[R/cla_secsse_loglik.R:1:37:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L48) *style:* **Variable and function name style should be snake_case.**
```r
  desRows <- which(phy$edge[, 1] == focal)
  ^~~~~~~
```
[R/cla_secsse_loglik.R:49:3:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  desNodes <- phy$edge[desRows, 2]
  ^~~~~~~~
```
[R/cla_secsse_loglik.R:50:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/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:145:47:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L145) *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:145:48:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L145) *style:* **Trailing whitespace is superfluous.**
```r
                                   )) %dopar% {
                                               ^
```
[R/cla_secsse_loglik.R:146:38:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
                                     ancesSub <- take_ancesSub[[ii]]
                                     ^~~~~~~~
```
[R/cla_secsse_loglik.R:147:41:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L147) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                                     for(i in 1:length(ancesSub)){
                                        ^
```
[R/cla_secsse_loglik.R:147:47:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L147) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
                                     for(i in 1:length(ancesSub)){
                                              ^
```
[R/cla_secsse_loglik.R:147:65:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L147) *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:148:49:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L148) *style:* **Trailing whitespace is superfluous.**
```r
                                       calcul <-
                                                ^
```
[R/cla_secsse_loglik.R:154:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
                                                          use_fortran = use_fortran,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:165:28:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L165) *style:* **Trailing whitespace is superfluous.**
```r
#' Logikelihood calculation
                           ^
```
[R/cla_secsse_loglik.R:168:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L168) *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:169:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L169) *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:170:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L170) *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:171:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L171) *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:172:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L172) *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:174:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L174) *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:174:35:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/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/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L175) *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:176:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L176) *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:178:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L178) *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:179:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L179) *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:180:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L180) *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:181:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L181) *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:182:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L182) *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:207:52:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L207) *style:* **Trailing whitespace is superfluous.**
```r
#'masterBlock <- matrix(4,ncol=3,nrow=3,byrow=TRUE)
                                                   ^
```
[R/cla_secsse_loglik.R:211:67:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L211) *style:* **Trailing whitespace is superfluous.**
```r
#'prepare_full_lambdas(traits,num_concealed_states,idparlist[[1]])
                                                                  ^
```
[R/cla_secsse_loglik.R:212:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L212) *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:217:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L217) *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:217:88:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L217) *style:* **Trailing whitespace is superfluous.**
```r
#'parameter[[1]] <- prepare_full_lambdas(traits,num_concealed_states,lambd_and_modeSpe)
                                                                                ^
```
[R/cla_secsse_loglik.R:219:55:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L219) *style:* **Trailing whitespace is superfluous.**
```r
#'masterBlock <- matrix(0.07,ncol=3,nrow=3,byrow=TRUE)
                                                      ^
```
[R/cla_secsse_loglik.R:223:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L223) *style:* **Lines should not be more than 80 characters.**
```r
#'                  use_fortran = FALSE, methode = "ode45", cond = "maddison_cond",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:230:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L230) *style:* **functions should have cyclomatic complexity of less than 15, this has 26.**
```r
cla_secsse_loglik <- function(parameter,
^
```
[R/cla_secsse_loglik.R:243:49:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L243) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
                              loglik_penalty = 0){
                                                ^~
```
[R/cla_secsse_loglik.R:247:3:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L247) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:248:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L248) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:249:5:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L249) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(run_parallel == TRUE){
    ^
```
[R/cla_secsse_loglik.R:249:26:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L249) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(run_parallel == TRUE){
                         ^~
```
[R/cla_secsse_loglik.R:249:27:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L249) *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:249:28:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L249) *style:* **Trailing whitespace is superfluous.**
```r
  if(run_parallel == TRUE){
                           ^
```
[R/cla_secsse_loglik.R:250:7:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L250) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.null(setting_calculation)){
      ^
```
