[R/CC_analysis_functions_additive_model.R:17:1:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L27) *style:* **Commas should always have a space after.**
```r
    op <- array(to.fill,c(length(prior$b.grid)))
                        ^
```
[R/CC_analysis_functions_additive_model.R:31:23:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                     ~^~
```
[R/CC_analysis_functions_additive_model.R:31:34:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                ~^~
```
[R/CC_analysis_functions_additive_model.R:31:46:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                            ~^~
```
[R/CC_analysis_functions_additive_model.R:35:1:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L35) *style:* **lines should not be more than 80 characters.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                       ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:35:59:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                              ~^~
```
[R/CC_analysis_functions_additive_model.R:35:96:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:37:18:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L37) *warning:* **no visible global function definition for ‘cc_llk_additive’**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:37:50:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                     ~^~
```
[R/CC_analysis_functions_additive_model.R:37:87:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:40:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:49:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                               ~^~
```
[R/CC_analysis_functions_additive_model.R:40:68:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:43:29:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L42) *style:* **Commas should always have a space after.**
```r
    t <- t[!t$coding %in% 99999,]
                                ^
```
[R/CC_analysis_functions.R:45:50:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L45) *style:* **Commas should always have a space after.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                 ^
```
[R/CC_analysis_functions.R:45:55:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L45) *style:* **Put spaces around all infix operators.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                     ~^~
```
[R/CC_analysis_functions.R:47:7:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L47) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(nrow(top.nodes) > 1 ) {
      ^
```
[R/CC_analysis_functions.R:55:26:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L55) *style:* **Only use double-quotes.**
```r
            selectable = 'N'
                         ^~~
```
[R/CC_analysis_functions.R:59:31:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                              ^~~~~~~~~~~
```
[R/CC_analysis_functions.R:59:47:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                                              ^~~~~~~
```
[R/CC_analysis_functions.R:62:22:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L62) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t,top.node)
                     ^
```
[R/CC_analysis_functions.R:64:58:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L64) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t[ ! t$node_id %in% top.nodes$node_id,],
                                                         ^
```
[R/CC_analysis_functions.R:68:27:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L68) *style:* **Commas should always have a space after.**
```r
    map <- match(t$coding,colnames(phens))
                          ^
```
[R/CC_analysis_functions.R:77:7:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L104) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                 ^
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L104) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L115) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:115:45:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L115) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^
```
[R/CC_analysis_functions.R:116:15:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L121) *style:* **Commas should always have a space after.**
```r
    t.ter <- t[t$ID %in% i.ter,]
                               ^
```
[R/CC_analysis_functions.R:123:21:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L123) *style:* **Commas should always have a space after.**
```r
    t2 <- t[nrow(t),,drop=F]
                    ^
```
[R/CC_analysis_functions.R:123:26:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L123) *style:* **Put spaces around all infix operators.**
```r
    t2 <- t[nrow(t),,drop=F]
                        ~^~
```
[R/CC_analysis_functions.R:126:10:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L126) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    while(cont) {
         ^
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L128) *style:* **Only use double-quotes.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^~~~
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L128) *style:* **Commas should always have a space after.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^
```
[R/CC_analysis_functions.R:131:43:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L131) *style:* **Commas should always have a space after.**
```r
        t2 <- rbind(t[t$ID %in% child.ids,],
                                          ^
```
[R/CC_analysis_functions.R:135:11:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L144) *style:* **Commas should always have a space after.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                          ^
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L144) *style:* **Only use double-quotes.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                                        ^~~~
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L191) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:192:10:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L192) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:193:10:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L193) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:194:10:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L194) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:195:10:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L195) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:196:10:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/R/CC_analysis_functions.R#L196) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:199:19:](https://github.com/shajoezhu/TreeWAS/blob/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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/b55c1860d659b4a5b70af709f1e9df4212ad67b2/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",
                                                              ^
```


Black Screen ?


Nope :v


test


In body i got this
>  got: "{\"error\":\"password is missing, role is invalid\"}"


I just patch some line, not all, thats not used for a6k


Kul
Black display Still present ;-; ?


even better!


