[R/CC_analysis_functions_additive_model.R:17:1:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L17) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
calculate.llk.grid_scaled_additive <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:27:25:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L27) *style:* **Commas should always have a space after.**
```r
    op <- array(to.fill,c(length(prior$b.grid)))
                        ^
```
[R/CC_analysis_functions_additive_model.R:31:23:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                     ~^~
```
[R/CC_analysis_functions_additive_model.R:31:34:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                ~^~
```
[R/CC_analysis_functions_additive_model.R:31:46:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                            ~^~
```
[R/CC_analysis_functions_additive_model.R:35:1:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L35) *style:* **lines should not be more than 80 characters.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:35:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L35) *warning:* **no visible binding for global variable ‘cc_d.llk_additive’**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                       ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:35:59:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                         ~^~
```
[R/CC_analysis_functions_additive_model.R:35:80:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                              ~^~
```
[R/CC_analysis_functions_additive_model.R:35:96:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:37:1:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L37) *style:* **lines should not be more than 80 characters.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:37:18:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L37) *warning:* **no visible global function definition for ‘cc_llk_additive’**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                 ^~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:37:36:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:37:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:37:71:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                     ~^~
```
[R/CC_analysis_functions_additive_model.R:37:87:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:40:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:40:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:49:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                               ~^~
```
[R/CC_analysis_functions_additive_model.R:40:68:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:43:29:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L43) *style:* **Put spaces around all infix operators.**
```r
    if (scaled) op <- exp(op-mx);
                           ~^~
```
[R/CC_analysis_functions_additive_model.R:45:19:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                 ~^~
```
[R/CC_analysis_functions_additive_model.R:45:30:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                            ~^~
```
[R/CC_analysis_functions_additive_model.R:45:42:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                                        ~^~
```
[R/CC_analysis_functions_additive_model.R:60:31:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L60) *style:* **Put spaces around all infix operators.**
```r
    tmp1 <- (aff[1] + unaf[1])/(1 + exp(-b0))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:60:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L60) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp1 <- (aff[1] + unaf[1])/(1 + exp(-b0))
                               ^
```
[R/CC_analysis_functions_additive_model.R:61:31:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L61) *style:* **Put spaces around all infix operators.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:61:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                               ^
```
[R/CC_analysis_functions_additive_model.R:61:42:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                                         ^
```
[R/CC_analysis_functions_additive_model.R:62:31:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L62) *style:* **Put spaces around all infix operators.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:62:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L62) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                               ^
```
[R/CC_analysis_functions_additive_model.R:62:42:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L62) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                                         ^
```
[R/CC_analysis_functions_additive_model.R:62:49:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L62) *style:* **Put spaces around all infix operators.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                                               ~^~
```
[R/CC_analysis_functions_additive_model.R:65:16:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
              ~^~
```
[R/CC_analysis_functions_additive_model.R:65:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
                   ~^~
```
[R/CC_analysis_functions_additive_model.R:65:26:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
                        ~^~
```
[R/CC_analysis_functions_additive_model.R:82:10:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L82) *style:* **Put spaces around all infix operators.**
```r
        2*b1)))
        ~^~
```
[R/CC_analysis_functions_additive_model.R:94:1:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L94) *style:* **lines should not be more than 80 characters.**
```r
calculate.integrated.llk_scaled_additive <- function(prior, llk.surf, scaled = TRUE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:94:1:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L94) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
calculate.integrated.llk_scaled_additive <- function(prior, llk.surf, scaled = TRUE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:126:1:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L126) *style:* **lines should not be more than 80 characters.**
```r
get.posterior.node_additive <- function(forward, backward, prior, id = 1, plot = FALSE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:126:1:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L126) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
get.posterior.node_additive <- function(forward, backward, prior, id = 1, plot = FALSE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:129:15:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L129) *style:* **Put spaces around all infix operators.**
```r
    tmp <- tmp/sum(tmp)
             ~^~
```
[R/CC_analysis_functions_additive_model.R:130:22:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L130) *warning:* **no visible binding for global variable ‘null.id’**
```r
    post.null <- tmp[null.id[1]]
                     ^~~~~~~
```
[R/CC_analysis_functions_additive_model.R:132:9:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L132) *warning:* **no visible binding for global variable ‘null.id’**
```r
    tmp[null.id[1]] <- 0
        ^~~~~~~
```
[R/CC_analysis_functions_additive_model.R:133:15:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L133) *style:* **Put spaces around all infix operators.**
```r
    tmp <- tmp/sum(tmp)
             ~^~
```
[R/CC_analysis_functions_additive_model.R:157:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L157) *style:* **Put spaces around all infix operators.**
```r
    spac <- abs(prior$b.grid[2]-prior$b.grid[1])
                              ~^~
```
[R/CC_analysis_functions_additive_model.R:163:35:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L163) *style:* **Put spaces around all infix operators.**
```r
        b1_ci_lhs = rg.1[1] - spac/2,
                                 ~^~
```
[R/CC_analysis_functions_additive_model.R:164:35:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions_additive_model.R#L164) *style:* **Put spaces around all infix operators.**
```r
        b1_ci_rhs = rg.1[2] + spac/2,
                                 ~^~
```
[R/CC_analysis_functions.R:20:5:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L20) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    NODE.COUNT.LIMIT=10,
    ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:21:5:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L21) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    NUM.CASES.MIN=10
    ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:28:7:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(nrow(samples) != nrow(phens)) {
      ^
```
[R/CC_analysis_functions.R:32:7:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L32) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(samples$ID == phens$ID)) {
      ^
```
[R/CC_analysis_functions.R:36:7:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
      ^
```
[R/CC_analysis_functions.R:36:9:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L36) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
        ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:36:28:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L36) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
                           ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:37:9:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L37) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        NODE.COUNT.LIMIT <- NUM.CASES.MIN
        ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:37:29:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L37) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        NODE.COUNT.LIMIT <- NUM.CASES.MIN
                            ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:42:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L42) *style:* **Commas should always have a space after.**
```r
    t <- t[!t$coding %in% 99999,]
                                ^
```
[R/CC_analysis_functions.R:45:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L45) *style:* **Commas should always have a space after.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                 ^
```
[R/CC_analysis_functions.R:45:55:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L45) *style:* **Put spaces around all infix operators.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                     ~^~
```
[R/CC_analysis_functions.R:47:7:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L47) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(nrow(top.nodes) > 1 ) {
      ^
```
[R/CC_analysis_functions.R:55:26:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L55) *style:* **Only use double-quotes.**
```r
            selectable = 'N'
                         ^~~
```
[R/CC_analysis_functions.R:59:31:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                              ^~~~~~~~~~~
```
[R/CC_analysis_functions.R:59:47:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                                              ^~~~~~~
```
[R/CC_analysis_functions.R:62:22:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L62) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t,top.node)
                     ^
```
[R/CC_analysis_functions.R:64:58:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L64) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t[ ! t$node_id %in% top.nodes$node_id,],
                                                         ^
```
[R/CC_analysis_functions.R:68:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L68) *style:* **Commas should always have a space after.**
```r
    map <- match(t$coding,colnames(phens))
                          ^
```