[R/cla_secsse_loglik.R:250:36:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L250) *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:251:26:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                         ^
```
[R/cla_secsse_loglik.R:251:30:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                             ^
```
[R/cla_secsse_loglik.R:251:48:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                                               ^
```
[R/cla_secsse_loglik.R:252:29:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L252) *style:* **Trailing whitespace is superfluous.**
```r
      setting_calculation <-
                            ^
```
[R/cla_secsse_loglik.R:253:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L253) *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:255:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L255) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:257:5:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L257) *style:* **Variable and function name style should be snake_case.**
```r
    forTime <- setting_calculation$forTime
    ^~~~~~~
```
[R/cla_secsse_loglik.R:258:5:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L258) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub1 <- setting_calculation$ancesSub1
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:259:5:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L259) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub2 <- setting_calculation$ancesSub2
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:260:5:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L260) *style:* **Variable and function name style should be snake_case.**
```r
    ancesRest <- setting_calculation$ancesRest
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:261:1:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L261) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:262:7:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L262) *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:262:59:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L262) *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:262:75:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L262) *style:* **Trailing whitespace is superfluous.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
                                                                          ^
```
[R/cla_secsse_loglik.R:263:28:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L263) *style:* **Trailing whitespace is superfluous.**
```r
      d <- ncol(states) / 2
                           ^
```
[R/cla_secsse_loglik.R:264:29:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L264) *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:264:41:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L264) *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:264:41:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L264) *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:265:29:](https://github.com/rsetienne/secsse/blob/870750c8f40d926e048fd976e7141be6ede3f2b7/R/cla_secsse_loglik.R#L265) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                            ^
```


Successfully deployed to following URLs:

* https://synthetix-community-ouv9jxs4l.now.sh
* https://synthetix-community.now.sh
* https://synthetix.community
* https://synthetix-community.michaelcohen716.now.sh
* https://synthetix-community-git-master.michaelcohen716.now.sh


SpriteBatch uses ``DXGI_ROTATION_MODE`` which is not defined unless you include dxgi.h

Model uses ``DXGI_FORMAT`` which is implicitly included, but added it for clarity.


New update 11/20 includes reactive table


Следует добавить private final


Successfully deployed to following URLs:

* https://website-k2edt7yom.now.sh
* https://keplersj.com
* https://website.keplersj.now.sh
* https://website-git-master.keplersj.now.sh


and we should migrate to JHipster organization too !


ambassador picture


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
> phantomjs-prebuilt@2.1.16 install /var/www/cms/node_modules/phantomjs-prebuilt
> node install.js

PhantomJS not found on PATH
Downloading https://github.com/Medium/phantomjs/releases/download/v2.1.1/phantomjs-2.1.1-linux-x86_64.tar.bz2
Saving to /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2
Receiving...

Received 22866K total.
Extracting tar contents (via spawned process)
Removing /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Copying extracted folder /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2-extract-1574279485378/phantomjs-2.1.1-linux-x86_64 -> /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Writing location.js file
Done. Phantomjs binary available at /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom/bin/phantomjs

> core-js@2.6.9 postinstall /var/www/cms/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 7.256s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/www/cms
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com 0
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Wed, 20 Nov 2019 19:51:29 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 19:51:34 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:** ip-10-247-97-26
- **In:** 01:55


Successfully deployed to following URLs:

* https://kinessapi-zv9thitp1.now.sh
* https://kinessapi-neon-beta.now.sh
* https://kinessapi.antelab.now.sh
* https://kinessapi-git-master.antelab.now.sh


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
> phantomjs-prebuilt@2.1.16 install /var/www/cms/node_modules/phantomjs-prebuilt
> node install.js

PhantomJS not found on PATH
Downloading https://github.com/Medium/phantomjs/releases/download/v2.1.1/phantomjs-2.1.1-linux-x86_64.tar.bz2
Saving to /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2
Receiving...

Received 22866K total.
Extracting tar contents (via spawned process)
Removing /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Copying extracted folder /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2-extract-1574279508428/phantomjs-2.1.1-linux-x86_64 -> /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Writing location.js file
Done. Phantomjs binary available at /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom/bin/phantomjs

> core-js@2.6.9 postinstall /var/www/cms/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 7.442s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/www/cms
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com 0
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/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://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Wed, 20 Nov 2019 19:51:52 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 19:51:58 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:** ip-10-247-35-104
- **In:** 02:03


А зачем здесь параметр **user** ?


That requires modification of `define runner_test_gen` which ended up with a lot more duplicate.


169840232_Issue7547 (Unknown) - x86_64-MacOS-10.13-clang: OK (2583 of 2583 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)


Revisar indentación del hash.