是发现了 puma restart 周期性重启会报错吗？就是类似

No such file or directory -- /xxx/.../releases/38/vendor/bundle/ruby/2.4.0/gems/puma-3.8.1/bin/puma-wild (LoadError)
？？？


In lockscreen ? idk bro, thats random incoming :3


jhgfds


![](https://github.trello.services/images/mini-trello-icon.png) [Setup NS in Trello](https://trello.com/c/dXja1lkh/39-setup-ns-in-trello)


Chrome and Opera, I'm thinking that I need to test to see if it's actually that styles.css is in the edge cache since it's not using a cache busting technique, it's possible that the html being served is getting out of sync temporarily with the css being served. temporarily for a cdn cache can be measured in quite a long time.


Yo! @GUYVER91 I have merged some more chacha20 commits from linux-4.9.
I think you will like them.


"Use simple algorithm of timestamp handling in InnoDB instead of TRX_SEES"


A small app where you can call, Check about sports, learnings many more


Still keeps comming back ?


While I setOutputFile to the named pipe made by mkfifo, MediaRecorder.start cannot work and will throw IllegalStateException. Did you have this issue and do you know why? Thanks.


Not for now


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2387](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=28701&buildTypeId=ota_plus_RviSotaServer_Ci) outcome was **FAILURE**
Summary: Tests failed: 2 (2 new), passed: 288, ignored: 3 Build time: 00:15:57
### Failed tests
```
APIFunTests.test adding packages: <no details avaliable>

APIFunTests.test searching packages: <no details avaliable>

```


68725136fad8 alias cosimo


Do me a favour when that lockscreen freeze happens collect kernel logs


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2388](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=28703&buildTypeId=ota_plus_RviSotaServer_Ci) outcome was **FAILURE**
Summary: Tests failed: 2 (2 new), passed: 274, ignored: 3 Build time: 00:14:17
### Failed tests
```
org.genivi.sota.device_registry.DeviceResourceSpec.POST request on 'ping' should update 'lastSeen' field for device.: <no details avaliable>

org.genivi.sota.device_registry.DeviceResourceSpec.POST request on ping gets counted: <no details avaliable>

```


Vague condition. Use `versioned_by_engine()`.


or use lollipop dtb data from wt86528's dtbs it may fix flickering


u:object_r:fingerprint_device:s0

unknown fingerprint_device


Trying to get this pull & commit change section done


I wanted to import the spells to a new game, but the window wouldn't even show up.
Anyways, dunno what it was, but got fixed with the last update on this file.


I'm getting this:

```
==> default: chmod:
==> default: cannot access ‘.pgpass’
==> default: : No such file or directory
```


Hey @vinitkumar I will send a PR as soon as I can confirm that it works with both `python2` and `python3`. Good to know that the project is still actively maintained! :+1:


comment from the void: since you are including a `typings` property in your package.json file within the `autodiscover-activesync` lib, this line shouldn't be needed as TS should find the correct typings. (happy to debug if this is not working).


@shindig


Aye, was probably resolved by #25.


@pascalberger why is this needed?  That DLL will always be resolved by the installation of Cake.


I will update this soon.


Okey, we have same dtb just otg different bro


See the available entropy https://goo.gl/photos/Dpw4hc9WcUFUGpAGA


Instead of the number 720, probably you should have a variable and just use that. Such as WIDTH and HEIGHT


Only pick init.target.rc


the same as above


yep that makes sense.


It's only generating a partial migration at the moment, so it's not useful.


I would say that you commit way to often. Maybe it is not even necessary.


`rm -rf` does not fail when directory does not exist, so this is unnecessary.


Do #6


Like this solution. Easy to read.


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2389](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=28705&buildTypeId=ota_plus_RviSotaServer_Ci) is now running


You shouldn't have outcommented lines.


@jncd interesting find! So it's an orphaned page that's not linked from the subnav?


bla bla


Use fifo_active here and below instead of depth == 0


This needs to be non-blocking assignment.


interesting soul


@miguel456 You forgot the new-player translation at top.


You forgot to remove #Needs translation.


yes, still need to do that :)


Not sure what you mean here..