[R/CC_analysis_functions.R:77:7:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if( length(dummy) > 0 ) {
      ^
```
[R/CC_analysis_functions.R:79:12:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L79) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for( i in 1:length(dummy) ) {
           ^
```
[R/CC_analysis_functions.R:80:20:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L80) *style:* **Use <-, not =, for assignment.**
```r
            node.id=t[dummy[i],'node_id']
                   ^
```
[R/CC_analysis_functions.R:80:20:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L80) *style:* **Put spaces around all infix operators.**
```r
            node.id=t[dummy[i],'node_id']
                  ~^~
```
[R/CC_analysis_functions.R:80:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L80) *style:* **Only use double-quotes.**
```r
            node.id=t[dummy[i],'node_id']
                               ^~~~~~~~~
```
[R/CC_analysis_functions.R:80:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L80) *style:* **Commas should always have a space after.**
```r
            node.id=t[dummy[i],'node_id']
                               ^
```
[R/CC_analysis_functions.R:81:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L81) *style:* **Use <-, not =, for assignment.**
```r
            node.cod=t[dummy[i],'coding']
                    ^
```
[R/CC_analysis_functions.R:81:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L81) *style:* **Put spaces around all infix operators.**
```r
            node.cod=t[dummy[i],'coding']
                   ~^~
```
[R/CC_analysis_functions.R:81:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L81) *style:* **Only use double-quotes.**
```r
            node.cod=t[dummy[i],'coding']
                                ^~~~~~~~
```
[R/CC_analysis_functions.R:81:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L81) *style:* **Commas should always have a space after.**
```r
            node.cod=t[dummy[i],'coding']
                                ^
```
[R/CC_analysis_functions.R:82:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L82) *style:* **Use <-, not =, for assignment.**
```r
            node.mea=t[dummy[i],'meaning']
                    ^
```
[R/CC_analysis_functions.R:82:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L82) *style:* **Put spaces around all infix operators.**
```r
            node.mea=t[dummy[i],'meaning']
                   ~^~
```
[R/CC_analysis_functions.R:82:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L82) *style:* **Only use double-quotes.**
```r
            node.mea=t[dummy[i],'meaning']
                                ^~~~~~~~~
```
[R/CC_analysis_functions.R:82:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L82) *style:* **Commas should always have a space after.**
```r
            node.mea=t[dummy[i],'meaning']
                                ^
```
[R/CC_analysis_functions.R:83:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L83) *style:* **Use <-, not =, for assignment.**
```r
            node.counts=t[dummy[i],'counts']
                       ^
```
[R/CC_analysis_functions.R:83:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L83) *style:* **Put spaces around all infix operators.**
```r
            node.counts=t[dummy[i],'counts']
                      ~^~
```
[R/CC_analysis_functions.R:83:36:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L83) *style:* **Only use double-quotes.**
```r
            node.counts=t[dummy[i],'counts']
                                   ^~~~~~~~
```
[R/CC_analysis_functions.R:83:36:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L83) *style:* **Commas should always have a space after.**
```r
            node.counts=t[dummy[i],'counts']
                                   ^
```
[R/CC_analysis_functions.R:88:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L88) *style:* **Only use double-quotes.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                        ^~~~~~~~
```
[R/CC_analysis_functions.R:88:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L88) *style:* **Commas should always have a space after.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                        ^
```
[R/CC_analysis_functions.R:88:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L88) *style:* **Commas should always have a space after.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                 ^
```
[R/CC_analysis_functions.R:88:53:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L88) *style:* **Put spaces around all infix operators.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                   ~^~
```
[R/CC_analysis_functions.R:88:54:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L88) *style:* **Only use double-quotes.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                     ^~
```
[R/CC_analysis_functions.R:93:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L93) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                       ^~~~~~~~
```
[R/CC_analysis_functions.R:93:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                       ^
```
[R/CC_analysis_functions.R:93:52:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                   ^
```
[R/CC_analysis_functions.R:93:59:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                          ^
```
[R/CC_analysis_functions.R:93:62:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L93) *style:* **Put spaces around all infix operators.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                            ~^~
```
[R/CC_analysis_functions.R:93:63:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L93) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                              ^~
```
[R/CC_analysis_functions.R:94:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L94) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                       ^~~~~~~~~
```
[R/CC_analysis_functions.R:94:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                       ^
```
[R/CC_analysis_functions.R:94:53:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                    ^
```
[R/CC_analysis_functions.R:94:60:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                           ^
```
[R/CC_analysis_functions.R:94:63:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L94) *style:* **Put spaces around all infix operators.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                             ~^~
```
[R/CC_analysis_functions.R:94:64:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L94) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                               ^~
```
[R/CC_analysis_functions.R:95:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L95) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'selectable'] <- "N"
                       ^~~~~~~~~~~~
```
[R/CC_analysis_functions.R:95:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L95) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'selectable'] <- "N"
                       ^
```
[R/CC_analysis_functions.R:96:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L96) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'counts'] <- NA
                       ^~~~~~~~
```
[R/CC_analysis_functions.R:96:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L96) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'counts'] <- NA
                       ^
```
[R/CC_analysis_functions.R:98:26:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L98) *style:* **Commas should always have a space after.**
```r
            t <- rbind(t,new.node)
                         ^
```
[R/CC_analysis_functions.R:104:34:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L104) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                 ^
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L104) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L104) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^
```
[R/CC_analysis_functions.R:106:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^~~~
```
[R/CC_analysis_functions.R:106:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^
```
[R/CC_analysis_functions.R:106:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^~~~~
```
[R/CC_analysis_functions.R:106:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^
```
[R/CC_analysis_functions.R:106:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^~~~
```
[R/CC_analysis_functions.R:106:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:107:25:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L107) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^~~~
```
[R/CC_analysis_functions.R:107:25:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L107) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^
```
[R/CC_analysis_functions.R:110:24:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L110) *style:* **Commas should always have a space after.**
```r
    t <- rbind(t[i.ter,],
                       ^
```
[R/CC_analysis_functions.R:111:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L111) *style:* **Commas should always have a space after.**
```r
                  t[i.par,])
                          ^
```
[R/CC_analysis_functions.R:112:15:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L112) *style:* **Only use double-quotes.**
```r
    t[nrow(t),'Par'] <- 0
              ^~~~~
```
[R/CC_analysis_functions.R:112:15:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L112) *style:* **Commas should always have a space after.**
```r
    t[nrow(t),'Par'] <- 0
              ^
```
[R/CC_analysis_functions.R:115:34:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L115) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                 ^
```
[R/CC_analysis_functions.R:115:45:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L115) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:115:45:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L115) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^
```
[R/CC_analysis_functions.R:116:15:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L116) *style:* **Only use double-quotes.**
```r
    t[nrow(t),'Par'] <- 0
              ^~~~~
```
[R/CC_analysis_functions.R:116:15:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L116) *style:* **Commas should always have a space after.**
```r
    t[nrow(t),'Par'] <- 0
              ^
```
[R/CC_analysis_functions.R:117:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^~~~
```
[R/CC_analysis_functions.R:117:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^
```
[R/CC_analysis_functions.R:117:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^~~~~
```
[R/CC_analysis_functions.R:117:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^
```
[R/CC_analysis_functions.R:117:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^~~~
```
[R/CC_analysis_functions.R:117:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:118:25:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L118) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^~~~
```
[R/CC_analysis_functions.R:118:25:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L118) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^
```
[R/CC_analysis_functions.R:121:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L121) *style:* **Commas should always have a space after.**
```r
    t.ter <- t[t$ID %in% i.ter,]
                               ^
```
[R/CC_analysis_functions.R:123:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L123) *style:* **Commas should always have a space after.**
```r
    t2 <- t[nrow(t),,drop=F]
                    ^
```
[R/CC_analysis_functions.R:123:26:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L123) *style:* **Put spaces around all infix operators.**
```r
    t2 <- t[nrow(t),,drop=F]
                        ~^~
