[R/cla_secsse_loglik.R:1:37:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L1) *style:* **Commas should always have a space after.**
```r
cla_secsse_loglik_rhs <- function(t,y,parameter){
                                    ^
```
[R/cla_secsse_loglik.R:1:39:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L1) *style:* **Commas should always have a space after.**
```r
cla_secsse_loglik_rhs <- function(t,y,parameter){
                                      ^
```
[R/cla_secsse_loglik.R:1:48:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L1) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
cla_secsse_loglik_rhs <- function(t,y,parameter){
                                               ^~
```
[R/cla_secsse_loglik.R:3:10:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L3) *style:* **Put spaces around all infix operators.**
```r
  d <- ly/2
        ~^~
```
[R/cla_secsse_loglik.R:4:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  Es <- y[1:d]
  ^~
```
[R/cla_secsse_loglik.R:5:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
  Ds <- y[(d+1):ly]
  ^~
```
[R/cla_secsse_loglik.R:5:13:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L5) *style:* **Put spaces around all infix operators.**
```r
  Ds <- y[(d+1):ly]
           ~^~
```
[R/cla_secsse_loglik.R:8:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L8) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:10:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L10) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:11:26:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L11) *style:* **Commas should always have a space after.**
```r
  all_states <- cbind(Ds,Es)
                         ^
```
[R/cla_secsse_loglik.R:12:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L12) *warning:* **local variable ‘mus’ assigned but may not be used**
```r
  mus <- parameter[[2]]
  ^~~
```
[R/cla_secsse_loglik.R:12:26:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                         ^
```
[R/cla_secsse_loglik.R:12:29:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                            ^
```
[R/cla_secsse_loglik.R:12:41:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                                        ^
```
[R/cla_secsse_loglik.R:14:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  cross_D_E <- a%*%b
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:14:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L14) *warning:* **local variable ‘Q’ assigned but may not be used**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:14:17:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L14) *style:* **Put spaces around all infix operators.**
```r
  cross_D_E <- a%*%b
               ~^~~~
```
[R/cla_secsse_loglik.R:15:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L15) *warning:* **local variable ‘nb_node’ assigned but may not be used**
```r
  nb_node <- phy$Nnode
  ^~~~~~~
```
[R/cla_secsse_loglik.R:16:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:16:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
  ^~
```
[R/cla_secsse_loglik.R:16:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *warning:* **local variable ‘mus’ assigned but may not be used**
```r
  mus <- parameter[[2]]
  ^~~
```
[R/cla_secsse_loglik.R:16:10:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
         ^
```
[R/cla_secsse_loglik.R:16:34:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                 ^
```
[R/cla_secsse_loglik.R:16:62:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                             ^
```
[R/cla_secsse_loglik.R:16:73:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Put spaces around all infix operators.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                        ^~
```
[R/cla_secsse_loglik.R:16:74:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                         ^
```
[R/cla_secsse_loglik.R:16:75:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                          ^
```
[R/cla_secsse_loglik.R:16:84:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:118:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:122:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:133:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:17:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
  ^~
```
[R/cla_secsse_loglik.R:17:10:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
         ^
```
[R/cla_secsse_loglik.R:17:34:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                 ^
```
[R/cla_secsse_loglik.R:17:62:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                             ^
```
[R/cla_secsse_loglik.R:17:76:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                           ^
```
[R/cla_secsse_loglik.R:17:85:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:125:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:129:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:131:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Put spaces around all infix operators.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ~^~~~
```
[R/cla_secsse_loglik.R:17:141:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:18:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L18) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:18:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L18) *warning:* **local variable ‘hmax’ assigned but may not be used**
```r
  hmax <- NULL
  ^~~~
```
[R/cla_secsse_loglik.R:18:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L18) *warning:* **local variable ‘Q’ assigned but may not be used**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:19:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L19) *warning:* **local variable ‘ly’ assigned but may not be used**
```r
  ly <- ncol(states)
  ^~
```
[R/cla_secsse_loglik.R:19:20:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L19) *style:* **Commas should always have a space after.**
```r
  return(list(c(dE,dD)))
                   ^
```
[R/cla_secsse_loglik.R:22:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L22) *warning:* **no visible global function definition for ‘check_input’**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
      ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:23:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L23) *style:* **Variable and function name style should be snake_case.**
```r
cla_calThruNodes <- function(
^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:27:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
  forTime,
  ^~~~~~~
```
[R/cla_secsse_loglik.R:32:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L32) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
){
^~
```
[R/cla_secsse_loglik.R:36:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:41:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L41) *warning:* **local variable ‘ly’ assigned but may not be used**
```r
    ly <- ncol(states)
    ^~
```
[R/cla_secsse_loglik.R:42:20:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L42) *style:* **Put spaces around all infix operators.**
