[R/DEploidR.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L20) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                   ^
```
[R/DEploidR.R:20:38:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/DEploidR.R:23:12:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:35:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L49) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                   ^
```
[R/DEploidR.R:49:38:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:57:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L57) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:61:13:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L61) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:73:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:96:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L108) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractPLAF <- function ( plafFileName ){
                        ^
```
[R/DEploidR.R:108:27:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
                          ^~~~~~~~~~~~
```
[R/DEploidR.R:109:12:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L109) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( read.table(plafFileName, header = T)$PLAF )
           ^
```
[R/DEploidR.R:115:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L115) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot the MCMC samples of the proportion, indexed by the MCMC chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:117:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
#' @param proportions Matrix of the MCMC proportion samples. The matrix size is number of the MCMC samples by the number of strains.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:130:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L130) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:131:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
#' panelFile = system.file("extdata", "labStrains.test.panel.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:137:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
#' plotProportions( PG0390CoverageTxt.deconv$Proportions, "PG0390-C proportions" )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:139:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:141:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:184:21:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:189:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:232:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L243) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                     ^
```
[R/DEploidR.R:243:24:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:246:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:248:9:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L248) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:250:12:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:295:36:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:298:10:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:302:16:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:310:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:350:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:381:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


логика верная. оформите как функцию


Oops, it seems I didn't push my change (regarding checking `PvNode`); this test is unintentional.


It doesn't make sense to change the overhang angle of a support mesh. The overhang angle determines where support will be generated, but support meshes don't generate support - they *are* support. I think overhang angle is a particularly bad example. However, maybe the same reasoning holds for other support settings?

I think there will be additional cost of generating support per supprot mesh rather than for all support meshes at the same time. There's probably some computations on outlines of models which you would have to do voer again when you generate support for each support mesh separately.

Rewriting the feature to support those settings will requirte a lot of work.
Can you think of a setting which people would likely want to alter per support mesh?


@satamas `LanguageVersion` is the version of the language (e.g. 1.0, 1.1), `TargetPlatformVersion` is the version of the platform of generated binary files (e.g. JVM 1.6, JVM 1.8). Either this method should be named `getTargetPlatformVersion`, or it should return `LanguageVersion`


Should be > -1 as like this you can have instances where its '0' and you return false.

Or rather use .startsWith


You don't need to compute the overhang for either.


Looks awesome!


Die Colorramp verbessert das Käfigmaterial auf alle Fälle enorm, weiter so


What do you mean?


Learn from past mistakes!
Leaking credentials again 😑


I wanted to accumulate a bit more changes for the next release, but that's OK, I will release today.


I'm really enjoying these :+1:


верно. а почему у переменной суффикс `_1`?


چیه خب به این خوبی 😂


I'll add a brief explanation RE: @glimmer/env to the README shortly.

RE: runInDebug,  it is not forgotten, you would just use if (DEBUG) like in the example below. I can try to explain that better in the README also.


Salut Paul-Etienne,

Désolé mais c'est le seul moyen que j'ai trouvé pour te contacter. Premièrement, je trouve ton article très utile étant donné que beaucoup de monde a rencontré ce pb moi y compris. A l'époque, j'avais fais une solution semblable à la tienne à part le @MapsId que je ne connaissais pas. J'ai deux questions pour toi :
1 - A quoi ressemble le changeset liquibase d'une colonne avec un @MapsId ?
2 - Comment récupérer les informations exta de l'utilisateur avec SpringSecurity (si c'est possible) ?

Voilà, si ce n'est pas le bon moyen, je reposterai sur stackoverflow en anglais cette fois ;)

Merci,

Issam


Issue #210


Why is it needed to set this with an external property?


This bit is dangerous. Because some of the other jest packages will be v18 which can cause issues. But if it works, then why not!? :)


they changed it yet again, now +lv30 accounts for iv moves (and ofc cp)

:(


Why not specify the default guard's actual name?


TeamCity Code :: 1. Development :: DDK :: Feature [Build 262](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=21789&buildTypeId=Code_Development_Ddk_Feature) is now running


@ianfab Here is the corrected code (to only not skip quiets on the PV); I'll submit a new test.