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* https://assignment-blue-beta.now.sh
* https://assignment.mledot.now.sh
* https://assignment-git-master.mledot.now.sh


I get the following error:

#######
 Error in names(x) <- value :
  'names' attribute [100] must be the same length as the vector [50]

3. `colnames<-`(`*tmp*`, value = lefse_tax)
2. `colnames<-`(`*tmp*`, value = lefse_tax)
1. phyloseq_to_lefs(ps1)

#####


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Each "leaf" is actually a collection of cells, so for each batch I'm selecting a random cell from this set resulting a set of indices of length len(self.leaves). I.e. we're training on one cell per 'leaf' each iteration


Looks good.


What about to add this step (@yuya-oc should have push permissions to [the repo](https://github.com/flathub/com.mattermost.Desktop)):
- Build flatpak version and release it into Flathub


@purbon @rhauch ^ typo.


IntelliJ files should be added to .gitignore


I have a feeling, you have this itch to fix this thoroughly throughout the codebase ;-) Go for it, I won't keep you from doing it...


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Use Singular for class names


@eddelbuettel `paste0()` is already used in a few places within Rcpp.

https://github.com/RcppCore/Rcpp/search?q=paste0&unscoped_q=paste0


@rouault - I've been running git bisect (thanks for the suggestion!), building and testing. It looks like this is the commit where FastCGI stops working. I'll try reverting some of the changes to see which causes the issue.


SpriteBatch uses ``DXGI_MODE_ROTATION`` which is only defined by DXGI headers.

RenderTargetState uses ``DXGI_SWAP_CHAIN_DESC`` which requires the DXGI header.

EffectPipelineStateDescription, Model, and ResourceUploadBatch use ``DXGI_FORMAT`` which is implicitly included, but added it for clarity.


Ah well.  You needed to tell me that three hours ago :)   Anyway, this issue is good now.  No point chasing windmills.  Or `paste(..., sep="")`.


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* https://demo-sync-moltin-to-shipengine-git-master.particular.now.sh


cc @amyblais @deanwhillier


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Who ever originally changed this made a breaking change as the code would not retry correctly on a 401.  I was not aware of this previous change but it has been impacting us for months.


Quên xóa thư mục node_modules


Deployment failed with the following error:

~~~
Unexpected error. Please try again later. ()
~~~


//  logcat 창에서 Main 태크로 검색
    public void println(String data) {
        Log.d("Main", data);
    }


Menghapus barang dari keranjang


The following doc(s) have been deployed to the [5255lighth](https://5255lighth-static-docs.pantheonsite.io/docs) Multidev environment:
- [gatsby/tests/lighthouse/lighthouse-constants.js](https://github.com/pantheon-systems/documentation/commit/b49bb00feef3d236c7fd2bcb209b88003b00ac17/gatsby/tests/lighthouse/lighthouse-constants.js)
- [.circleci/config.yml](https://github.com/pantheon-systems/documentation/commit/a56da9fa8a577a92a19c818e2fb767fc45a2e46c/.circleci/config.yml)
- [.circleci/scripts/set-env.sh](https://github.com/pantheon-systems/documentation/commit/3f298f60be676ff0f828f26fa88c90861e0afc7f/.circleci/scripts/set-env.sh)
- [gatsby/package-lock.json](https://github.com/pantheon-systems/documentation/commit/069e8b89cb92a52f58260de8c20dcd976041366f/gatsby/package-lock.json)
- [gatsby/package.json](https://github.com/pantheon-systems/documentation/commit/069e8b89cb92a52f58260de8c20dcd976041366f/gatsby/package.json)
- [gatsby/tests/lighthouse/createPullRequestComment.js](https://github.com/pantheon-systems/documentation/commit/99e15898ff99e21b283a8b66068e1f5181bbaeda/gatsby/tests/lighthouse/createPullRequestComment.js)


//  현재 입력상자에 입력된 데이터를 저장
//  데이터를 저장할 때는 SharedPreferences 사용 - 데이터를 저장할 수 있도록 edit() 메서드 제공
//  SharedPreferences 객체를 사용하려면 getSharedPreferences() 메서드 참조
//  edit() 메서드를 호출한후 putString()메서드로 저장하려는 데이터를 설정
//  데이터를 저장한 후에는 commit()를 호출해야 실제로 저장
    protected void saveState() {
        SharedPreferences pref = getSharedPreferences("pref", Activity.MODE_PRIVATE);
        SharedPreferences.Editor editor = pref.edit();
        editor.putString("name", nameInput.getText().toString());
        editor.commit();
    }


default path `/tmp/nebula-importer.log`


@Mark-H released new update on modx.com for this.