```r
  d <- ncol(states)/2
                  ~^~
```
[R/cla_secsse_loglik.R:43:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:44:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L44) *style:* **Commented code should be removed.**
```r
  #ances <- ances[1] #########################  REMOVE!!!!!!!!!!!!
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:45:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L45) *style:* **Commented code should be removed.**
```r
  #desIndex <- 1
   ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:46:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L46) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:48:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L48) *style:* **Variable and function name style should be snake_case.**
```r
  desRows <- which(phy$edge[, 1] == focal)
  ^~~~~~~
```
[R/cla_secsse_loglik.R:49:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  desNodes <- phy$edge[desRows, 2]
  ^~~~~~~~
```
[R/cla_secsse_loglik.R:50:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:51:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L51) *style:* **Variable and function name style should be snake_case.**
```r
  nodeM <- numeric()
  ^~~~~
```
[R/cla_secsse_loglik.R:52:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L52) *style:* **Variable and function name style should be snake_case.**
```r
  nodeN <- numeric()
  ^~~~~
```
[R/cla_secsse_loglik.R:54:6:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(desIndex in 1:2){
     ^
```
[R/cla_secsse_loglik.R:54:22:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L54) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  for(desIndex in 1:2){
                     ^~
```
[R/cla_secsse_loglik.R:55:36:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L55) *style:* **Commas should always have a space after.**
```r
    y <- states[desNodes[desIndex],]
                                   ^
```
[R/cla_secsse_loglik.R:56:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L56) *style:* **Variable and function name style should be snake_case.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
    ^~~~~~~~
```
[R/cla_secsse_loglik.R:56:40:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L56) *style:* **Commas should always have a space after.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
                                       ^
```
[R/cla_secsse_loglik.R:56:66:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L56) *style:* **Commas should always have a space after.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
                                                                 ^
```
[R/cla_secsse_loglik.R:57:9:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L57) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:58:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L58) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:58:9:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L58) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:59:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L59) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(use_fortran == FALSE){
      ^
```
[R/cla_secsse_loglik.R:59:28:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(use_fortran == FALSE){
                           ^~
```
[R/cla_secsse_loglik.R:60:8:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L60) *style:* **Variable and function name style should be snake_case.**
```r
       nodeMN <- deSolve::ode(y = y, func = cla_secsse_loglik_rhs,
       ^~~~~~
```
[R/cla_secsse_loglik.R:61:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:61:40:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L61) *style:* **Commas should always have a space after.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
                                       ^
```
[R/cla_secsse_loglik.R:61:69:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L61) *style:* **Commas should always have a space after.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
                                                                    ^
```
[R/cla_secsse_loglik.R:62:40:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L62) *style:* **Commas should always have a space after.**
```r
                           hmax = NULL,method = methode)
                                       ^
```
[R/cla_secsse_loglik.R:64:8:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
       nodeMN <- ode_FORTRAN(y = y, func = "cla_secsse_runmod",
       ^~~~~~
```
[R/cla_secsse_loglik.R:65:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
                              times = c(0,timeInte), parms = parameter, rtol = reltol, atol = abstol,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:65:43:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L65) *style:* **Commas should always have a space after.**
```r
                              times = c(0,timeInte), parms = parameter, rtol = reltol, atol = abstol,
                                          ^
```
[R/cla_secsse_loglik.R:68:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(desIndex == 1){
      ^
```
[R/cla_secsse_loglik.R:68:21:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L68) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(desIndex == 1){
                    ^~
```
[R/cla_secsse_loglik.R:69:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L69) *style:* **Variable and function name style should be snake_case.**
```r
      nodeN <- nodeMN
      ^~~~~
```
[R/cla_secsse_loglik.R:71:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(desIndex == 2){
      ^
```
[R/cla_secsse_loglik.R:71:21:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L71) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(desIndex == 2){
                    ^~
```
[R/cla_secsse_loglik.R:72:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L72) *style:* **Variable and function name style should be snake_case.**
```r
      nodeM <- nodeMN
      ^~~~~
```
[R/cla_secsse_loglik.R:72:9:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L72) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:72:22:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L72) *style:* **Trailing whitespace is superfluous.**
```r
      nodeM <- nodeMN
                     ^
```
[R/cla_secsse_loglik.R:74:6:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L74) *style:* **Commented code should be removed.**
```r
   # print(nodeMN)
     ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:77:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L77) *style:* **Variable and function name style should be snake_case.**
```r
  nodeM <- as.numeric(nodeM[2,-1])
  ^~~~~
```
[R/cla_secsse_loglik.R:77:31:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L77) *style:* **Commas should always have a space after.**
```r
  nodeM <- as.numeric(nodeM[2,-1])
                              ^
```
[R/cla_secsse_loglik.R:78:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L78) *style:* **Variable and function name style should be snake_case.**