[R/DEploidR.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L20) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                   ^
```
[R/DEploidR.R:20:38:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/DEploidR.R:23:12:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:35:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L49) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                   ^
```
[R/DEploidR.R:49:38:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:57:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L57) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:61:13:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L61) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:73:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:96:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L108) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractPLAF <- function ( plafFileName ){
                        ^
```
[R/DEploidR.R:108:27:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
                          ^~~~~~~~~~~~
```
[R/DEploidR.R:109:12:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L109) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( read.table(plafFileName, header = T)$PLAF )
           ^
```
[R/DEploidR.R:115:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L115) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot the MCMC samples of the proportion, indexed by the MCMC chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:117:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
#' @param proportions Matrix of the MCMC proportion samples. The matrix size is number of the MCMC samples by the number of strains.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:130:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L130) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:131:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
#' panelFile = system.file("extdata", "labStrains.test.panel.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:137:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
#' plotProportions( PG0390CoverageTxt.deconv$Proportions, "PG0390-C proportions" )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:139:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:141:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:184:21:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:189:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:232:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L243) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                     ^
```
[R/DEploidR.R:243:24:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:246:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:248:9:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/R/DEploidR.R#L248) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:250:12:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:295:36:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:298:10:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:302:16:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:310:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:350:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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:381:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/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/d8a3e8b4de26b9c53d52c026b2487746c18fa6db/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


It's highly coupled with `preparePublication` task, here it looks out of context.


There's a fabsf, no? fabs still returns double.


여러가지로 신경 써 주셔서 갑사합니다!!ㅠㅠ
더 열심히 하겠습니다!

-----Original Message-----
From: "Suh Chansu"<notifications@github.com>
To: "jsme11/HwanBlog"<HwanBlog@noreply.github.com>;
Cc: "jsme11"<jsme111@naver.com>; "Author"<author@noreply.github.com>;
Sent: 2017-04-28 (금) 23:56:26
Subject: Re: [jsme11/HwanBlog] 게시판 수정기능 + 삭제기능 추가 (a901005)

다양한 예제를 연습한것 같네

잘하고 있다

오늘도 수고 많았어!

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


no, regular path.

`/var/www/html/mailscanner/functions.php`

I just upgraded the files with last PR and got this error message.


Releases 1.1.2


Seems it won't let me remove that.


Refactorato


TeamCity Code :: 1. Development :: DDK :: Feature [Build 262](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=21789&buildTypeId=Code_Development_Ddk_Feature) outcome was **SUCCESS**
Summary: Tests passed: 68 Build time: 00:02:35


Doesn't seem avoidable on GitHub editor


The following doc(s) have been deployed to the [freehttps](https://freehttps-static-docs.pantheonsite.io/docs) Multidev environment:
- [docs/free-https](https://freehttps-static-docs.pantheonsite.io/docs/free-https)


Yeah it's receiver dependend. At the time setting that value I had one candidate where going lower value did not convince the AVR to stay powered, that's what it is like it is.


Yes, thats fine. The outer `i` is the position of the bell character and the inner `i` is the position of the newline character. Line 280 needs to return if no bell character was found.


TeamCity Platform Services :: Environment Manager 2 :: Package [Build 3.42.4-pre-5-geba774f](http://infra.teamcity.ci.ttldev/viewLog.html?buildId=59935&buildTypeId=PlatformServices_EnvironmentManager2_Package) outcome was **SUCCESS**
Summary: Running Build time: 00:00:40


Please, follow our guidelines, this is supposed to be English-only, so everyone can understand what you say