* include


this is 72 instead of 71


It is. Master branch has version `1.1.0` for whisper, carbon and graphite-web. So, ceres too.
Carbonate not using separate branches, we're tagging releases from master branch there.


![](https://github.trello.services/images/mini-trello-icon.png) [v1.42](https://trello.com/c/fxf0rLy4/1193-v1-42)


As far as I could tell, that flag defaults to true and it includes the fields not annotated with the view also by default. In this case, I wanted to make sure that the view was kicking in by testing that name was in the resulting json string and not age. But maybe there is a better way to do that.


一个model不同的管理器


@gep13 I just added it for documentation purposes, so that it is visible on the package against which Cake version the addin was built.


10/10 Great Commit Message!


De comment ging niet helemaal goed, maar ik heb alleen Camille's instructies opgevolgd. Dus Camille is hier de loser. Groetjes!


Text was too common.


Le commit a planté, il a pas tt envoyé.... merde...


Yeah forget it, I meant keep a handle for `this.objectMapper.writerFor(getType(type))` that you'd update only when a view is set rather than copy/pasting the whole chain for the two cases.


you can write this: 'public BufferedImage FLOOR, WALL, HERO_UP, HERO_DOWN, HERO_LEFT, HERO_RIGHT, SKELETON, BOSS;'


@poad42 why use kanged commits when you can get the original one's from here https://github.com/LineageOS/android_kernel_cyanogen_msm8916/commits/cm-14.1/drivers/input/misc/ltr553.c


I really like the name of this commit 😆


naming should be isWallAtPosition look at this:
tile.isWall(1, 2) what it says that I check if the tile is a wall and I dont know the parameters are what for
map.hasWallAtPosition(1, 2) now I know what I'm asking from the map, what the parameters should be
or more like:
map.movablePosition(1, 2)


@pascalberger ah, I see.  This will now be resolved into the Addin folder when the nuget restore is executed.


really good example of why we need objects. in about 1 month from now you wont actually remember what have you stored in the String[][] thing. probably bunch of strings. why equals "1"? we don't want to store them as strings with descriptive values like "1", also what happens when we need to actually change the map at some point? thats really hard like this.


instead we can have a list of tiles. containing walls and tiles with positions. we can find the one in the specified position and check if its actually a Wall or a Floor


missing return, right ?


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2389](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=28705&buildTypeId=ota_plus_RviSotaServer_Ci) outcome was **UNKNOWN**
Summary: Canceled (Tests failed: 2, passed: 48) Build time: 00:11:23
### Failed tests
```
org.genivi.sota.device_registry.DeviceResourceSpec.POST request on 'ping' should update 'lastSeen' field for device.: <no details avaliable>

org.genivi.sota.device_registry.DeviceResourceSpec.POST request on ping gets counted: <no details avaliable>

```


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2390](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=28708&buildTypeId=ota_plus_RviSotaServer_Ci) is now running


It turns out that it was: "send_group(group, message), a callable that takes two positional arguments; the group to send to, as a unicode string, and the message to send, as a serializable dict. It may raise MessageTooLarge but cannot raise ChannelFull."


I didn't know that thanks for pointing it out :) Fixing now.


@gep13 Yes, I noticed that too. Does this lead to any current or possible future problems?


Shouldn't this be `.nil?` instead of `.blank?`?


nice solutions


i have undervolted Some regulator Pins according to general msm8916 schema as on Qualcomnns website merge them & check


Are you sure that this assert is right? As far as I understand, you want the code to fail if you are doing a conversion to HF from other type. But on that situation, the left side of the || is false, the right side is true, so true as a whole.

I guess that what you want is an && instead of an ||


@mattkrick this the right thing to do? I’m not sure what the criteria is for adding to the list. But I had to yank the packages that we are using anymore.


Après réflxion : est-ce vraiment une bonne idée de mettre les snapshots dans un seul document ? Pour une machine qui tournera des jours ? Le tableau CPU sera énorme ce qui peut être un problème pour l'afficher sur une page web par la suite, alors mongodb propose [$slice](https://docs.mongodb.com/manual/reference/operator/projection/slice/) qui peut résoudre le problème, a voir.