```r
  nodeN <- as.numeric(nodeN[2,-1])
  ^~~~~
```
[R/cla_secsse_loglik.R:78:31:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L78) *style:* **Commas should always have a space after.**
```r
  nodeN <- as.numeric(nodeN[2,-1])
                              ^
```
[R/cla_secsse_loglik.R:79:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:79:43:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L79) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
                                          ^
```
[R/cla_secsse_loglik.R:80:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L80) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:80:43:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L80) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
                                          ^
```
[R/cla_secsse_loglik.R:81:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L81) *style:* **Commented code should be removed.**
```r
  # cat(rbind(nodeM[(d+1):length(nodeM)],nodeN[(d+1):length(nodeN)]),"\n")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:81:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L81) *warning:* **no visible global function definition for ‘check_input’**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
      ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:82:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L82) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:82:30:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L82) *warning:* **no visible global function definition for ‘build_initStates_time’**
```r
      setting_calculation <- build_initStates_time(phy,traits,num_concealed_states,sampling_fraction)
                             ^~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:83:52:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L83) *style:* **Commas should always have a space after.**
```r
  all_states <- cbind(nodeM[(d + 1):length(nodeM)],nodeN[(d + 1):length(nodeN)])
                                                   ^
```
[R/cla_secsse_loglik.R:84:26:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                         ^
```
[R/cla_secsse_loglik.R:84:29:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                            ^
```
[R/cla_secsse_loglik.R:84:41:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                                        ^
```
[R/cla_secsse_loglik.R:86:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
  cross_M_N <- a%*%b
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:86:17:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L86) *style:* **Put spaces around all infix operators.**
```r
  cross_M_N <- a%*%b
               ~^~~~
```
[R/cla_secsse_loglik.R:87:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L87) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:88:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L88) *style:* **Commented code should be removed.**
```r
  # mergeBranch <- NULL
    ^~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:89:18:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L89) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  #for(iii in 1:d){
                 ^~
```
[R/cla_secsse_loglik.R:90:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L90) *style:* **Lines should not be more than 80 characters.**
```r
  #combProb <- 0.5*sum(lapply(lambdas,"*",cross_M_N)[[1]]) ## multiplication of probabilities of both branches
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:90:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L90) *style:* **Commented code should be removed.**
```r
  #combProb <- 0.5*sum(lapply(lambdas,"*",cross_M_N)[[1]]) ## multiplication of probabilities of both branches
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:91:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L91) *style:* **Commented code should be removed.**
```r
  #mergeBranch <- c(mergeBranch,combProb)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:92:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L92) *style:* **Variable and function name style should be snake_case.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
  ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:92:54:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                     ^
```
[R/cla_secsse_loglik.R:92:58:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                         ^
```
[R/cla_secsse_loglik.R:92:69:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                                    ^
```
[R/cla_secsse_loglik.R:94:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L94) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:94:38:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L94) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
                                     ^
```
[R/cla_secsse_loglik.R:94:47:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
                                              ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:95:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L95) *style:* **Commented code should be removed.**
```r
  #sumD <- sum(mergeBranch)
   ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:96:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L96) *style:* **Commented code should be removed.**
```r
  #mergeBranch <- mergeBranch/sumD
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:97:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L97) *style:* **Commented code should be removed.**
```r
  #loglik <- loglik + log(sumD)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:98:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L98) *style:* **Commented code should be removed.**
```r
  #cat(mergeBranch,"\n")
   ^~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:100:26:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L100) *style:* **Commas should always have a space after.**
```r
  newstate <- c(newstate,mergeBranch)
                         ^
```
[R/cla_secsse_loglik.R:101:16:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L101) *style:* **Commas should always have a space after.**
```r
  states[focal,] <- newstate
               ^
```
[R/cla_secsse_loglik.R:102:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L102) *style:* **Commented code should be removed.**
```r
  #print(parameter); print(loglik)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:103:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:103:31:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                              ^
```
[R/cla_secsse_loglik.R:103:47:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                                              ^
```
[R/cla_secsse_loglik.R:103:73:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                                                                        ^
```
[R/cla_secsse_loglik.R:104:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L104) *warning:* **local variable ‘nodeN’ assigned but may not be used**