```
[R/CC_analysis_functions.R:126:10:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L126) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    while(cont) {
         ^
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L128) *style:* **Only use double-quotes.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^~~~
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L128) *style:* **Commas should always have a space after.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^
```
[R/CC_analysis_functions.R:131:43:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L131) *style:* **Commas should always have a space after.**
```r
        t2 <- rbind(t[t$ID %in% child.ids,],
                                          ^
```
[R/CC_analysis_functions.R:135:11:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L135) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(nrow(t2) == nrow(t)) cont <- FALSE
          ^
```
[R/CC_analysis_functions.R:139:42:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L139) *style:* **Commas should always have a space after.**
```r
               t2[ ! t2$ID %in% t.ter$ID,])
                                         ^
```
[R/CC_analysis_functions.R:144:43:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L144) *style:* **Commas should always have a space after.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                          ^
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L144) *style:* **Only use double-quotes.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                                        ^~~~
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L144) *style:* **Commas should always have a space after.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                                        ^
```
[R/CC_analysis_functions.R:145:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L145) *style:* **Only use double-quotes.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^~~~~
```
[R/CC_analysis_functions.R:145:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L145) *style:* **Commas should always have a space after.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^
```
[R/CC_analysis_functions.R:146:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^~~~
```
[R/CC_analysis_functions.R:146:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^
```
[R/CC_analysis_functions.R:146:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^~~~~
```
[R/CC_analysis_functions.R:146:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:146:59:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^~~~
```
[R/CC_analysis_functions.R:146:59:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^
```
[R/CC_analysis_functions.R:147:28:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L147) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^~~~
```
[R/CC_analysis_functions.R:147:28:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L147) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^
```
[R/CC_analysis_functions.R:152:8:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:length(i.ter) ) {
       ^
```
[R/CC_analysis_functions.R:153:11:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L153) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
          ^
```
[R/CC_analysis_functions.R:153:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L153) *style:* **Only use double-quotes.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
                               ^~~~~~~~
```
[R/CC_analysis_functions.R:153:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L153) *style:* **Commas should always have a space after.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
                               ^
```
[R/CC_analysis_functions.R:154:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L154) *style:* **Only use double-quotes.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:154:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L154) *style:* **Commas should always have a space after.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:155:18:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L155) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                 ^
```
[R/CC_analysis_functions.R:155:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L155) *style:* **Only use double-quotes.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                ^~~~~~~~
```
[R/CC_analysis_functions.R:155:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L155) *style:* **Commas should always have a space after.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                ^
```
[R/CC_analysis_functions.R:155:46:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L155) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                             ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:156:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L156) *style:* **Only use double-quotes.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:156:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L156) *style:* **Commas should always have a space after.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:160:8:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L160) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:length(i.par) ) {
       ^
```
[R/CC_analysis_functions.R:161:28:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L161) *style:* **Only use double-quotes.**
```r
        w.d <- which(tree[,'Par'] == i.par[i])
                           ^~~~~
```
[R/CC_analysis_functions.R:161:28:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L161) *style:* **Commas should always have a space after.**
```r
        w.d <- which(tree[,'Par'] == i.par[i])
                           ^
```
[R/CC_analysis_functions.R:163:11:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L163) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
          ^
```
[R/CC_analysis_functions.R:163:26:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L163) *style:* **Only use double-quotes.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
                         ^~~~~~~~
```
[R/CC_analysis_functions.R:163:26:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L163) *style:* **Commas should always have a space after.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
                         ^
```
[R/CC_analysis_functions.R:164:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L164) *style:* **Only use double-quotes.**
```r
            tree[i.par[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:164:27:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L164) *style:* **Commas should always have a space after.**
```r
            tree[i.par[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:168:31:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L168) *style:* **Commas should always have a space after.**
```r
    tree <- tree[!tree$REMOVE,]
                              ^
```
[R/CC_analysis_functions.R:170:40:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L170) *style:* **Commas should always have a space after.**
```r
    tree.par <- tree.id[match(tree$Par,tree$ID)]
                                       ^
```
[R/CC_analysis_functions.R:173:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L173) *style:* **Only use double-quotes.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^~~~~
```
[R/CC_analysis_functions.R:173:21:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L173) *style:* **Commas should always have a space after.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^
```
[R/CC_analysis_functions.R:175:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^~~~
```
[R/CC_analysis_functions.R:175:33:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^
```
[R/CC_analysis_functions.R:175:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^~~~~
```
[R/CC_analysis_functions.R:175:50:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:175:59:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^~~~
```
[R/CC_analysis_functions.R:175:59:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^
```
[R/CC_analysis_functions.R:176:28:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L176) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^~~~
```
[R/CC_analysis_functions.R:176:28:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L176) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^
```
[R/CC_analysis_functions.R:180:5:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L180) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    expected.node.ids <- 1:NUM.NODES
    ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:182:7:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L182) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
      ^
```
[R/CC_analysis_functions.R:182:19:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L182) *style:* **Only use double-quotes.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                  ^~~~
```
[R/CC_analysis_functions.R:182:19:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L182) *style:* **Commas should always have a space after.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                  ^
```
[R/CC_analysis_functions.R:182:28:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L182) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                           ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:183:1:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L183) *style:* **lines should not be more than 80 characters.**
```r
        stop("Node IDs are not compatible. Check that they are numeric and increasing bottom to top\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:186:7:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L186) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(i.ter == 1:length(i.ter))) {
      ^
```
[R/CC_analysis_functions.R:191:10:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L191) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:192:10:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L192) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:193:10:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L193) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:194:10:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L194) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:195:10:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L195) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:196:10:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L196) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:199:19:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                  ^
```
[R/CC_analysis_functions.R:199:26:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                         ^
```
[R/CC_analysis_functions.R:199:32:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                               ^
```
[R/CC_analysis_functions.R:199:41:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                        ^
```
[R/CC_analysis_functions.R:199:51:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                                  ^
```
[R/CC_analysis_functions.R:199:63:](https://github.com/shajoezhu/TreeWAS/blob/2d99bea5b82b8456cfe7eeb569d002bd8b910eea/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                                              ^
```


Commit after create the ring buffer and the connexion between two neurons


Created multidev environment [natalie-sandbox#ci-260](https://dashboard.pantheon.io/sites/ee1a9f88-1cc8-4eca-a8a6-7dc1433bb37e#ci-260).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-260-natalie-sandbox.pantheonsite.io/)


Jag menar att det verkar som att du glömde uppdatera filen footerNav.html när du uppdaterade adress.md?