Sinon une autre solution serai de faire une collection snapshot au lieu de machine avec les valeurs des métriques à un instant t, ainsi on peut controler le nombres de valeurs avec limit ou between...


Thats for what ? screen flicker ?


Can you check that this test pass when mode=FAST_COMPILE?


здесь тоже можно без self


@Fasse ping


good commit message :)


**abc**


@pascalberger I am not sure.

@devlead @patriksvensson can you offer anything here?

My normal guidance is simply not to include teh dependency, but I understand why you need it.


Too many comments. You already moved this part to a separate method called setImage. Let it go, Ramin.


Consumer ? Servers are producers (They produce metrics), calling this route consume seems wrong in my opinion.


Indentation seems wrong (3 chars on most places, 4 here)


if you get your self to 5000000 blocks you can see what happens


add line plz


rm line plz


rm plz


leave an extra line at the end


not required


Informative variable names 👍


``@ORM\Entity(repositoryClass="ClassSymfonyRepository")``


Good commitmessages 👍


``@ORM\Entity(repositoryClass="InterfaceSymfonyRepository")``


``@ORM\Entity(repositoryClass="NamespaceSymfonyRepository")``


麻烦问下dll将第三方库打包，如果不是PSA，是不是引入生成的文件就将所有打包后的第三方都引入了？还是可以按需引入？


``class NamespaceSymfonyrepository extends EntityRepository`` and use ``use``


since these are all the same type variables, they can and should all go into one line like this:

public BufferedImage FLOOR, WALL, HERO_UP, HERO_DOWN, HERO_LEFT, HERO_RIGHT, BOSS;


Tested, both tests pass:
```
(python2) ~/mila/dev/git/theano$ theano-cache purge
(python2) ~/mila/dev/git/theano$ THEANO_FLAGS=mode=FAST_COMPILE nosetests -xvs theano/gpuarray/tests/test_opt.py:test_local_lift_cholesky
Using cuDNN version 5105 on context None
Mapped name None to device cuda: GeForce 840M (0000:0A:00.0)
theano.gpuarray.tests.test_opt.test_local_lift_cholesky ... ok

----------------------------------------------------------------------
Ran 1 test in 6.755s

OK
(python2) ~/mila/dev/git/theano$ THEANO_FLAGS=mode=FAST_COMPILE nosetests -xvs theano/gpuarray/tests/test_opt.py:test_gpu_cholesky_not_inplace
Using cuDNN version 5105 on context None
Mapped name None to device cuda: GeForce 840M (0000:0A:00.0)
theano.gpuarray.tests.test_opt.test_gpu_cholesky_not_inplace ... ok

----------------------------------------------------------------------
Ran 1 test in 22.242s

OK
```