desuperheater_remain_issues (yzhou601) - x86_64-MacOS-10.13-clang: OK (2567 of 2581 tests passed, 0 test warnings)

Messages:\n
 * 14 tests had: EIO diffs.
 * 4 tests had: ERR diffs.
 * 12 tests had: ESO big diffs.
 * 4 tests had: MTR small diffs.
 * 14 tests had: Table big diffs.
 * 5 tests had: MTR big diffs.

Failures:\n

regression Test Summary
 * Passed: 655
 * Failed: 14

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.46%25-yellow.png)


an array ?


This is just temporary and will be changed later on


TeamCity Bvcms / Build [Build 2825](https://builds.tpsdb.com/viewLog.html?buildId=9944&buildTypeId=Bvcms_Build) is now running


TeamCity Bvcms / Build [Build 2824](https://builds.tpsdb.com/viewLog.html?buildId=9946&buildTypeId=Bvcms_Build) outcome was **FAILURE**
Summary: Tests failed: 2 (2 new), passed: 161 Build time: 00:24:30
### Failed tests
```
Webapp collection (1): IntegrationTests.Areas.OnlineReg.Models.OnlineRegPerson.EnrollTests.Should_Store_and_Populate_RegEmail: OpenQA.Selenium.WebDriverTimeoutException : Timed out after 5 seconds
   at OpenQA.Selenium.Support.UI.DefaultWait`1.ThrowTimeoutException(String exceptionMessage, Exception lastException)
   at OpenQA.Selenium.Support.UI.DefaultWait`1.Until[TResult](Func`2 condition)
   at IntegrationTests.Support.FeatureTestBase.WaitForElement(String css, Int32 maxWaitTimeInSeconds, Boolean visible) in C:\TeamCity\buildAgent\work\de2c4e6ef697cb99\IntegrationTests\Support\FeatureTestBase.cs:line 553
   at IntegrationTests.Areas.OnlineReg.Models.OnlineRegPerson.EnrollTests.Should_Store_and_Populate_RegEmail() in C:\TeamCity\buildAgent\work\de2c4e6ef697cb99\IntegrationTests\Areas\OnlineReg\Models\OnlineRegPerson\EnrollTests.cs:line 56

Webapp collection (1): IntegrationTests.Areas.Reports.Views.Reports.ApplicationTests.Application_Report_Should_Have_Answers: Shouldly.ShouldAssertException : PageSource
    should contain (case insensitive comparison)
"ThisTextMustAppearInTests"
    but was actually
"<html lang="en-US"><head>
    <link rel="shortcut icon" href="/favicon.ico?v=3">
    <meta charset..."
   at IntegrationTests.Areas.Reports.Views.Reports.ApplicationTests.Application_Report_Should_Have_Answers() in C:\TeamCity\buildAgent\work\de2c4e6ef697cb99\IntegrationTests\Areas\Reports\Views\Reports\ApplicationTests.cs:line 103

```


@pierre Check out the `https://docs.killbill.io/latest/getting_started.html` for instance, i think this is way better, although there are a few things we could think of tweaking


Hi David, I followed the all steps.. however after copying all the scripts in at target host it is unable to run the script saying oracle not available... can you pls suggest . Appreciate your help.