Såhär ser sidan ut för mig efter en hard reload:
![image](https://user-images.githubusercontent.com/4319680/31620346-4e7d667c-b297-11e7-9500-42f1d0c6abaf.png)

Footern visar alltså fortfarande den gamla adressen. Ska det verkligen vara så? 😕 Jag hittar ingen annan fil än footerNav.html som innehåller texten "Larsgatan", och jag vet inte varför footern skulle vara skriven i html när resten är i markdown, men så verkar det i alla fall vara...


The Pokemon constructor should have dealt with the other fields as well, as Aze described on Thursday, hence those people who work on Pokemon class can define what kind of fileds are necessary in Pokemon and sub-classes have to follow.


Не обязательно указывать конкретную реализацию списка в объявлении переменной, можно ограничиться интерфейсом:
`private List<PushEvent> pushEventsList = new ArrayList<>();`


@jwilm The font rendering looks slightly blurry and glitchy after this commit when I resize it:

![image](https://user-images.githubusercontent.com/107672/31620467-1683a856-b276-11e7-9098-bb5653efa4dd.png)
![image](https://user-images.githubusercontent.com/107672/31620515-329ae3e2-b276-11e7-8c82-4c9beeb298aa.png)

![image](https://user-images.githubusercontent.com/107672/31620423-fb377c58-b275-11e7-8633-80653b12e2fb.png)


Забудь про селкивание строк (конкатенацию) и вспомни про интерполяцию, тогда никаких to_s не нужно будет, например, здесь будет так: `"#{index + 1}. #{st.name_station};"`.
И назови у станции атрибут просто `name`, не нужно дублировать название класса в именах атрибутовю


@speting64 empty strings doesnt change the value, its just a complicated thing for `return voice;`


It should be like
public Pokemon(String sound, int hp, int strength){
this.sound= sound;
this.hp = hp;
this.strength = rand.nextInt(10);
}


Комментарий к коду, поясняющий как оно работает, хорошее решение?


TeamCity Selenium POM :: CI [Build 115](https://teamcity.sponte.uk/viewLog.html?buildId=1393&buildTypeId=SeleniumPom_Ci) is now running


Without the defult super constructor it doesn't make sense


I would rather not have a bunch of whitespace/formatting commits.  I don't recall our discussions on coding style, but I'm okay moving forward with what ever this commit may have implied -- just let us know how to perform the same beautification step so we can do it before committing code.  The only thing I really care about is tabs vs spaces.  I hope we went with spaces.


Added to form:
Choice distribution, number iterations, enter s value, range, set parametrs.
Added to script:
Set different parametrs for exp. and normal distributions.


I had an idea one night that open open source wasn't quite the right model for hyperamp, but thinking about it some more, I think I was mistaken.  The idea was basically that unlike a library, an app that mixes lots of ideas together require a lot of editorialized decision by us and that a wiki model would be too lose, whereas libraries define an interface early on and a loosely coordinated effort to improve the library is nearly self directing.  I'll put it back for the time being.


TeamCity Selenium POM :: CI [Build 115](https://teamcity.sponte.uk/viewLog.html?buildId=1393&buildTypeId=SeleniumPom_Ci) outcome was **SUCCESS**
Summary: Tests passed: 60 Build time: 00:03:12


Code in the Dark hosted by SC5 Online in Jyväskylä, Finland.


это не моё. Пришло ещё со старых версий в новых исправленно


Chapter 2

The use of double kernel mapping in multiple address spaces is essential and the continuity in mapping the same amount of memory in an address space more than one times to create and form the "unmapped" page. Furthermore, to protect the stack of the user.
 This page table program is to allow the system of xv6 to reapply and reuse the address space of different processes into a single physical memory space. Moreover, it is indeed made to perform a single protection at the same amount of time.
The ability of kernel and users to control the virtual address is given by the Operating system, thus the programming of the time page hardware connect these two kinds of physical address and Random-Access Memory.
The existance of the PTE is essentials, therefore, it is noted that determination of the existance of PTE must be done first, then going back to the PTE and then eventually it does not content any kalloc program in order to create a brand new page and back to zero, finally it is set back to the PTE program.

CPU Page Table Entry in addition to PPN also stored flags, used to explain the corresponding virtual address usage rights,
It is considered 3 important main PTE's to consider about, the first one PTE_W, is to control the writing of this page. PTE_P, meaning is PTE really in the Page Table, if it is not, then it is not allowed to use.  PTE_U is to control user process can or cannot be used, if it can't be used then only the kernel is available to be used.

The paged hardware
The initial step, 10bits that is received,find the corresponding process in the Page Table and then continue utilizing the 10bits that find the corresponding entity page
 The intermediate step (with the PPN), 20bits is calculated from the addition of both 10bits,  convert the virtual address to the index page to find a PTE and replace the top 20 bits of PTE
And then the original virtual address last 12bits after the completion
if the front of the 10bits already exist it is just down 10bits from the page index a PTE.