I wasn't able to retrieve PDD puzzles from the code base (if you think that it's a bug on your our side, please submit it to [yegor256/0pdd](https://github.com/yegor256/0pdd/issues):

```
cd /tmp/0pdd/extsoft/insight && pdd -q -f /tmp/pdd.xml20170412-17326-se2523: 256 (not zero):
/app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/lib/pdd/source.rb:143:in `rescue in puzzles': ["in /tmp/0pdd/extsoft/insight/git/git-utils.bash", #<PDD::Error: Space expected>] (PDD::Error)
	from /app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/lib/pdd/source.rb:141:in `puzzles'
	from /app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/lib/pdd.rb:97:in `block (3 levels) in xml'
	from /app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/lib/pdd.rb:96:in `each'
	from /app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/lib/pdd.rb:96:in `block (2 levels) in xml'
	from /app/vendor/bundle/ruby/2.2.0/gems/nokogiri-1.6.8.1/lib/nokogiri/xml/builder.rb:391:in `call'
	from /app/vendor/bundle/ruby/2.2.0/gems/nokogiri-1.6.8.1/lib/nokogiri/xml/builder.rb:391:in `insert'
	from /app/vendor/bundle/ruby/2.2.0/gems/nokogiri-1.6.8.1/lib/nokogiri/xml/builder.rb:375:in `method_missing'
	from /app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/lib/pdd.rb:95:in `block in xml'
	from /app/vendor/bundle/ruby/2.2.0/gems/nokogiri-1.6.8.1/lib/nokogiri/xml/builder.rb:293:in `initialize'
	from /app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/lib/pdd.rb:93:in `new'
	from /app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/lib/pdd.rb:93:in `xml'
	from /app/vendor/bundle/ruby/2.2.0/gems/pdd-0.17.3/bin/pdd:90:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.2.0/bin/pdd:23:in `load'
	from /app/vendor/bundle/ruby/2.2.0/bin/pdd:23:in `<main>'

/app/objects/exec.rb:38:in `run'
/app/objects/git_repo.rb:60:in `xml'
/app/objects/puzzles.rb:46:in `deploy'
/app/objects/job.rb:42:in `proceed'
/app/objects/job_starred.rb:35:in `proceed'
/app/objects/job_recorded.rb:33:in `proceed'
/app/objects/job_emailed.rb:36:in `proceed'
/app/objects/job_commiterrors.rb:36:in `proceed'
/app/objects/job_detached.rb:51:in `block in exclusive'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:89:in `block in timeout'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:34:in `block in catch'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:34:in `catch'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:34:in `catch'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:104:in `timeout'
/app/objects/job_detached.rb:49:in `exclusive'
/app/objects/job_detached.rb:39:in `block in proceed'
/app/objects/job_detached.rb:39:in `fork'
/app/objects/job_detached.rb:39:in `proceed'
/app/0pdd.rb:201:in `block in <top (required)>'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1611:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1611:in `block in compile!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `[]'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `block (3 levels) in route!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:994:in `route_eval'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `block (2 levels) in route!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1015:in `block in process_route'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in `catch'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in `process_route'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:973:in `block in route!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in `each'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in `route!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1085:in `block in dispatch!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `block in invoke'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `catch'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `invoke'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1082:in `dispatch!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in `block in call!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `block in invoke'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `catch'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `invoke'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in `call!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:895:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/xss_header.rb:18:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/path_traversal.rb:16:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/json_csrf.rb:18:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/base.rb:49:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/base.rb:49:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/frame_options.rb:31:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/logger.rb:15:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/commonlogger.rb:33:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:219:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:212:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/head.rb:13:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/methodoverride.rb:22:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:182:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:2013:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in `block in call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1787:in `synchronize'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/handler/webrick.rb:88:in `service'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/webrick/httpserver.rb:138:in `service'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/webrick/httpserver.rb:94:in `run'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/webrick/server.rb:294:in `block in start_thread'
```


Yep, not using a cache busting technique. If you're serving your site from your own origin server, you could try sending `cache-control: proxy-revalidate` HTTP header so that CDNs are "required" to make sure the resource is fresh. I don't use CDNs (on purpose), so I'm not sure how this works.


Nice :)


Quelle est la différence entre `actual_user` et `request.user` ?


nice catch! yeah, the more the merrier, every name on the list will make the webpack build just a little bit faster


rm line


You could add the characters to the charactersOnBoard list right away in their constructor.


JENKINS_HOME=/var/lib/jenkins
MAIL=/var/mail/jenkins
USER=jenkins
RUN_CHANGES_DISPLAY_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/2/display/redirect?page=changes
NODE_LABELS=master
HUDSON_URL=http://54.187.110.28:8080/
SHLVL=1
HOME=/var/lib/jenkins
BUILD_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/2/
HUDSON_COOKIE=7ae73870-726d-4686-a964-84cba2600df0
JENKINS_SERVER_COOKIE=durable-85d2a6fdbec4f8e1d5bdf18574029419
WORKSPACE=/var/lib/jenkins/workspace/testJenkinsfile_feature_dev-VO6KWFN7KDF6Z73JSKS4MD3CJJPSLWSLONTRLYUFEAKQ4PID6CHQ
LOGNAME=jenkins
NODE_NAME=master
_=/usr/bin/daemon
EXECUTOR_NUMBER=1
XDG_SESSION_ID=c13
BUILD_DISPLAY_NAME=#2
HUDSON_HOME=/var/lib/jenkins
JOB_BASE_NAME=feature%2Fdev
PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/bin
BUILD_ID=2
XDG_RUNTIME_DIR=/run/user/112
BUILD_TAG=jenkins-testingGHO-testJenkinsfile-feature%2Fdev-2
LANG=en_US.UTF-8
JENKINS_URL=http://54.187.110.28:8080/
JOB_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/
BUILD_NUMBER=2
NODE_PATH=/usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript
SHELL=/bin/bash
RUN_DISPLAY_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/2/display/redirect
HUDSON_SERVER_COOKIE=b063ccf2922c0e12
JOB_DISPLAY_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/display/redirect
JOB_NAME=testingGHO/testJenkinsfile/feature%2Fdev
PWD=/var/lib/jenkins/workspace/testJenkinsfile_feature_dev-VO6KWFN7KDF6Z73JSKS4MD3CJJPSLWSLONTRLYUFEAKQ4PID6CHQ
BRANCH_NAME=feature/dev