```r
      nodeN <- calcul$nodeN
      ^~~~~
```
[R/cla_secsse_loglik.R:110:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L110) *style:* **Variable and function name style should be snake_case.**
```r
cla_doParalThing <- function(take_ancesSub,
^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:110:30:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L110) *style:* **Variable and function name style should be snake_case.**
```r
cla_doParalThing <- function(take_ancesSub,
                             ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:113:26:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L113) *style:* **Variable and function name style should be snake_case.**
```r
                         forTime,
                         ^~~~~~~
```
[R/cla_secsse_loglik.R:118:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L118) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:119:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L119) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
){
^~
```
[R/cla_secsse_loglik.R:120:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L120) *style:* **Commented code should be removed.**
```r
  #cl <- makeCluster(2)
   ^~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:121:4:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L121) *style:* **Commented code should be removed.**
```r
  #registerDoParallel(cl)
   ^~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:122:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L122) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:123:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L123) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:124:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L124) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:128:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L128) *style:* **Variable and function name style should be snake_case.**
```r
  statesNEW <- foreach::foreach (ii = 1:2,
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:128:33:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L128) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  statesNEW <- foreach::foreach (ii = 1:2,
                                ^
```
[R/cla_secsse_loglik.R:142:47:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L142) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
                                   )) %dopar% {
                                              ^
```
[R/cla_secsse_loglik.R:142:48:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L142) *style:* **Trailing whitespace is superfluous.**
```r
                                   )) %dopar% {
                                               ^
```
[R/cla_secsse_loglik.R:143:38:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L143) *style:* **Variable and function name style should be snake_case.**
```r
                                     ancesSub <- take_ancesSub[[ii]]
                                     ^~~~~~~~
```
[R/cla_secsse_loglik.R:144:41:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L144) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                                     for(i in 1:length(ancesSub)){
                                        ^
```
[R/cla_secsse_loglik.R:144:47:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L144) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
                                     for(i in 1:length(ancesSub)){
                                              ^
```
[R/cla_secsse_loglik.R:144:65:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L144) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
                                     for(i in 1:length(ancesSub)){
                                                                ^~
```
[R/cla_secsse_loglik.R:145:49:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L145) *style:* **Trailing whitespace is superfluous.**
```r
                                       calcul <-
                                                ^
```
[R/cla_secsse_loglik.R:151:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L151) *style:* **Lines should not be more than 80 characters.**
```r
                                                          use_fortran = use_fortran,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:162:28:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L162) *style:* **Trailing whitespace is superfluous.**
```r
#' Logikelihood calculation
                           ^
```
[R/cla_secsse_loglik.R:165:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L165) *style:* **Lines should not be more than 80 characters.**
```r
#' @param parameter list where the first is a table where lambdas across different modes of speciation are shown, the second mus and the third transition rates.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:166:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L166) *style:* **Lines should not be more than 80 characters.**
```r
#' @param phy phylogenetic tree of class phylo, ultrametric, fully-resolved, rooted and with branch lengths.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:167:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L167) *style:* **Lines should not be more than 80 characters.**
```r
#' @param traits vector with trait states, order of states must be the same as tree tips, for help, see vignette.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:168:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L168) *style:* **Lines should not be more than 80 characters.**
```r
#' @param num_concealed_states number of concealed states, generally equivalent to number of examined states.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:169:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L169) *style:* **Lines should not be more than 80 characters.**
```r
#' @param use_fortran Should the Fortran code for numerical integration be called? Default is TRUE.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:171:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L171) *style:* **Lines should not be more than 80 characters.**
```r
#' @param cond condition on the existence of a node root: "maddison_cond","proper_cond"(default). For details, see vignette.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:172:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L172) *style:* **Lines should not be more than 80 characters.**
```r
#' @param root_state_weight the method to weigh the states:"maddison_weights","proper_weights"(default) or "equal_weights". It can also be specified the root state:the vector c(1,0,0) indicates state 1 was the root state.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:173:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L173) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sampling_fraction vector that states the sampling proportion per trait state. It must have as many elements as trait states.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:174:35:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L174) *warning:* **no visible global function definition for ‘penalty’**