  "preupgrd": {
        "changed": true,
        "cmd": "echo exit | sqlplus / as sysdba @preupgrd.sql",
        "delta": "0:00:01.533505",
        "end": "2019-11-19 20:04:04.182302",
        "failed": false,
        "rc": 0,
        "start": "2019-11-19 20:04:02.648797",
        "stderr": "",
        "stderr_lines": [],
        "stdout": "\nSQL*Plus: Release 12.1.0.2.0 Production on Tue Nov 19 20:04:03 2019\n\nCopyright (c) 1982, 2014, Oracle.  All rights reserved.\n\nConnected to an idle instance.\n\nSP2-0310: unable to open file \"preupgrd.sql\"\nSQL> Disconnected",
        "stdout_lines": [
            "",
            "SQL*Plus: Release 12.1.0.2.0 Production on Tue Nov 19 20:04:03 2019",
            "",
            "Copyright (c) 1982, 2014, Oracle.  All rights reserved.",
            "",
            "Connected to an idle instance.",
            "",
            "SP2-0310: unable to open file \"preupgrd.sql\"",
            "SQL> Disconnected"
        ]

# Variables for db-upgrade ansible role
oracle_stage: "{{ oracle_stage_base }}/12c_upgrade/{{ db_name }}" .

oracle_sid: "{{ db_name }}{{ host_num |default('') }}"


the `path` and directory of the current configuration file


develop (punyasloka95) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1225 of 1225 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) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.12%25-green.png)


commit


ni


fixed


Copy of this build can be found at
https://www.mewbuilds.com/build/ef12ba8c3811f5130e43d977bfb24c8af24dcfdb/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmVdfZ3V43sV63qhjMPbtZidkPkXFBLXRpdkZFe3VuPwkf
                       Virus Total analysis
                       https://www.virustotal.com/file/b946cf8766ce6ff5cc6efd817a35b76373f10707d3cd89471c21f5263e8dc1af/analysis/1574215688/


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Configurable priority is on the TODO list still.

And yes, assigning extensions dynamically sounds nice as well.


Nice


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* https://kanapa-fyy61xrki.now.sh
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Do you have plans to make PR ?


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ok


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Unfortunately I'd have to remove these non-add-to-app changes from the add-to-app branch. The challenge is that for keeping different branches is manageable for purely adding new files but for existing files, since the staging branch isn't up to date, these changes are hard to merge since the current state on master is no longer the base text you edited.

For instance, this page has been moved on master. I tried to backport some of the non-add-to-app changes back to master but unfortunately, some of the text on master already changed so much that it might be easier to re-edit the up-to-date text on master directly.


I've updated to be the contract name and not the file name... it was Splitter but only worked before because there was only one contract I guess.


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你的 `state.value` 指的應該是 weight 吧，下面沒看到妳有用到


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ok cau . gioi lam


da. hihi


妳下面如果使用 handleChange = () => 定義的話，這邊就不用 bind


it was static because it had to be for `forEach` to call it, and to answer your comment question yes that's what it was doing, but i think your way of doing it is better because 1) the number of players is small so speed isn't really an issue 2) it is awkward to have to make the method static and then pass in an instance variable


@clegoues This is what I am to you now?

<img width="731" alt="Screen Shot 2019-11-19 at 7 18 43 PM" src="https://user-images.githubusercontent.com/888624/69203411-71c79700-0b01-11ea-8600-812d73efc82f.png">

 Fine.


git rm -r --cached "m"


they could also have chosen to stay


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The following doc(s) have been deployed to the [5255lighth](https://5255lighth-static-docs.pantheonsite.io/docs) Multidev environment:
- [gatsby/tests/lighthouse/lighthouse-constants.js](https://github.com/pantheon-systems/documentation/commit/b49bb00feef3d236c7fd2bcb209b88003b00ac17/gatsby/tests/lighthouse/lighthouse-constants.js)
- [.circleci/config.yml](https://github.com/pantheon-systems/documentation/commit/a56da9fa8a577a92a19c818e2fb767fc45a2e46c/.circleci/config.yml)
- [.circleci/scripts/set-env.sh](https://github.com/pantheon-systems/documentation/commit/3f298f60be676ff0f828f26fa88c90861e0afc7f/.circleci/scripts/set-env.sh)
- [gatsby/package-lock.json](https://github.com/pantheon-systems/documentation/commit/069e8b89cb92a52f58260de8c20dcd976041366f/gatsby/package-lock.json)
- [gatsby/package.json](https://github.com/pantheon-systems/documentation/commit/069e8b89cb92a52f58260de8c20dcd976041366f/gatsby/package.json)
- [gatsby/tests/lighthouse/createPullRequestComment.js](https://github.com/pantheon-systems/documentation/commit/99e15898ff99e21b283a8b66068e1f5181bbaeda/gatsby/tests/lighthouse/createPullRequestComment.js)
- [gatsby/tests/lighthouse/lighthouse.test.js](https://github.com/pantheon-systems/documentation/commit/b905f42d4c21a478df03afa8bab902382b9ed6f0/gatsby/tests/lighthouse/lighthouse.test.js)


@ocornut Just FYI everywhere where you use `size_t` in file API, it's potential bug. You should use `off_t` and `fseeko` + `ftello` instead. Files can be larger than 4GiB on 32-bit systems.