BTW, http://edas.info redirects you to the HTTPS version of the site right away (and HTTPS is what you should be using in the first place anyway 😃...)


Why not use the `$badfilter` directive instead of creating an exception filter ?


JENKINS_HOME=/var/lib/jenkins
MAIL=/var/mail/jenkins
USER=jenkins
RUN_CHANGES_DISPLAY_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/3/display/redirect?page=changes
NODE_LABELS=master
HUDSON_URL=http://54.187.110.28:8080/
SHLVL=1
HOME=/var/lib/jenkins
BUILD_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/3/
HUDSON_COOKIE=17f5786c-a0df-4657-a925-19eec6ae802a
JENKINS_SERVER_COOKIE=durable-85d2a6fdbec4f8e1d5bdf18574029419
WORKSPACE=/var/lib/jenkins/workspace/testJenkinsfile_feature_dev-VO6KWFN7KDF6Z73JSKS4MD3CJJPSLWSLONTRLYUFEAKQ4PID6CHQ
LOGNAME=jenkins
NODE_NAME=master
_=/usr/bin/daemon
EXECUTOR_NUMBER=1
XDG_SESSION_ID=c13
BUILD_DISPLAY_NAME=#3
HUDSON_HOME=/var/lib/jenkins
JOB_BASE_NAME=feature%2Fdev
PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/bin
BUILD_ID=3
XDG_RUNTIME_DIR=/run/user/112
BUILD_TAG=jenkins-testingGHO-testJenkinsfile-feature%2Fdev-3
LANG=en_US.UTF-8
JENKINS_URL=http://54.187.110.28:8080/
JOB_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/
BUILD_NUMBER=3
NODE_PATH=/usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript
SHELL=/bin/bash
RUN_DISPLAY_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/3/display/redirect
HUDSON_SERVER_COOKIE=b063ccf2922c0e12
JOB_DISPLAY_URL=http://54.187.110.28:8080/job/testingGHO/job/testJenkinsfile/job/feature%252Fdev/display/redirect
JOB_NAME=testingGHO/testJenkinsfile/feature%2Fdev
PWD=/var/lib/jenkins/workspace/testJenkinsfile_feature_dev-VO6KWFN7KDF6Z73JSKS4MD3CJJPSLWSLONTRLYUFEAKQ4PID6CHQ
BRANCH_NAME=feature/dev


Error in validate, unlock & generate when channel is missing
500 Internal Error thrown but should be 404 NOT_FOUND


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2390](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=28708&buildTypeId=ota_plus_RviSotaServer_Ci) outcome was **SUCCESS**
Summary: Tests passed: 290, ignored: 3 Build time: 00:13:21


you should define multiple variables in one line if they are from same type, so it is makes your code shorter, like "BufferdImage FLOOR, WALL, HERO_UP, etc.;"


So there are 4 layers but velocities are are defined 6, how it works?

thanks


I like this solution for drawing all the characters 👍


Nice commit message :)


#2 把xls 另存成 xlsx檔就不會有亂碼了。


Initial Commit


tile size should be 72, if you have 720 size canvas and have 10 tile.


Because the filter was not bad? It's a specific filter, it just needed a specific exception.