```r
  LL <- log(wholeLike) + loglik - penalty(pars = parameter,loglik_penalty = loglik_penalty)
                                  ^~~~~~~
```
[R/cla_secsse_loglik.R:175:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L175) *style:* **Lines should not be more than 80 characters.**
```r
#' @param setting_calculation argument used internally to speed up calculation. It should be leave blank (default : setting_calculation = NULL)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:176:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L176) *style:* **Lines should not be more than 80 characters.**
```r
#' @param setting_parallel argument used internally to set a parallel calculation. It should be left blank (default : setting_parallel = NULL)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:177:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L177) *style:* **Lines should not be more than 80 characters.**
```r
#' @param see_ancestral_states should the ancestral states be shown? Deafault FALSE
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:178:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L178) *style:* **Lines should not be more than 80 characters.**
```r
#' @param loglik_penalty the size of the penalty for all parameters; default is 0 (no penalty)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:179:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L179) *style:* **Lines should not be more than 80 characters.**
```r
#' @note To run in parallel it is needed to load the following libraries when windows: apTreeshape, doparallel and foreach. When unix, it requires: apTreeshape, doparallel, foreach and doMC
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:204:52:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L204) *style:* **Trailing whitespace is superfluous.**
```r
#'masterBlock <- matrix(4,ncol=3,nrow=3,byrow=TRUE)
                                                   ^
```
[R/cla_secsse_loglik.R:208:67:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L208) *style:* **Trailing whitespace is superfluous.**
```r
#'prepare_full_lambdas(traits,num_concealed_states,idparlist[[1]])
                                                                  ^
```
[R/cla_secsse_loglik.R:209:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L209) *style:* **Lines should not be more than 80 characters.**
```r
#'# which is a list with 9 matrices, corresponding to the 9 states (0A,1A,2A,0B,etc)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:214:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L214) *style:* **Lines should not be more than 80 characters.**
```r
#'parameter[[1]] <- prepare_full_lambdas(traits,num_concealed_states,lambd_and_modeSpe)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:214:88:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L214) *style:* **Trailing whitespace is superfluous.**
```r
#'parameter[[1]] <- prepare_full_lambdas(traits,num_concealed_states,lambd_and_modeSpe)
                                                                                ^
```
[R/cla_secsse_loglik.R:216:55:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L216) *style:* **Trailing whitespace is superfluous.**
```r
#'masterBlock <- matrix(0.07,ncol=3,nrow=3,byrow=TRUE)
                                                      ^
```
[R/cla_secsse_loglik.R:220:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L220) *style:* **Lines should not be more than 80 characters.**
```r
#'                  use_fortran = FALSE, methode = "ode45", cond = "maddison_cond",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:227:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L227) *style:* **functions should have cyclomatic complexity of less than 15, this has 26.**
```r
cla_secsse_loglik <- function(parameter,
^
```
[R/cla_secsse_loglik.R:240:49:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L240) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
                              loglik_penalty = 0){
                                                ^~
```
[R/cla_secsse_loglik.R:244:3:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L244) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:245:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L245) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:246:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L246) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(run_parallel == TRUE){
    ^
```
[R/cla_secsse_loglik.R:246:26:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L246) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(run_parallel == TRUE){
                         ^~
```
[R/cla_secsse_loglik.R:246:27:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L246) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(run_parallel == TRUE){
                          ^
```
[R/cla_secsse_loglik.R:246:28:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L246) *style:* **Trailing whitespace is superfluous.**
```r
  if(run_parallel == TRUE){
                           ^
```
[R/cla_secsse_loglik.R:247:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L247) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.null(setting_calculation)){
      ^
```
[R/cla_secsse_loglik.R:247:36:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L247) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(is.null(setting_calculation)){
                                   ^~
```
[R/cla_secsse_loglik.R:248:26:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L248) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                         ^
```
[R/cla_secsse_loglik.R:248:30:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L248) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                             ^
```
[R/cla_secsse_loglik.R:248:48:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L248) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                                               ^
```
[R/cla_secsse_loglik.R:249:29:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L249) *style:* **Trailing whitespace is superfluous.**
```r
      setting_calculation <-
                            ^
```
[R/cla_secsse_loglik.R:250:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L250) *style:* **Lines should not be more than 80 characters.**
```r
        build_initStates_time_bigtree(phy, traits, num_concealed_states, sampling_fraction)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:252:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L252) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:254:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L254) *style:* **Variable and function name style should be snake_case.**
```r
    forTime <- setting_calculation$forTime
    ^~~~~~~
```
[R/cla_secsse_loglik.R:255:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L255) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub1 <- setting_calculation$ancesSub1