@jensens Jenkins CI reporting about code analysis
See the full report here: http://jenkins.plone.org/job/package-plone.app.z3cform/17/violations
```
plone/app/z3cform/inline_validation.py:15:1: C901 'InlineValidationView.__call__' is too complex (15)
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


The idea is. it should be applied to `libraries` and not to `gradle-tools`, that's why it's left here out of `commonConfiguration.gradle`.


Take an another look


Ok, thanks. I have approved the test.


@moshonk You do not need a new identifier - this one already exists its called HIV_CARE_NUMBER


If the pidfile contains a PID for a process that doesn't exist any more, the status code in glusterd can easily detect that with a kill(0) and there shouldn't be a problem with showing the correct status.  On the flip side, if we unlink one pidfile it should not affect any other brick regardless of whether their pidfile is linked to or copied from the first.  Either way, it will still exist and still contain the correct PID.  If there's a problem with brick status, I suspect it's somewhere else.  The only problem I see here is that we're not unlinking *enough* pidfiles.  If the process is going away, then either the process itself or glusterd (from a SIGCLD handler) should loop over all of the bricks associated with it and remove all of those pidfiles - not just one.


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170428-153713 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170428-153713") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170428-153722 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170428-153722") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


It's better to change the determiners to "the" or "its owner's" instead of "your", in the unlikely event your opponent controls those creatures, so if they do eventually return to the hand or gets put in the mana zone, there won't be any confusion.

*Aqua Commando* :
`str0 = Return this creature to the` [its owner's] `hand instead of banishing it.`

*Karate Carrot* :
`str0 = Put this creature into the` [its owner's] `mana zone instead of banishing it.`


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-Prod-20170428-153727 "deployed-2-env-Prod-20170428-153727") to [Prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "There was a problem retrieving the space name"), including this commit


*[Hook UI build recap](http://ci.perseids.org/repo/OpenGreekAndLatin/First1KGreek/155)*


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170428-153737 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170428-153737") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testrepo-traceability](https://github.com/idsdev/testrepo-traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170428-153747 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170428-153747") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Remember any details ?


TeamCity libpalaso :: palaso-win32-master Continuous [Build 4.0.51.6143a870ad2cd40dac60b426fd4821eefa2fd51b](http://build.palaso.org/viewLog.html?buildId=89214&buildTypeId=Libpalaso_PalasoWin32masterContinuous) outcome was **FAILURE**
Summary: Compilation error: SIL.Windows.Forms\SIL.Windows.Forms.csproj; compilation error: SIL.DblBundle\SIL.DblBundle.csproj Build time: 00:00:41


I guess this could have been `a.__getitem__`, but this is clearer.


This same patch adds gf_is_pid_running with the same sprintf/access code.


This is failing for me. "faultException does not exist in the current context."

![image](https://cloud.githubusercontent.com/assets/1640591/25536010/1d3d1d08-2c07-11e7-9573-8e0ed2bc75f1.png)


not really. it's actually a `!` in my current experiment


Was some Teufel speakers connected to a Denon AVR. That one just turned off the pcm signal when we went further down.

Can be reevaluated of course. Just change the default to 10x lower and wait if someone complains :-)


#6028-PTAC-heating-coil-undersized-for-ventilation-load-when-zone-design-heating-load-is-zero (EnergyArchmage) - x86_64-Linux-Ubuntu-14.04-custom_check: OK (0 of 0 tests passed, 0 test warnings)

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


<!-- PMABOT:SOB -->
This commit is missing Signed-Off-By line to indicate that you agree with phpMyAdmin Developer's Certificate of Origin. Please check [contributing documentation](https://github.com/phpmyadmin/phpmyadmin/blob/master/CONTRIBUTING.md) for more information.


heh :)


*[Hook UI build recap](http://ci.perseids.org/repo/OpenGreekAndLatin/First1KGreek/157)*


@FernetMenta strange - in krypton branch i still get the high load with this patch applied ...


- [ ] asd
- [ ] asd

- [ ] asd


Các lệnh với cả Synopsis gồm những gì thế mấy anh
e chạy python validate.py bvhs/Example1.bvh rồi mà sao chưa thấy gì nhỉ ?


@tcg96 GitHub Pages doesn't support PHP 😆


indentation issue


remove spaces


TeamCity libpalaso :: palaso-win32-libpalaso-3.1 Continuous [Build 3.1.317.6143a870ad2cd40dac60b426fd4821eefa2fd51b](http://build.palaso.org/viewLog.html?buildId=89216&buildTypeId=bt223) outcome was **SUCCESS**
Summary: Tests passed: 3600, ignored: 128 Build time: 00:03:47


TeamCity libpalaso :: palaso-precise64-libpalaso-2.6 Continuous [Build 2.6.1311.6143a870ad2cd40dac60b426fd4821eefa2fd51b](http://build.palaso.org/viewLog.html?buildId=89215&buildTypeId=PalasoPrecise64v26Cont) outcome was **FAILURE**
Summary: Tests failed: 2, passed: 3576, ignored: 111 Build time: 00:06:19
### Failed tests
```
SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreIfDisposed): <no details avaliable>

SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreAll): <no details avaliable>

```


TeamCity libpalaso :: palaso-precise64-master Continuous [Build 4.0.40.6143a870ad2cd40dac60b426fd4821eefa2fd51b](http://build.palaso.org/viewLog.html?buildId=89218&buildTypeId=Libpalaso_PalasoPrecise64masterContinuous) outcome was **FAILURE**
Summary: Failed to resolve artifact dependency Build time: 00:00:10


Just had another check, as I wasn't completely sure myself, and this is wat I can find;

`local_action` is identical to `delegate_to: localhost`, so I would prefer the delegate version, as this preserves the highlighting and structure.

`connection: local` will use the vars from the targeted host, and will use the system installed python. So in most cases this will be fine, but the fact it will use the system installed python could indeed cause trouble in edge cases.


del


A brick doesn't correspond to any particular thread or set of threads, because sharing resources across multiple bricks is why multiplexing exists.  Also, since thread stacks account for a significant portion of total memory use, sharing threads is critical to reducing memory use as well.  If we need to take action for a single brick, then we need to do it at the same level as attach/detach.  Often this means looping over the children of the top-level translator (protocol/server) to find the brick we're interested in.  See e.g. the notify code for an example.


Maybe it's better to leave that ? Removing this method broke backward compatibility, at least one good module as Mojolicious::Plugin::Webtail will fail to install


is both version of qt5-quickcontrols really needed?


Is this needed


From something you mentioned I believe this isn't needed anymore


Is this needed, or is it automatic?


Love it! <3


TeamCity libpalaso :: palaso-trusty64-lfmerge Continuous [Build 2.6.303.6143a870ad2cd40dac60b426fd4821eefa2fd51b](http://build.palaso.org/viewLog.html?buildId=89217&buildTypeId=PalasoTrusty64lfmergeContinuous) outcome was **FAILURE**
Summary: Tests failed: 2, passed: 3576, ignored: 111 Build time: 00:05:44
### Failed tests
```
SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreIfDisposed): <no details avaliable>

SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreAll): <no details avaliable>

```


No, the only configuration is on Jenkins.  Can I merge this now?


Agencies had problems integrating their HTML into the Aimeos subparts structure. This is now gone :-)


Man what a fucking moron you are


TeamCity libpalaso :: palaso-precise64-libpalaso-3.1 Continuous [Build 3.1.270.6143a870ad2cd40dac60b426fd4821eefa2fd51b](http://build.palaso.org/viewLog.html?buildId=89221&buildTypeId=bt322) outcome was **FAILURE**
Summary: Tests failed: 2, passed: 3576, ignored: 111 Build time: 00:06:11
### Failed tests
```
SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreIfDisposed): <no details avaliable>

SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreAll): <no details avaliable>

```


1) Do we plan on keeping this "just return the debug"
2) If so, do we need a better check, could we, could we ever get `self._play_context.remote_addr == ::1`?


TeamCity libpalaso :: palaso-win32-libpalaso-3.1 Continuous [Build 3.1.318.965c544c338778af0e85f30a60aa94d294757235](http://build.palaso.org/viewLog.html?buildId=89223&buildTypeId=bt223) outcome was **SUCCESS**
Summary: Tests passed: 3600, ignored: 128 Build time: 00:03:40


TeamCity Code :: 1. Development :: DDK :: Feature [Build 263](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=21795&buildTypeId=Code_Development_Ddk_Feature) is now running


Nice one :)


Above this line, there has to be an opening `div` with class `row`.


Ca veut dire quoi `homeBare` ?


Are these changes good to go? You haven't created a pull request.
Here's a tutorial about it:
https://help.github.com/articles/creating-a-pull-request/#creating-the-pull-request
Thanks!


Below this line, there has to be a closing `</div>` that corresponds to the `div` with class `row` that my previous comment is asking you to add.


*[Hook UI build recap](http://ci.perseids.org/repo/OpenGreekAndLatin/First1KGreek/159)*


TeamCity Code :: 1. Development :: DDK :: Feature [Build 263](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=21795&buildTypeId=Code_Development_Ddk_Feature) outcome was **SUCCESS**
Summary: Tests passed: 68 Build time: 00:01:18


Please open a PR. :)


TeamCity libpalaso :: palaso-win32-master Continuous [Build 4.0.52.965c544c338778af0e85f30a60aa94d294757235](http://build.palaso.org/viewLog.html?buildId=89228&buildTypeId=Libpalaso_PalasoWin32masterContinuous) outcome was **FAILURE**
Summary: Compilation error: SIL.Windows.Forms\SIL.Windows.Forms.csproj; compilation error: SIL.DblBundle\SIL.DblBundle.csproj Build time: 00:01:13


*[Hook UI build recap](http://ci.perseids.org/repo/OpenGreekAndLatin/First1KGreek/161)*


Does this have _any_ impact on anything (except you) ?


"home" comme la route "home" au dessus, et "bare" comme "sans rien", c'est le même mot que j'avais vu sur une autre route dans le code, je l'ai réutilisé


@taylorotwell, is this will be also reverted (#18987) ?


TeamCity libpalaso :: palaso-precise64-libpalaso-3.1 Continuous [Build 3.1.271.965c544c338778af0e85f30a60aa94d294757235](http://build.palaso.org/viewLog.html?buildId=89226&buildTypeId=bt322) outcome was **FAILURE**
Summary: Tests failed: 2, passed: 3576, ignored: 111 Build time: 00:05:56
### Failed tests
```
SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreIfDisposed): <no details avaliable>

SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreAll): <no details avaliable>

```


144488793-Correct-surface-convection-calculation-6037 (EnergyArchmage) - x86_64-MacOS-10.9-clang: OK (2488 of 2488 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)


lgtm


ok


Right, we do not want tests to silently pass while not testing things when no Postgres server is available.


src/universal/routes/home.js:2
  2: import type { Store } from 'universal/flowtypes/redux'
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^ universal/flowtypes/redux. Required module not found

src/universal/routes/home.js:4
  4: import App from 'universal/components/App'
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^ universal/components/App. Required module not found

src/universal/routes/index.js:3
  3: import type { Store } from 'universal/flowtypes/redux'
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^ universal/flowtypes/redux. Required module not found


TeamCity libpalaso :: palaso-trusty64-lfmerge Continuous [Build 2.6.304.965c544c338778af0e85f30a60aa94d294757235](http://build.palaso.org/viewLog.html?buildId=89224&buildTypeId=PalasoTrusty64lfmergeContinuous) outcome was **FAILURE**
Summary: Tests failed: 2, passed: 3576, ignored: 111 Build time: 00:05:25
### Failed tests
```
SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreIfDisposed): <no details avaliable>

SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreAll): <no details avaliable>

```


> planetx-boilerplate-crater@0.1.0 prod /Users/florian/Code/Public/PlanetX/boilerplate-crater
> babel-node scripts/prod.js

build/meteor is up to date
Meteor npm dependencies are up to date
Happy[1]: Version: 3.0.3. Using cache? no. Threads: 4
Happy[1]: Version: 3.0.3. Using cache? no. Threads: 4
Happy[1]: All set; signalling webpack to proceed.
Happy[1]: All set; signalling webpack to proceed.
Hash: 81743d89c90ff74c35e0
Version: webpack 2.4.1
Time: 3077ms
       Asset     Size  Chunks  Chunk Names
prerender.js  8.13 kB       0  prerender
chunk    {0} prerender.js (prerender) 15.3 kB [entry] [rendered]

ERROR in ./src/universal/routes/home.js
Module not found: Error: Can't resolve 'universal/components/App' in '/Users/florian/Code/Public/PlanetX/boilerplate-crater/src/universal/routes'
resolve 'universal/components/App' in '/Users/florian/Code/Public/PlanetX/boilerplate-crater/src/universal/routes'
  Parsed request is a module
  using description file: /Users/florian/Code/Public/PlanetX/boilerplate-crater/package.json (relative path: ./src/universal/routes)
  after using description file: /Users/florian/Code/Public/PlanetX/boilerplate-crater/package.json (relative path: ./src/universal/routes)
    resolve as module
      /Users/florian/Code/Public/PlanetX/node_modules doesn't exist or is not a directory
      /Users/florian/Code/Public/node_modules doesn't exist or is not a directory
      /Users/florian/Code/node_modules doesn't exist or is not a directory
      /Users/florian/node_modules doesn't exist or is not a directory
      /Users/node_modules doesn't exist or is not a directory
      /node_modules doesn't exist or is not a directory
      /Users/florian/Code/Public/PlanetX/boilerplate-crater/src/universal/routes/node_modules doesn't exist or is not a directory
      /Users/florian/Code/Public/PlanetX/boilerplate-crater/src/universal/node_modules doesn't exist or is not a directory
      /Users/florian/Code/Public/PlanetX/boilerplate-crater/src/node_modules doesn't exist or is not a directory
      looking for modules in /Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules
        using description file: /Users/florian/Code/Public/PlanetX/boilerplate-crater/package.json (relative path: ./node_modules)
        after using description file: /Users/florian/Code/Public/PlanetX/boilerplate-crater/package.json (relative path: ./node_modules)
          using description file: /Users/florian/Code/Public/PlanetX/boilerplate-crater/package.json (relative path: ./node_modules/universal/components/App)
