubuntu partitions and ran a series of scanimage commands to get some comparative data.
![ubuntu_test](https://cloud.githubusercontent.com/assets/13264393/26321916/0aa918e4-3ee6-11e7-93f8-2ac264d200a5.jpeg)

[Haiku_scanimage.txt](https://github.com/haikuports/haikuports/files/1019722/Haiku_scanimage.txt)
[Ubuntu_scanimage.txt](https://github.com/haikuports/haikuports/files/1019723/Ubuntu_scanimage.txt)


Can we using chinese?


@chetanmeh , yes, I'd add tests.. current is more like WIP and the direction of implementation.


Order = 2 two times.


@voleye: be aware that this commit introduces a nasty bug where the wrong translation of the attribute option is getting cached if you work with multiple storeviews. This is because the StoreResolver isn't the correct class to get the current store id, see https://github.com/magento/magento2/pull/9704 for more details.


Cool idea!


Sorry for reply late. Why we have PERF_TYPE_RAW here instead of PERF_TYPE_SOFTWARE?


you're welcome bro!


@mariuszs @adrian-wozniak @tkrzeminski Doesn't the following commit message look better than ordinary "[#DO_RELEASE]" in the Git history? ;)

```
git commit -m "Trigger release" -m "[#DO_RELEASE]" --allow-empty
```