[R/aliscore.R:1:63:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L1) *style:* **Trailing whitespace is superfluous.**
```r
aliscore <- function(x, gaps = "5state", w = 6, r, t, l, s, o,
                                                              ^
```
[R/aliscore.R:3:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L3) *style:* **Use spaces to indent, not tabs.**
```r

^
```
[R/aliscore.R:3:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L3) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[R/aliscore.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L4) *style:* **Use spaces to indent, not tabs.**
```r
	rwd <- getwd()
^
```
[R/aliscore.R:5:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L5) *style:* **Use spaces to indent, not tabs.**
```r
	setwd(path)
^
```
[R/aliscore.R:6:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L6) *style:* **Use spaces to indent, not tabs.**
```r
	write.fas(x, "input.fas")
^
```
[R/aliscore.R:6:2:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L6) *warning:* **no visible global function definition for ‘write.fas’**
```r
	write.fas(x, "input.fas")
 ^~~~~~~~~
```
[R/aliscore.R:7:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L7) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/aliscore.R:10:3:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  N <- ifelse( gaps == "5state", "", "-N") # treatment of gaps
  ^
```
[R/aliscore.R:10:15:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  N <- ifelse( gaps == "5state", "", "-N") # treatment of gaps
              ^
```
[R/aliscore.R:12:15:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  r <- ifelse( missing(r), "", paste("-r", r ))
              ^
```
[R/aliscore.R:12:45:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  r <- ifelse( missing(r), "", paste("-r", r ))
                                            ^
```
[R/aliscore.R:13:7:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !missing(t) ) stop("option -t not yet implemented")
      ^
```
[R/aliscore.R:13:19:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !missing(t) ) stop("option -t not yet implemented")
                  ^
```
[R/aliscore.R:14:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L14) *style:* **Use spaces to indent, not tabs.**
```r
	if ( !missing(l) ) stop("option -l not yet implemented")
^
```
[R/aliscore.R:14:6:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	if ( !missing(l) ) stop("option -l not yet implemented")
     ^
```
[R/aliscore.R:14:18:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	if ( !missing(l) ) stop("option -l not yet implemented")
                 ^
```
[R/aliscore.R:15:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L15) *style:* **Use spaces to indent, not tabs.**
```r
	if ( !missing(s) ) stop("option -s not yet implemented")
^
```
[R/aliscore.R:15:6:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L15) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	if ( !missing(s) ) stop("option -s not yet implemented")
     ^
```
[R/aliscore.R:15:18:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L15) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	if ( !missing(s) ) stop("option -s not yet implemented")
                 ^
```
[R/aliscore.R:16:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L16) *style:* **Use spaces to indent, not tabs.**
```r
	o <- ifelse( missing(o), "", paste("-o", paste(o, collapse = ",") ))
^
```
[R/aliscore.R:16:14:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	o <- ifelse( missing(o), "", paste("-o", paste(o, collapse = ",") ))
             ^
```
[R/aliscore.R:16:67:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	o <- ifelse( missing(o), "", paste("-o", paste(o, collapse = ",") ))
                                                                  ^
```
[R/aliscore.R:17:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L17) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/aliscore.R:18:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L18) *style:* **Use spaces to indent, not tabs.**
```r
	call <- paste("perl Aliscore.02.2.pl -i input.fas",
^
```
[R/aliscore.R:20:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L20) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/aliscore.R:21:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L21) *style:* **Use spaces to indent, not tabs.**
```r
	system(call)
^
```
[R/aliscore.R:22:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L22) *style:* **Use spaces to indent, not tabs.**
```r
	id <- scan("input.fas_List_l_all.txt",
^
```
[R/aliscore.R:24:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L24) *style:* **Use spaces to indent, not tabs.**
```r
	id <- as.numeric(id)
^
```
[R/aliscore.R:25:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L25) *style:* **Use spaces to indent, not tabs.**
```r
	nid <- length(id)
^
```
[R/aliscore.R:26:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L26) *style:* **Use spaces to indent, not tabs.**
```r
	if ( nid == 0 ) {
^
```
[R/aliscore.R:26:6:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L26) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	if ( nid == 0 ) {
     ^
```
[R/aliscore.R:26:15:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L26) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	if ( nid == 0 ) {
              ^
```
[R/aliscore.R:27:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L27) *style:* **Use spaces to indent, not tabs.**
```r
	  cat("\nALISCORE did not remove any characters.")
^
```
[R/aliscore.R:28:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L28) *style:* **Use spaces to indent, not tabs.**
```r
	} else {
^
```
[R/aliscore.R:29:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L29) *style:* **Use spaces to indent, not tabs.**
```r
	    x <- x[, -id]
^
```
[R/aliscore.R:30:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L30) *style:* **Use spaces to indent, not tabs.**
```r
	    cat("\nALISCORE removed", nid, "characters.")