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/4783b745-d26b-41fe-bb56-d39169880c89 "fitchain"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/420a436e-add5-49fe-9817-1556990ec503 "fitchain") deployed [health-blockchain](https://github.com/IBM-Bluemix/health-blockchain/releases/tag/deploy-ibm-yp-us-south-Dev-Advocates-demos-20170412-145315 "deploy-ibm-yp-us-south-Dev-Advocates-demos-20170412-145315") to [demos](https://console.ng.bluemix.net/apps/a40dc60e-7166-458d-af16-edeb22da5c9d "ibm:yp:us-south:Dev-Advocates:demos"), including this commit


much better solutions than the previous one :)


with open('{}.{}'.format(index, link.get('href')[len(link.get('href'))-3: len(link.get('href'))]), 'wb') as jpg:这段代码有没有bs4，request文档，


Añadir el pin de mostoles al mapa @githubteacher
closes #5459


Does not compile?


Actually this should be exec_type != BRW_REGISTER_TYPE_HF &&  inst->dst.type != BRW_REGISTER_TYPE_HF, so we don't do any to/from HF conversion.


Interesting, how did this crop up now? Did a blame, and it looks like the display property wasn't there as of 3 months ago?


> Upload handlers are initially defined in the FILE_UPLOAD_HANDLERS setting, which defaults to:
> ```python
> ["django.core.files.uploadhandler.MemoryFileUploadHandler",
>  "django.core.files.uploadhandler.TemporaryFileUploadHandler"]
> ```
>
> https://docs.djangoproject.com/en/1.10/topics/http/file-uploads/#upload-handlers


Nice to see you were able to move this to more appropriate classes. Make sure to clean up this class before commiting.


oups :D


Ok, I am going to fix it.


jejoeffewj


try not no leave commented out lines in the code, especially if i repeats twice.


Why have you disabled SD_DETECT_PIN?


grhrhhehe


Using hero moving methodes is a good idea 👍 👍


Always leave an empty line on the bottom of the file, otherwise neat!


Old Version, will mark...


I wasn't able to retrieve PDD puzzles from the code base (if you think that it's a bug on your our side, please submit it to [yegor256/0pdd](https://github.com/yegor256/0pdd/issues):

```
cd /tmp/0pdd/extsoft/insight && git reset --hard --quiet && git clean --force -d && git pull --quiet: 256 (not zero):
Auto-merging git/git-utils.bash
CONFLICT (add/add): Merge conflict in git/git-utils.bash
Automatic merge failed; fix conflicts and then commit the result.

/app/objects/exec.rb:38:in `run'
/app/objects/git_repo.rb:89:in `pull'
/app/objects/git_repo.rb:67:in `push'
/app/objects/job.rb:41:in `proceed'
/app/objects/job_starred.rb:35:in `proceed'
/app/objects/job_recorded.rb:33:in `proceed'
/app/objects/job_emailed.rb:36:in `proceed'
/app/objects/job_commiterrors.rb:36:in `proceed'
/app/objects/job_detached.rb:51:in `block in exclusive'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:89:in `block in timeout'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:34:in `block in catch'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:34:in `catch'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:34:in `catch'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/timeout.rb:104:in `timeout'
/app/objects/job_detached.rb:49:in `exclusive'
/app/objects/job_detached.rb:39:in `block in proceed'
/app/objects/job_detached.rb:39:in `fork'
/app/objects/job_detached.rb:39:in `proceed'
/app/0pdd.rb:201:in `block in <top (required)>'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1611:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1611:in `block in compile!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `[]'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `block (3 levels) in route!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:994:in `route_eval'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `block (2 levels) in route!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1015:in `block in process_route'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in `catch'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in `process_route'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:973:in `block in route!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in `each'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in `route!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1085:in `block in dispatch!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `block in invoke'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `catch'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `invoke'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1082:in `dispatch!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in `block in call!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `block in invoke'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `catch'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `invoke'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in `call!'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:895:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/xss_header.rb:18:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/path_traversal.rb:16:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/json_csrf.rb:18:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/base.rb:49:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/base.rb:49:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-protection-1.5.3/lib/rack/protection/frame_options.rb:31:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/logger.rb:15:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/commonlogger.rb:33:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:219:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:212:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/head.rb:13:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/methodoverride.rb:22:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:182:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:2013:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in `block in call'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1787:in `synchronize'
/app/vendor/bundle/ruby/2.2.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in `call'
/app/vendor/bundle/ruby/2.2.0/gems/rack-1.6.5/lib/rack/handler/webrick.rb:88:in `service'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/webrick/httpserver.rb:138:in `service'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/webrick/httpserver.rb:94:in `run'
/app/vendor/ruby-2.2.2/lib/ruby/2.2.0/webrick/server.rb:294:in `block in start_thread'
```