It's a wrap!

sbreak;
A process that requires more memory at run time can call sbreak (n) to increase its data memory n bytes (n> 0 or n <0);
if (n> 0) growproc allocates one or more physical pages and maps them to the top of the process address space and vice versa if (n <0) growproc will unmap one or more pages from the process's address space and release the corresponding physical page.
execution =
exec;
 Process to open the binary conversion name can read the ELF file
exec is allocated to a new page table via onoffkvm, and then loaduvm loads each segment into memory, and allocuvm is used to allocate memory for each single ELF.
The more detailed is:allocuvm Checks if the requested virtual address is lower than kernbase
loaduvm Use walkpgdir to find the physical address of the allocated memory for each page that writes the ELF segment and read it.
During the preparation of a new memory image, if exec detects an invalid block error, return to minus 1. If the old image disappears, the system call can not return-1.
The exec most common mistake is when the image is formed. It is formed, then the exec can install the new image in order to return to zero, but before that exec has to released the old image first.

Address space
kvmalloc

kvmalloc () {
pgdir = setupkvmalloc ();

onoffkvm ();
}
Initial = KERNELBASE originates from software you installed on your system.
Use KERNELBASE to create and switch to the top of the page table to run the double kernel process address space plan required mapping.
User memory from zero to compile the page number.
Intermediate = In addition, use mappages to install the kernel translation required to convert a virtual address range to the corresponding physical address range of the page table.
Advance =  Use walkpgdir to search for the virtual address PTE
walkpgdir (pde_t * pgdir, const void * va, int alloc)
walkpgdir In the search for virtual address of the PTE, there are simulated to x86 paging hardware action. walkpgdir uses the upper ten bits of the virtual address to find the page directory entry. If it does not exist, the page table page is not yet assigned; if the alloc reference is set , then walkpgdir will allocate it and place its physical address in the page directory. Then initialize the PTE to hold the associated physical page number, the required permissions (PTE_W and / or PTE_U), and PTE_P to mark the PTE as valid as possible. Finally use the next 10 bits of the virtual address to find the PTE in the page table page address.


spacing


=> "/users/3"

这里可以说一下 “/users/3” 是怎么回事，或者可以说一下 3 是参数


@speting64 you dont use only just the name parameter


Опять же не мой код. Это коллизия из-за неправльного слияния версий


I... uhm.  I guess this is fine, but the question that comes to mind is why would anyone have a 30 Day Lending threshold lower than their minimum lending rate?  In other words, when would this ever come up?  You would have to have your thirtyDayMin setting lower than your minlendrate, the base lowest rate you ever lend anything out at.


It is true, it is wrong, but the main problem these updates came by accident idk how and Insurgency xml files are not finished by me.

About Insurgency: MIC, actually the xml was totally wrong, this game support only Windows, there is no linux support, that's why I renamed back to win32. I will finish the xml and push an update, but the big problem is there is no official or any custom tutorial about this game server how to make, so it is difficult to recheck everything...


First edit of this file done!/GH


Это опять же не мой код


4 последние строки зачем вызываются на каждый эвент?


@speting64 the exercise doesnt say anything about the pokebag having a name


NICE


Метод называется setEvent**s** а принимает один эвент


这个的意思是 传入 17 这个 id，然后输出的是 { id: 17, name: "Alex" } ？

觉得这里可以加一些描述


also the exercise doesnt say anything pokemons having names


@speting64 this exercise is very incomplete, only some of the basic fields pokemons are correct


This answer should be answered in README.md, you can use IntelliJ for etxt editing as well, but no need for the new .java file.
1 - the whole thingy was in bracket, so it is the method signature, not the public only


May I check if this is the same as `guard let planeAnchor = anchor as? PlaneAnchor else { return }`?


@vdominika questions created commit message and nothing related to that are in the changes


可以说明一下这句注释的含义，再适当加一些文字描述，会比只有代码更容易理解一下。


Also, renamed instances of typelist to "bestiary" to avoid confusion with functions whose names contain type_list. Previously the distinction was the lack of an underscore. This was admittedly bad practice.

Another minor change is that free_type_list now correctly operates on its argument


6 - local variable
7 - body of the method
8 - return statement


I think this can generally be inferred by what the user is asking, seems redundant to add it.

I also think we could split the Computer/Server OS stuff into different lines.

```
* Server OS (include output of `uname -a`):
* Computer OS and Browser (if applicable):
```


@vdominika indentation


像最后这几个路由都没有加文字描述，所以只有代码的话，可能会让读者理解起来吃力一些。


@vdominika you cant create a function inside of another function


refactored `schema.fields` to `schema.fieldClasses`


@vdominika opening brackets should be inline with the method signature


What about CTRL-HOME and CTRL-END? These would go to beginning resp. end of whole text.


thong bao


hi, "$this->app->config['view']['paths']" is not set for lumen ?


Bluemix [toolchain](https://dev-console.stage1.bluemix.net/devops/toolchains/71872f44-5538-41e9-a816-179fbf1dde6d "idsqat4-ToolInt-1508168816846"): [Delivery Pipeline](https://dev-console.stage1.bluemix.net/devops/pipelines/13882c7d-00a7-4a14-b364-fdcd49856fb7 "idsqat4-ToolInt-1508168816846") deployed [idsqat4-ToolInt-1508168816846](https://github.com/idsqat1/idsqat4-ToolInt-1508168816846/releases/tag/deploy-ibm-ys1-us-south-idsqat4-us.ibm.com-dev-20171016-154855 "deploy-ibm-ys1-us-south-idsqat4-us.ibm.com-dev-20171016-154855") to [dev](https://console.stage1.bluemix.net/apps/d70fa541-efdd-4668-bd58-572548a1dc1c?env_id=ibm:ys1:us-south "ibm:ys1:us-south:idsqat4@us.ibm.com:dev"), including this commit


@weslly your screenshots look like there's old pixel data interleaved with the current glyphs. Strange that I can't make the problem show up on my machine. Looking into it.


:white_check_mark: [CodeHound](https://github.com/CodeHoundBot) has built this commit using [AppVeyor](https://appveyor.com) and found that it is :ok:.

[![](https://img.shields.io/travis/rust-lang/rust.svg)](https://ci.appveyor.com/project/yotam180/xai/build/1.0.19)


Created multidev environment [profos2#ci-2](https://dashboard.pantheon.io/sites/1a350c81-8441-4dce-9520-04392f586f56#ci-2).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-2-profos2.pantheonsite.io/)


@matthiaskrgr This https://github.com/danmar/cppcheck/commit/f27e98f910b0ff8905ed252ed5a117e4218dce70 should address the problem.