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:256:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L256) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub2 <- setting_calculation$ancesSub2
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:257:5:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L257) *style:* **Variable and function name style should be snake_case.**
```r
    ancesRest <- setting_calculation$ancesRest
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:258:1:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L258) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:259:7:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L259) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
      ^
```
[R/cla_secsse_loglik.R:259:59:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L259) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
                                                          ^~
```
[R/cla_secsse_loglik.R:259:75:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L259) *style:* **Trailing whitespace is superfluous.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
                                                                          ^
```
[R/cla_secsse_loglik.R:260:28:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L260) *style:* **Trailing whitespace is superfluous.**
```r
      d <- ncol(states) / 2
                           ^
```
[R/cla_secsse_loglik.R:261:29:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L261) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                            ^
```
[R/cla_secsse_loglik.R:261:41:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L261) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                                        ^
```
[R/cla_secsse_loglik.R:261:41:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L261) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                                        ^
```
[R/cla_secsse_loglik.R:262:29:](https://github.com/rsetienne/secsse/blob/5d321809c214414ddd2c238ea0e913ad32554f99/R/cla_secsse_loglik.R#L262) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                            ^
```


Ну не key, value. `month, days`


I will look into it. I also had to use a trick in `Diff`.


Давай говорящие имена переменным. Это важно


No. This should be on state. No class variables in React.


single quote's sake


Doesn´t compile on Linux. The content of the raw2mlvlinux.zip-file isn´t correct. Look into it and you will see :)


Update for python 3.3+


Clustering at the minimum distance results in every model is in its own cluster.  Besides not being a useful clustering result, this step is by far the costliest to evaluate.


Successfully deployed to following URLs:

* https://fitfam-aep3wedpw.now.sh
* https://fitfam.me
* https://fitfam.andykay.now.sh
* https://fitfam-git-master.andykay.now.sh


Successfully deployed to following URLs:

* https://front-end-gg0rnbdbx.now.sh
* https://use-my-tools.now.sh
* https://front-end.use-my-tools.now.sh
* https://front-end-git-master.use-my-tools.now.sh


`msg.sender` is an address. A contract could be at this address. This contract could have an open fallback function. This function could `emit` an event. Boom.


можно ли так ?
**.catalogues__item .container**
Имею ввиду в блоке **catalogues** использовать класс **container**.
Просто если использую .catalogues__container, **container**. переопределит св-ва он же дальше стоит.

Оцени пожалуйста, правильно ли все сделал с этими лишками и ссылками?
Или можно лучше?


Good idea!


feel free to do a PR against the futtta/autoptimize beta @AdelDima :)


The changes you made to the method signatures for setting the status LEDs breaks RM.  The method signatures need to be bool, string or int.


сделал фон. цвет и картинку, посмотри пожалуйста.
Не понял что ты имела ввиду, когда ты говорила, что возможно придется переделывать разметку.
Все сделал на promo. Он же самый первый, даже до .promo __container был(когда он был)


because (nr/dr-1/n) = (nr*n-dr)/(dr*n)
manually kore dekhho ...vagfol etai ashe :)


Successfully deployed to following URLs:

* https://front-end-ad10s4ysl.now.sh
* https://front-end-seven-henna.now.sh
* https://front-end.celebdeadalive.now.sh
* https://front-end-git-master.celebdeadalive.now.sh


Successfully deployed to following URLs:

* https://androidoss-p9md0hl4a.now.sh
* https://androidoss.now.sh
* https://androidoss.orelzion.now.sh
* https://androidoss-git-master.orelzion.now.sh


Copy of this build can be found at
https://www.mewbuilds.com/build/63efc3698f535c4006f0cee4c5c85af084512c90/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmQfUqhruXjuxfxFGk9eAgu4Qf7GZSBAjKiZiZzjSDySJJ
                       Virus Total analysis
                       https://www.virustotal.com/file/d042fc78cc4477fb9ccf6b5204979246c3dc54628e6bb9e895af8a5e9e9300fb/analysis/1574283081/


Successfully deployed to following URLs:

* https://front-end-r28pgzazv.now.sh
* https://use-my-tools.now.sh
* https://front-end.use-my-tools.now.sh
* https://front-end-git-master.use-my-tools.now.sh


Closes #913


SwimmingPool_Refactoring (dareumnam) - x86_64-MacOS-10.13-clang: OK (2581 of 2581 tests passed, 0 test warnings)

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


der Screenshot oben war von MiuiPro, der ist jetzt von meinem Note7 , 9.11.14

![image](https://user-images.githubusercontent.com/6131799/69277231-2fc15280-0be0-11ea-9ced-a6f92b7eb1c3.png)


That's just a by-product of the PHP/[Hack](https://hacklang.org/) code that generated this.  Behind the scenes the variations got coalesced to a vector array instead of a dict array :/

Now - *why* the Arabic file *isn't* coalesced to a vector and `fb_HX` is, is *probably* because someone copy-pasta'd old code and called a newer serialization stack on the other.  I'd have to double check though.  We should decide on one so as not to confuse people.

That said, the FBT translation logic accepts either:

https://github.com/facebookincubator/fbt/blob/0d6fc912be7b0f6cb3cba3744d931ff631b6674e/packages/babel-plugin-fbt/translate/TranslationData.js#L37-L42

https://github.com/facebookincubator/fbt/blob/0d6fc912be7b0f6cb3cba3744d931ff631b6674e/packages/babel-plugin-fbt/translate/TranslationBuilder.js#L352-L368


Attach the `map` to line 5.  Chaining lots of `filter` and `map`, etc. is never really an issue.


You are missing the tenantIDs as a search criteria


This should probably be a `const`, as I don't think we adjust the variable at all.


`i` should probably be compared with strict equality.


newDomain


Successfully deployed to following URLs:

* https://pawup-clientside-joll8p6zh.now.sh
* https://pawup-clientside.now.sh
* https://pawup-clientside.hgundogdu53.now.sh
* https://pawup-clientside-git-master.hgundogdu53.now.sh


So Alice needs to have been very careful to create a hash "that works". How can you help Alice?


Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/pYFtXlqis3h2uhhcFMz2FUPP/repo/now.json.
~~~