            as directory
              /Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules/universal/components/App doesn't exist
            no extension
              /Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules/universal/components/App doesn't exist
            .js
              /Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules/universal/components/App.js doesn't exist
            .json
              /Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules/universal/components/App.json doesn't exist
[/Users/florian/Code/Public/PlanetX/node_modules]
[/Users/florian/Code/Public/node_modules]
[/Users/florian/Code/node_modules]
[/Users/florian/node_modules]
[/Users/node_modules]
[/node_modules]
[/Users/florian/Code/Public/PlanetX/boilerplate-crater/src/universal/routes/node_modules]
[/Users/florian/Code/Public/PlanetX/boilerplate-crater/src/universal/node_modules]
[/Users/florian/Code/Public/PlanetX/boilerplate-crater/src/node_modules]
[/Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules/universal/components/App]
[/Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules/universal/components/App]
[/Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules/universal/components/App.js]
[/Users/florian/Code/Public/PlanetX/boilerplate-crater/node_modules/universal/components/App.json]
 @ ./src/universal/routes/home.js 7:11-46
 @ ./src/universal/routes/index.js
 @ ./src/server/createSSR.js
 @ ./src/server/index.js
Hash: 9a54a3423120f99b0789


em pull code về chưa ?


неверно
проверьте на значениях
zero=3, minus_one=4, one=1


Could you elaborate a bit why it was necessary to kill all this code? Was the test result caching fundamentally broken or was it just hard to get right? Wouldn't it had been enough to just disable it by default and allow enabling it selectively? I'd very much like to use this functionality for some tests and now it looks like I'll need to fork Buck :(


Thanks!


TeamCity libpalaso :: palaso-win32-master Continuous [Build 4.0.53.2f3243d8ec0801a3c55d0454cd1c5a2fe618661c](http://build.palaso.org/viewLog.html?buildId=89239&buildTypeId=Libpalaso_PalasoWin32masterContinuous) outcome was **FAILURE**
Summary: Compilation error: SIL.Windows.Forms\SIL.Windows.Forms.csproj; compilation error: SIL.DblBundle\SIL.DblBundle.csproj Build time: 00:00:37


Yes, I think this can be merged. Depending on how the tests run I will add more tests for different sizes of instance terms later on. Currently I am only testing for terms of size one. Is this OK?


TeamCity libpalaso :: palaso-precise64-libpalaso-2.6 Continuous [Build 2.6.1312.965c544c338778af0e85f30a60aa94d294757235](http://build.palaso.org/viewLog.html?buildId=89229&buildTypeId=PalasoPrecise64v26Cont) outcome was **FAILURE**
Summary: Tests failed: 2, passed: 3576, ignored: 111 Build time: 00:06:28
### Failed tests
```
SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreIfDisposed): <no details avaliable>

SIL.Windows.Forms.Tests.dll: SIL.Windows.Forms.Tests.ControlExtensionsTests.ControlExtensionsTests.SafeInvoke_DisposedAfterInvokingOnUiThread_InvokedActionDequeued(IgnoreAll): <no details avaliable>

```


TeamCity libpalaso :: palaso-precise64-master Continuous [Build 4.0.41.965c544c338778af0e85f30a60aa94d294757235](http://build.palaso.org/viewLog.html?buildId=89230&buildTypeId=Libpalaso_PalasoPrecise64masterContinuous) outcome was **FAILURE**
Summary: Failed to resolve artifact dependency Build time: 00:00:04


Pas mal, un truc cool également est de lier une route à un modèle.

```diff
-public function show ( $id ) {
-    $task = Task::find($id);
+public function show ( $task ) {
```

https://laravel.com/docs/5.4/routing#route-model-binding


Just a quick question: Is this the fix for the reported AppleTalk problem here: https://forum.armbian.com/index.php?/topic/3236-appletalkagain/&do=findComment&comment=30443


Ohh I love it!