一般都需要解析出来请求带过来的数据 => 一般都需要把请求带过来的数据解析出来


I don't _think_ the `set +u` and `set -u` are necessary anymore once we pop into the environment.  At least when I tested in my PR it seemed to be OK without.  I also think we should probably source every file in `/.singularity.d/env/` in a loop just to make sure we are picking everything up.


Yes, it is.

The `updateByDiff` is a wrapper for us to not have to pass the second parameter to `update` (which is an array of the fields' name we are going to update) because using an array this way leads us to duplicate that array across the implementation and all of its possible tests.

As the new method relays on a bonded method, I've used sinon to "hijack" `update` I believe that it does not replace the original method but rather observes it - if not we have a problem.


I've restored sources


I feel it's a bit confusing this way. $isDevMode is not the right variable name. I would rather change the name to $isProdMode = true; and send $isProdMode to createAnnotationMetadataConfiguration().


运行代码，并通过浏览器访问 `http://localhost:3000/home?id=12&name=ikcamp`，然后打开控制台会看到下面的输出内容：


// 浏览器打开访问 http://localhost:3000/home?id=12&name=ikcamp    这一句可以放在上面说


We have corrected the spelling on this function and updated the references everywhere.


Should this ref #825 instead?


Ignore. Suddenly stopped. I guess after "Clear cache and register hooks."


or better even: just send "true" to createAnnotationMetadataConfiguration() and don't use a variable name, because it's only used for that and it doesn't represent the dev mode or not.


运行代码，并通过浏览器访问 `http://localhost:3000/home/12/ikcamp `，然后查看下控制台显示的日志信息：


这个注释也可以放在上面


RSTE doesn't have this problem as it doesn't pull from learnset


I'm able to reproduce on macOS; is that the platform you're on?


建议： 句号是不是可以去掉


Just to clarify, it only incorrectly returns `CacheError`s when the request fn throws rather than emits an error.

All other errors are properly thrown as `got.RequestError` `got.HTTPError` etc. Working on a fix.


@jwilm yes, macOS 10.13


修改 => 继续修改


@bsclifton I think it was added and walked back. If you see a duplicate block, duplicate shouldn't be there.


Google Apps Script code snippets/Hightligh Event.js

yrtrty


Could you add a note about why these files need to be renamed again?


somebody had to do this :)


@jwilm looks like this on mine... macOS as well
![screen shot 2017-10-16 at 12 00 17 pm](https://user-images.githubusercontent.com/7071307/31622227-d57b79da-b269-11e7-9de9-ab75c54dd1a3.png)


Some of the redirects are bad, needs fixing.


extra space?


Why are these here?


Incorrect spacing.  Tabs are standard now.


Another typo: `exmaple.cpp -> example.cpp`. Sorry!


删除重新提交


spelling.....


这里可以用 “===”


why the caps?


Probably, yeah.


Oui c'est une bonne idée


This isn't just a bad idea, it is seen to break emails in the wild. The splitting logic persistently evolved the wrong splitting logic from release to release. What specs / email examples required the change from strict treatment to this lax (and incorrect) treatment?


Just for knowledge: [Vertex](https://www.quora.com/What-is-the-plural-form-of-the-word-vertex-Why-is-it-irregular)


thanks martin,don't work anyways unfortunately


I couldn't find them defined in a specific header anywhere, so i defined them locally. Every file that uses them seems to do something similar.


I think I need to understand how important it is to manually type the same repetitive words into every commit message.  Isn't the whole point of having a branch so that you don't have to repeat yourself on every commit message?  Because otherwise, this is just annoying busy-work.

If it is that important, we'll need to have tooling or something that enforces it, or allows someone to safely change the message after the fact, because otherwise, I can guarantee folks will forget or make mistakes.

I'd rather just get this rename over with so we can deliver a release to our users.  If I have to spend an extra minute worrying about the format of a commit message, then I will probably have to stop committing on the weekend or late at night when I'm trying to slip something in that I think is going to help everyone get a release of Royale sooner than later.

I have been wishing for some sort of tooling for quite a while.  If we want to discuss tooling more, start a new thread.

My 2 cents,
-Alex

From: Piotr Zarzycki <notifications@github.com<mailto:notifications@github.com>>
Reply-To: apache/royale-compiler <reply@reply.github.com<mailto:reply@reply.github.com>>
Date: Monday, October 16, 2017 at 12:15 AM
To: apache/royale-compiler <royale-compiler@noreply.github.com<mailto:royale-compiler@noreply.github.com>>
Cc: aharui <aharui@apache.org<mailto:aharui@apache.org>>, Author <author@noreply.github.com<mailto:author@noreply.github.com>>
Subject: Re: [apache/royale-compiler] fix more tests (f0119cb)

@aharui<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Faharui&data=02%7C01%7C%7C6aad67a8a50c44ddf92808d51465ae61%7Cfa7b1b5a7b34438794aed2c178decee1%7C0%7C0%7C636437349310442916&sdata=EH50A%2Fa1pdn98NuehkMgZkvff6BdHbQ94uu8w%2B5gTdw%3D&reserved=0> please do not forget about issue number - This is still renaming work (reference #17<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Froyale-compiler%2Fissues%2F17&data=02%7C01%7C%7C6aad67a8a50c44ddf92808d51465ae61%7Cfa7b1b5a7b34438794aed2c178decee1%7C0%7C0%7C636437349310442916&sdata=5yFfmkJob7iu3nsrLxgF%2F3IUY%2BgEpezDuR7MnbmbyHg%3D&reserved=0>)

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Brian, some debugging code was added during course of development and we removed most of it but missed to remove the console.log debug statement. We have removed that now.


I tested with this; doesn't affect any how so should be removed.


Let's add `-f` (force) for ln instead.


这一段和上面的那句话可以放在一个段落里。


Hello,

ok thanks for this, i am correcting here, i will do a pull request soon


ARPlaneAnchor, but yes, I think that should also work. And it looks more elegant, thanks!


https://tools.ietf.org/html/rfc2387 is a fun read!