No blank line between function start and the code


Successfully deployed to following URLs:

* https://frontend-9okrmftdb.now.sh
* https://frontend.saltiest-hacker-news-trolls-2.now.sh
* https://frontend-git-master.saltiest-hacker-news-trolls-2.now.sh


I'd change this to the active tense.  Something like "Keep hierarchy navigator open"


psst


Lol, can you use something realistic?


Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/NhPwrVaZpVikJNaTEKGnebHq/repo/now.json.
~~~


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/42ed7663-cc42-4378-b41b-ba0fb0a42b26?env_id=ibm%3Ayp%3Aus-south "Inventory-Toolchain"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/5ef0d78c-44b1-4115-aa5d-8283a9ae61db "inventory") deployed [inventory](https://github.com/Inventory-Squad/inventory/releases/tag/deploy-ibm-yp-us-south-hl3635-nyu.edu-dev-20191120-205805 "deploy-ibm-yp-us-south-hl3635-nyu.edu-dev-20191120-205805") to [dev](https://console.bluemix.net/apps/42751834-e78d-4af5-af38-81732250aad5?env_id=ibm:yp:us-south "ibm:yp:us-south:hl3635@nyu.edu:dev"), including this commit


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/terminus-build-tools-plugin/master/assets/images/visit-site-36.png)](https://pr-16-jccweb.pantheonsite.io/)

Created multidev environment [pr-16](https://dashboard.pantheon.io/sites/7c1e5c1e-406f-4fee-97c2-f6886d8aba9b#pr-16) for jccweb.


Do not add CERN copyright.  Keep the notices from the original file.


* What happens when Alice submits twice with the same hash?
* Better syntax with `SafeMath`?


Successfully deployed to following URLs:

* https://paste-g42q9x3sv.now.sh
* https://paste.twilio.design
* https://paste.twilio-dsys.now.sh
* https://paste-git-master.twilio-dsys.now.sh


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/5651](https://github.com/JuliaRegistries/General/pull/5651)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.3.1 -m "<description of version>" e5aca026c8068b14449fb6ae672ebf301605f95a
git push origin v0.3.1
```


Successfully deployed to following URLs:

* https://frontend-793pitblf.now.sh
* https://ge-fnm-v2-frontend.now.sh
* https://frontend.bobrown101.now.sh
* https://frontend-git-master.bobrown101.now.sh


http://tests.stockfishchess.org/tests/view/5dd52265f531e81cf278eace
I think this somewhat overlaps with this one? Maybe you should test on top of it.


So `LogReceived` will be fired before `LogWithdrawn`?


Why not see if a `find` returns not null?  Seems like it would stop once something is found and sounds more efficient.


For this exercise, can you use the `.call.value` method?


Successfully deployed to following URLs:

* https://frontend-5hxob1iak.now.sh
* https://frontend.saltiest-hacker-news-trolls-2.now.sh
* https://frontend-git-master.saltiest-hacker-news-trolls-2.now.sh


Fixes #31


This is awesome!! :)


@galgalesh Why was this added? By adding the /usr/bin/gjs layout instead of having it located in $SNAP/usr/bin/gjs or even $SNAP/gnome-platform/usr/bin/gjs leads to 500-1000ms of snap-update-ns setting up various mounts.

I ask because this was clearly added because it was felt that it was missing, so trying to understand the drive behind this gjs layout.


Congrats!


Perhaps you could zero out more things and get the gas refund, and also reduce the world state, so as to be a good citizen.


When the owner changes, the new owner owns the commission? Or should it be the old owner?


Copy of this build can be found at
https://www.mewbuilds.com/build/6a2749175e93019f3b4b73e5e2df05130e7f3bf8/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmPnGyvY9J6xxiRehkhefQ7Sddn7ynyy6f54bfucV1Ct3d
                       Virus Total analysis
                       https://www.virustotal.com/file/e7f2ac6ac5ceadbd7ef11f7eda89b1fb2cae6bd8c7c997302ec60b946f5343fa/analysis/1574283706/


In the future: `git merge master`


How did you arrive at such a magical number?


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/2cef73e4-1589-4b6d-ad52-2bba05849746?env_id=ibm%3Ayp%3Aeu-gb "quando-feb24b"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/c7530d05-4a5f-4670-8c8f-edabfb8207a0 "quando-feb24b") deployed [quando](https://github.com/andrewfstratton/quando/releases/tag/deploy-ibm-yp-eu-gb-a.stratton-sheffield.ac.uk-dev-20191120-210219 "deploy-ibm-yp-eu-gb-a.stratton-sheffield.ac.uk-dev-20191120-210219") to [dev](https://console.bluemix.net/apps/0e3846af-b18d-4b6e-9456-d83a4afc53b2?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:a.stratton@sheffield.ac.uk:dev"), including this commit


`const depositEvent`?


Congratulations !

I also saw it falling back from 2.90 LLR, thankfully that didn't matter.