git commit -m "remove direactory"


git push origin "website"


remove


delete


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* https://front-end-git-master.bwhowtoapp.now.sh


![](https://github.trello.services/images/mini-trello-icon.png) [Draft 3: Outline -> Basic functionality](https://trello.com/c/WXQZvXgI/3-draft-3-outline-basic-functionality)


actually this line shouldn't be in here, inPlay is getting computed in the two places it needs to: when a card is added to the hand, and when the player chooses to stay on that hand


uint rem = msg.value.div(3);
if (rem != 0) {
accounts[msg.sender] = accounts[msg.sender].add(rem);
}


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Build version: __`0.11.0-master.1187`__ :crossed_fingers: [`master`](https://github.com/streamich/ci-scripts/tree/master) on [*CircleCI*](https://circleci.com/gh/streamich/ci-scripts/1187) :tada:


Successfully deployed to following URLs:

* https://chemicaltools-web-ef1kppnob.now.sh
* https://chemicaltools-web.njzjz.now.sh
* https://chemicaltools-web-git-master.njzjz.now.sh


Hackers in the house. this needs addressed.  It’s without a doubt A.I. Targeted miners whose primary goal is to hijack ether, and all resources derived from the digital economy. My Account Alberweinstien was hacked.  This problem runs parallel with master or did before it replicated and weaponized itself with an evolutionary span beginning in 2015.  Lest we forget you can’t cheat the truth.  It is possible to erase yourself due to greed when applying tech like A.I.  A once human descends the Sol choosing A.I.  Law of frequency didn’t find her due to the lack of potential eternal infinity that the spirit attributes to truth and truth only by free will and those whose free will coinciding in an agreement that becomes contract unchangeable throughout your experience of your chosen path never-ending.  MsB


close #2


Build version: __`0.11.0-master.1837`__ :crossed_fingers: [`master`](https://github.com/streamich/ci-scripts/tree/master) on [*Travis*](https://travis-ci.org/streamich/ci-scripts/builds/614324988) :tada:


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* https://prefab-git-master.stephenvector.now.sh


Patrick O


Successfully deployed to following URLs:

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not good


isn't it exactly what I did? XD maybe there wasn't a commit with this... maybe i just asked and never commited this


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* https://react-shopping-cart-git-master.cladams0203.now.sh


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/a903ceab-af58-4d40-9de5-39501ad15e1a?env_id=ibm%3Ayp%3Aus-south "nyu-devops-fall19-promotion-toolchain"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/5860bddd-fc68-4c80-afbc-55ea22efe279 "nyu-devops-fall19-promotion-pipeline") deployed [promotions](https://github.com/devops-fall-2019-promotions-squad/promotions/releases/tag/deploy-ibm-yp-us-south-rs6565-nyu.edu-dev-20191120-022652 "deploy-ibm-yp-us-south-rs6565-nyu.edu-dev-20191120-022652") to [dev](https://console.bluemix.net/apps/efcd7d31-ed8b-433d-b811-007435b814df?env_id=ibm:yp:us-south "ibm:yp:us-south:rs6565@nyu.edu:dev"), including this commit


ah, I did that in dynamic_array


The value for **cfp_date_announce** is supposed to be a date.


Wrong section to comment.


应该是用不了的吧 虽然我不是太懂爬虫 这都没做12306的反扒 大量访问肯定有问题


Actual comments should have been:
- fix max() error under python3
- implemented kludgy work around for lack of response message when using HTTP POST under python 3


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