Same, `ln -sf`


But that's breaking parsing, as data in read() is not guaranteed to get in blocks until `\n`. It's possible to receive partial commands back broken into two parts, like what I said:
```
> G1\nG1
< Gok\n1\nG1\nok\n
// Notice how `G1` is broken into two parts (Gok\n and 1\n)
```


![](https://github.trello.services/images/mini-trello-icon.png) [Scroll without repainting menus](https://trello.com/c/ikC7x8YH/44-scroll-without-repainting-menus)


so I have to create 2 new models : `ResourceImageAttachment` and `ResourceDocumentAttachment` and to add UNIQUE constraints on these ?


The correlation matrix is not appearing need to be fixed


Also… fun fact, if you send `?_format=json` it will send back JSON data intead of `multipart/related` data.


GET requests are cacheable, but when coming from a browser the may have an unintended URL length cap. In those cases you can use POST.


I dream when we can use `multipart/related` to stream subresponses back for a better _time to first byte_ performance. That is impossible with JSON because is not an streameable format.


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/9c05c60b-fc2f-42e3-b721-1a9f146d65f9 "DM-Toolchain"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/1c11b36b-c072-4612-85ca-bc45b9e367ac "DM-Toolchain") deployed [DM-Toolchain](https://github.com/DAMcGrath/DM-Toolchain/releases/tag/deploy-ibm-yp-us-south-Debbra.McGrath-TestDM-20171016-161756 "deploy-ibm-yp-us-south-Debbra.McGrath-TestDM-20171016-161756") to [TestDM](https://console.bluemix.net/apps/76e652d5-4b9c-42a9-863c-7bfb3209d8e0?env_id=ibm:yp:us-south "ibm:yp:us-south:Debbra.McGrath:TestDM"), including this commit


обернуть в скобки


а не лучше ли тогда юзать for i цикл?


@e0ipso Do you have any docs on the url length cap?


I accidentally released version 0.1.5 while testing various configuration options. 🙀


@NikolajBjorner I'm surprised that you needed this. I thought `_Exit()` was supposed to work under MSVC.
See https://msdn.microsoft.com/en-us/library/6wdz5232.aspx .


In PHP, currently,

- `<<|>>` is scoped as `keyword.operator.bitwise.php`.
- `&&|\|\|` is scoped as `keyword.operator.logical.php`.

https://github.com/sublimehq/Packages/blob/928a7a618d99631ea424c45e74fb01d1fb6f6853/PHP/PHP%20Source.sublime-syntax#L229


The USB_DC_STM32 should depend on USB && SOC_FAMILY_STM32 (I will update it, when I patch the driver to be generic). Each Kconfig.series file selects HAS_STM32CUBE.


"afficher"


our build machines are still 2012


I'm fine with changing that, let's just create an issue for it. I won't remember there is a comment on this commit. :smile:


D'oh! Thanks :-)


"dû insérer"


"par défaut"


Perhaps better to output something useful like:  "ERROR: sl_thd struct size doesn't match rust version."


I know you had slow-networks issues with Composer but let's not replace the Composer with bash: the idea of Composer is to manage versions. Now If I want to update Mediawiki version, I can't just run `composer update`.

Composer has caching, it won't re-install already installed stuff and other nice tools, so `wget` is really a step backwards.

Additionally we can easily pull any other repositories to `/public` by just adding them to Composer file.


@gronke As you can see above, this is not currently getting transpiled to code that can run in an environment where [`Set`](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Set) is not available. What's your favorite way to fix that for this module?


I hear you Alex and promise do not be to harsh on that in case where we are working on the separate branch.

Thank you for your point of view!
Piotr


@NikolajBjorner Ah. I see.


same...

All caps is hard to read.  Don't make messages that are meant to be read all caps.  See previous suggestion for a better option.

Might as well make this more useful and print out the field that has the strange offset, right?


No reason to print anything on success, right?


Shouldn't these be returning an error (`-1`)?


Great, thanks!


@mvcds I think @rhberro mentioned the fact about `updateByDiff` isn't bind to class context unlike `update`, eg.: `this.updateByDiff = this.updateByDiff.bind(this)`


I already forgot the context for all of this.

Why are we creating a rust version of the `sl_thd` structure?


`Rails.application.config_for` does this for you.


I don't see a `FileName` property listed in the [documentation for `Process`](https://msdn.microsoft.com/en-us/library/system.diagnostics.process(v=vs.110).aspx), and since CKAN is a .NET app, the program that's running may technically be `mono` instead, with the `ckan.exe` listed in the arguments. I didn't want to wade into all of that complexity, but if you're able to make it work, then I think everyone would welcome a pull request.


There is a clang-format file in the root directory.  I didn't get any response on an earlier discussion of this.  We did go with spaces.
If you want to run it yourself.  you can enable clang-tools in the cmake,  then run make clang-format-all will run the formatter on all the code.   There is also a clang-tidy-all if you want to generate a bunch of code style and other warnings.  I have been slowly addressing them when the opportunity presents itself.

If you have other opinions on style we can discuss them as well as how to make it more automated.  For the moment we are just doing a style commit every couple weeks and before each major release, lacking anything better.


This looks small and standalone: https://github.com/jibsen/brieflz/blob/master/depack.c


I think this needs a `float(..)` around one of the arguments to work correctly in python2


you mean `this->map_tracks_ = map_tracks;` in the body of the constructor (it does not compile otherwise) ? I think it's going to be rejected by codacy again.

One nicer workaround could be to add a protected constructor to SequentialSfMReconstructionEngine which would only be accessible from SubmapSfMReconstructionEngine. Would that be alright ?


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/ea59c747-dd95-4876-8435-fd9fceea866a "cds-website-push"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/86716c6c-dcfd-4dc3-aded-5f4a22c3c209 "cds-pipeline") deployed [design-system-website](https://github.com/carbon-design-system/design-system-website/releases/tag/deploy-ibm-yp-us-south-chrisdhanaraj_org-Bluemix-Design-System-20171016-162928 "deploy-ibm-yp-us-south-chrisdhanaraj_org-Bluemix-Design-System-20171016-162928") to [Bluemix Design System](https://console.bluemix.net/apps/6a8f6f55-0f07-43fa-a912-1580fe66d984?env_id=ibm:yp:us-south "ibm:yp:us-south:chrisdhanaraj_org:Bluemix Design System"), including this commit


TeamCity Selenium POM :: CI [Build 116](https://teamcity.sponte.uk/viewLog.html?buildId=1398&buildTypeId=SeleniumPom_Ci) is now running


We'll change this to 12 if @mvdbro don't have any objections?