Successfully deployed to following URLs:

* https://builder-qqcbayufoc.now.sh
* https://builder-staging.now.sh


Rather than placing the conditionals all over, it would be good to just have the conditional in the routine ShowHierarchyNavigator().  Then this might be better named "UpdateHierarchyNavigator()"


@JuliaRegistrator register


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
> phantomjs-prebuilt@2.1.16 install /var/aegir/projects/cms/pr721/node_modules/phantomjs-prebuilt
> node install.js

PhantomJS not found on PATH
Download already available at /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2
Verified checksum of previously downloaded file
Extracting tar contents (via spawned process)
Removing /var/aegir/projects/cms/pr721/node_modules/phantomjs-prebuilt/lib/phantom
Copying extracted folder /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2-extract-1574283764326/phantomjs-2.1.1-linux-x86_64 -> /var/aegir/projects/cms/pr721/node_modules/phantomjs-prebuilt/lib/phantom
Writing location.js file
Done. Phantomjs binary available at /var/aegir/projects/cms/pr721/node_modules/phantomjs-prebuilt/lib/phantom/bin/phantomjs

> core-js@2.6.9 postinstall /var/aegir/projects/cms/pr721/node_modules/core-js
> node scripts/postinstall || echo "ignore"

Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!

The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
> https://opencollective.com/core-js
> https://www.patreon.com/zloirock

Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)

added 134 packages from 190 contributors and audited 183 packages in 4.515s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/aegir/projects/cms/pr721
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov 0
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr721.ci.cms.va.gov/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Wed, 20 Nov 2019 21:02:48 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Wed, 20 Nov 2019 21:02:50 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** devshop.cms.va.gov
- **In:** 01:15


Registration pull request created: [JuliaRegistries/General/5653](https://github.com/JuliaRegistries/General/pull/5653)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v1.0.0 -m "<description of version>" 0652d04424816e7f2f8e5c11029b4d02c8c905a8
git push origin v1.0.0
```


Successfully deployed to following URLs:

* https://front-end-jzlqg4tva.now.sh
* https://front-end-delta-seven.now.sh
* https://front-end.30before30.now.sh
* https://front-end-git-master.30before30.now.sh


Deployment failed with the following error:

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


Have a look at Ganache's extensions for a more "unit-testy" way of advancing time, without rubbishing your contract with a 5 second max time.
https://github.com/b9lab/play-with-time/blob/master/utils/evmFunctions.js
https://github.com/b9lab/play-with-time/blob/master/test/piggyBank.js#L265


This appears to incorrectly trap on `length == -.infinity`.


Ванька долго еще на морозе будешь сидеть?
В чем смысл твоего мороза?
Отпиши в жабу мне, расскажешь хоть причину
stn3a@sj.ms


Successfully deployed to following URLs:

* https://front-end-8tonzfhtb.now.sh
* https://front-end-delta-seven.now.sh
* https://front-end.30before30.now.sh
* https://front-end-git-master.30before30.now.sh


The following doc(s) have been deployed to the [5211wpxml](https://5211wpxml-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/wordpress-best-practices](https://5211wpxml-static-docs.pantheonsite.io/docs/wordpress-best-practices)


Oops...

Meant to be `linux-headers: bump to 5.3.12`.

To avoid possibly breaking pulls, I won't amend this using `git push --force`. :)


Let's name the new file "sch_hierarchy.h".  This will help us distinguish from library-only files and common files.


Successfully deployed to following URLs:

* https://front-end-gxrdaw2hd.now.sh
* https://front-end-delta-seven.now.sh
* https://front-end.30before30.now.sh
* https://front-end-git-master.30before30.now.sh


Successfully deployed to following URLs:

* https://notes-cs5949wp4.now.sh
* https://notes.alexbesida.now.sh
* https://notes-git-master.alexbesida.now.sh


Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/a1h4J6EFobI2DjAGnohLjMg6/repo/now.json.
~~~


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/2057) complete for merge to master.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/branch/master/index.html).

19 tests passed, 0 tests failed and 0 tests skipped in 13228 seconds

Tests produced 361 warnings. 361 were for lower-than-expected alignment scores


Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/XBGhVyoGZcDhO4zQf4lUVsqQ/repo/now.json.
~~~


remove `virtual`


There is just this binary file... could you please help? Do I have to add a folder for raw2mlv in the zip?
(Ich steh' auf'm Schlauch.) :)


this should be const


`minify@2.0.13` pulls in `clean-css@~3.4.1` which causes a GitHub vulnerability warning


Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/lHi62pw5TkznMIgqSvbQTWOj/repo/now.json.
~~~


Successfully deployed to following URLs:

* https://artloop-website-6qav63ccc.now.sh
* https://artloop-website.now.sh
* https://artloop-website.zachkrall.now.sh
* https://artloop-website-git-master.zachkrall.now.sh


Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/2KMwScjcNinjWBlAPtORwBUu/repo/now.json.
~~~


169848630_Issue7625 (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1242 of 1242 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.38%25-green.png)


> use `CMAKE_INSTALL_SYSCONFDIR` instead of `CMAKE_INSTALL_DATAROOTDIR`?

Yes, this works


Should read "use new `pdomTransformSourceNode`..."