you should pay attention and leave an empty line at the bottom of your code so it won't get messed up when we will work on the projects together


Adding assets might be better as separate commit(s).
(But I'm not sure what's the official guideline here.)

Nice, clean code! :+1:
Also, god descriptive commit message. :slightly_smiling_face:


I do understand what you are trying to do here, and actually I tried to solve the hero movement problem in a similar way first, but as Aze said on Monday, the Hero class should not contain any operational / movement related methods or functions at all. Anything that is related to the manipulation of events or characters in the game should belong to a Handler or similar class.


You may do these as not static methods inside a distinct class.


chinese


725? I wonder where did that number came from.


Fixes #513


wow, this is a long one :D you might want to consider moving a few lines out of here under different classes?


wrong indentation here, "}"


Fixes #514


gtgyuhug


very very very few commits today....


When you create a hero object, I think you don't have to pass all the images as parameters, as you can reach them from the hero class as well. Or at least it worked for me. :) Maybe we should ask a mentor about it. :)


too many empty lines


I like the way you structure your code, it's really clean, readable. :)


extra line


imageloader is nice solution... I should implement as well


explicitly check for `ErrNoCookie`


Looks great, I'll try it out. Thanks


hopefully adding this again works


hbgtfctfcyghkbhujn


This commit message seems to mee too long. Maybe you should commit separately the two changes.


hopefull this works too erd


<3 empty classes.


nice boolean :)


Think about disposing of the tile size here. A lot of other objects use this size as well.


Amazing job @Gouterman! 👍


I sense Skeletons in the walls. There should be a method to check position.


In my example there are 5 boundaries that is 6 layers thus 6 velocities.

------- 0 ------
layer 1
----wbz=0.1---
layer 2
------0.35------
layer 3
------0.95------
layer 4
-------1.20-----
layer 5
------1.90----
layer 6
------2.00----


two -> too 💯


`hw` is always a single letter by convention. Same below.


not a criticism, just maybe a good idea: you could ask for a BufferedImage parameter in your Character constructor instead of defining the image inside the constructor so you could create skeletons and bosses with different images easily in the future.


you don't need  this extra line


This doesn't have to be public, does it? Change to `stickyHeader` if not.


extra line


Hi @pachacamac , thank you for this project! Feel free to use and promote this list :)


can you get this from a canonical source?


nope


Read this from an environment variable.

A decent way to do this would be to define a `vars.js` that grabs it from a `TOKEN` environment variable

```
//vars.js

export const LOGIN_TOKEN = process.env.TOKEN;
```


you should also pay attention to leave an empty line at the bottom of your code so when we will work on the projects together it won't get messed up


I like this solution, I don't know if it's working yet but I think you're on the right track.


I'll add a variable PROD then and set that to T/F accordingly


Very clean and tight code. I am tempted to read some more of it! ;-)


AddChecksumReport (JasonGlazer) - x86_64-MacOS-10.9-clang: OK (2488 of 2488 tests passed, 241 test warnings)

 * 241 tests had: EIO diffs.

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


Fixed.


Could define this method on `*backendHeaderWriter` and avoid passing the `Header`


I don't get it, that it's the position of what? If it's the position of the hero, than I think that they should be the fields of the hero.


you could save the magic number 72 into a field such as tileSize, so in case you have to change it you wouldn't need to go through all your code to change number 72.


commit error:
"import collections" for standard deviation calculation


Done.


I'd recommend adding the dotenv package to the very top so that environment variables can be read from the file really easily.

```
require('dotenv').config()
```

https://www.npmjs.com/package/dotenv