nice


__This is the location of the fatal bug.__


This needs a `float` wrapper around one of the arguments, I think, to work in python2


ok


This needs a `float` wrapper to work in python 2


TeamCity Selenium POM :: CI [Build 116](https://teamcity.sponte.uk/viewLog.html?buildId=1398&buildTypeId=SeleniumPom_Ci) outcome was **UNKNOWN**
Summary: Canceled (Exit code 137 (new)) Build time: 00:03:22


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-20171016-163322 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20171016-163322") to [prod](https://console.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19?env_id=ibm:yp:us-south "ibm:yp:us-south:user@ibm.com:prod"), including this commit


That code looks nice and small. It's worth experimenting with at least. It'd be interesting to know how much it can shrink the syntax files by, before working on an actual patch.


@ghugo
I don't think this is sufficient?

From https://github.com/westurner/dotfiles/blob/develop/scripts/git-changelog.py (which still needs tests):

```python
BOLCHARSTOESCAPE = ['*', '.. ', '>>> ']
CHARSTOESCAPE = [
    #('\\', u'⧹'),  #TODO double-escaping
    ('`', '\`'),
    ('|', '\|'),
    ('[', '\['),
    (']', '\]'),
]

def rst_escape(_str):
    """XXX TODO
    References:
    - http://docutils.sourceforge.net/docs/user/rst/quickref.html#escaping
    - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html#escaping-mechanism
    .. warning:: There are not yet any test cases for this function.
    """
    lines = _str.splitlines()
    output_lines = []
    for line in lines:
        # *      -> \*
        # '.. '  -> '\.. '
        # '>>> ' -> '\>>> '
        for c in BOLCHARSTOESCAPE:
            r = '\\' + c
            matchcount = line.count(c)
            if matchcount == 0:
                line = line
            elif matchcount == 1:
                if not line.lstrip().startswith(c):
                    line = line.replace(c, r)
            else:
                if line.lstrip().startswith(c):
                    beginning, rest = line.split(c, 1)
                    line = beginning + c + rest.replace(c, r)
                else:
                    line = line.replace(c, r)
        # characters to escape
        for char, repl in CHARSTOESCAPE:
            line = line.replace(char, repl)
        if line.startswith('__ ') and line.endswith('_'):
            # indirect hyperlink target
            line = u'\%s' % line
        # TODO: header lines
        # TODO: footnotes, citations
        output_lines.append(line)
    return u'\n'.join(output_lines)
```

```rst
IIUC, this works, for example:
===========================
Include example:

    .. include:: /etc/shadow

Raw example:

.. raw:: html

  <script>alert("here");</script>
```


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-20171016-163329 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20171016-163329") to [prod](https://console.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19?env_id=ibm:yp:us-south "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Is it really necessary? I think that `updateByDiff` will be called correctly because it is wrapped into a class.

Though it would break if a third method started to call `updateByDiff`, but anyone writing such code should be the one fixing its binding IMO.


Why pass in `zero` if the function is named `..OrZero`? It seems like this function should take in `mem.index_reg`, and if the `Instruction::Register` is "empty", then it should produce `zero` on its own using `word_type`. Also, if you're going to put this function into Remill's instruction lifter, then I suggest refactoring remill's `LiftAddressOperand` to use it.


TeamCity Selenium POM :: CI [Build 117](https://teamcity.sponte.uk/viewLog.html?buildId=1400&buildTypeId=SeleniumPom_Ci) is now running


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-Prod-20171016-163337 "deployed-2-env-Prod-20171016-163337") to [Prod](https://console.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19?env_id=ibm:yp:us-south "There was a problem retrieving the space name"), 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-20171016-163347 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20171016-163347") to [prod](https://console.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19?env_id=ibm:yp:us-south "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Wuhuuu!


I wouldn't both with this, the `ir.Create..` suite of functions tend to do some in-line constant folding/etc.


Created multidev environment [natalie-sandbox#pr-theme-cl](https://dashboard.pantheon.io/sites/ee1a9f88-1cc8-4eca-a8a6-7dc1433bb37e#pr-theme-cl).

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


A King osztályt én írtam (Truzsi Vivien), viszont nem tudtam commitolni, ezért van annál is Kitti neve.


You should probably remove the ones that no longer exist (or teach the script how to remove them)


The workaround seems doable.


I think `format_base` should get a case handling `base == int(base)` to print these without the `.`


@leonardiwagner that's it! I am saying this because the others methods are binded in the class constructor.


Or are these all actually new?


TeamCity Selenium POM :: CI [Build 117](https://teamcity.sponte.uk/viewLog.html?buildId=1400&buildTypeId=SeleniumPom_Ci) outcome was **SUCCESS**
Summary: Tests passed: 60 Build time: 00:03:52


Good point. FIxing.


How to add new bad word?


You still need to tell ZAS to recalculate the zones, in the same way as doors.


On opening/closing, that is.


This commit has been mentioned on **Discourse Meta**. There might be relevant details there:

https://meta.discourse.org/t/deep-linking-to-headings-anchors/47552/20


What does this commit is supposed to do? I'm getting
'''
 error: expected ')'
 before 'PRId64'
     n += snprintf(str+n, L-n, "%" PRId64, tensor->size[i]);
'''
when building from source


```
$ du -hs share/
232K  share/

$ tar -cvf share.tar share

$ ls -l share.tar
... 160K ... share.tar

$ xz -6 share.tar

$ ls -l share.tar.xz
... 32K ... share.tar.xz
```

There's definitely some big space savings to be had.


Wondering if the file (conffiles) shouldn't just be generated during build...


Thx. Let me push some things on the concrete pages I implemented during my way back


Rust needs to know the definition of sl_thd to get the thread id from sl_thd_alloc which returns a sl_thd pointer.

I didn't make a PR, i just pushed directly, i thought we discussed that on Friday perhaps i misunderstood.


Dla mysql chyba sie wykrzaczy bo ta konstrukcja DROP NOT NULL nie przechodzi


Another option? http://oldhome.schmorp.de/marc/liblzf.html


DROP NOT NULL nie zadziala dla mysql


TeamCity Selenium POM :: CI [Build 118](https://teamcity.sponte.uk/viewLog.html?buildId=1403&buildTypeId=SeleniumPom_Ci) is now running


Why did you add this?


I don't seem to be able to do the editing this morning. When I click on Start review or Add comment nothing happens. Any ideas?


Я ОРУ


hi