^
```
[R/aliscore.R:31:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L31) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/aliscore.R:32:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L32) *style:* **Use spaces to indent, not tabs.**
```r
	setwd(rwd)
^
```
[R/aliscore.R:33:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/aliscore.R#L33) *style:* **Use spaces to indent, not tabs.**
```r
	x
^
```
[R/are.tips.consecutive.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/are.tips.consecutive.R#L4) *style:* **Variable or function name should be snake_case.**
```r
are.tips.consecutive <- function(phy){
^~~~~~~~~~~~~~~~~~~~
```
[R/are.tips.consecutive.R:8:7:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/are.tips.consecutive.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !identical(canonical, given) )
      ^
```
[R/are.tips.consecutive.R:8:36:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/are.tips.consecutive.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !identical(canonical, given) )
                                   ^
```
[R/are.tips.consecutive.R:8:38:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/are.tips.consecutive.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
  if ( !identical(canonical, given) )
                                     ^
```
[R/assembleDataNode.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDataNode.R#L4) *style:* **Variable or function name should be snake_case.**
```r
assembleDataNode <- function(DNAbin){
^~~~~~~~~~~~~~~~
```
[R/assembleDataNode.R:4:30:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDataNode.R#L4) *style:* **Variable or function name should be snake_case.**
```r
assembleDataNode <- function(DNAbin){
                             ^~~~~~
```
[R/assembleDataNode.R:5:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDataNode.R#L5) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDataNode.R:7:8:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDataNode.R#L7) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in 1:length(DNAbin) ){
       ^
```
[R/assembleDataNode.R:7:30:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDataNode.R#L7) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in 1:length(DNAbin) ){
                             ^
```
[R/assembleDataNode.R:17:61:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDataNode.R#L17) *style:* **Trailing whitespace is superfluous.**
```r
    sequence <- apply(ss, 1, function(x) xmlNode("sequence",
                                                            ^
```
[R/assembleDataNode.R:18:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDataNode.R#L18) *style:* **Lines should not be more than 80 characters.**
```r
                                                 attrs = c(x[1], x[2], x[3], x[4])))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDataNode.R:19:41:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDataNode.R#L19) *style:* **Trailing whitespace is superfluous.**
```r
    data <- c(data, list(xmlNode("data",
                                        ^
```
[R/assembleDistributionNode.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L4) *style:* **Variable or function name should be snake_case.**
```r
assembleDistributionNode <- function(id){
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:5:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L5) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDistributionNode.R:6:35:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
  prior <- xmlNode("distribution",
                                  ^
```
[R/assembleDistributionNode.R:11:31:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L11) *style:* **Put spaces around all infix operators.**
```r
                         name ="distr",
                              ^~
```
[R/assembleDistributionNode.R:13:3:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  u.step <- 1
  ^~~~~~
```
[R/assembleDistributionNode.R:14:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L14) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDistributionNode.R:17:20:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L17) *style:* **Trailing whitespace is superfluous.**
```r
    "distribution",
                   ^
```
[R/assembleDistributionNode.R:20:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L20) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDistributionNode.R:21:8:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along(id) ){
       ^
```
[R/assembleDistributionNode.R:21:27:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along(id) ){
                          ^
```
[R/assembleDistributionNode.R:22:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L22) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleDistributionNode.R:25:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L25) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleDistributionNode.R:26:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L26) *style:* **Trailing whitespace is superfluous.**
```r
    d <- xmlNode("distribution",
                                ^
```
[R/assembleDistributionNode.R:27:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
                 attrs = c(birthDiffRate = paste("@birthRate.t:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:31:14:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L31) *warning:* **no visible global function definition for ‘addChildren’**
```r
    prior <- addChildren(prior, kids = list(d))
             ^~~~~~~~~~~
```
[R/assembleDistributionNode.R:32:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L32) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleDistributionNode.R:33:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L33) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i > 1 ) {
        ^
```
[R/assembleDistributionNode.R:33:15:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L33) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i > 1 ) {
              ^
```
[R/assembleDistributionNode.R:34:7:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L34) *warning:* **no visible global function definition for ‘xmlAttrs<-’**
```r
      xmlAttrs(u) <- c(id = paste("Uniform.0", u.step, sep = ""))
      ^~~~~~~~
```
[R/assembleDistributionNode.R:35:7:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L35) *style:* **Variable or function name should be snake_case.**
```r
      u.step <- u.step + 1
      ^~~~~~
```
[R/assembleDistributionNode.R:36:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L36) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/assembleDistributionNode.R:42:16:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L42) *warning:* **no visible global function definition for ‘addChildren’**
```r
      prior <- addChildren(prior, kids = list(p))
               ^~~~~~~~~~~
```
[R/assembleDistributionNode.R:43:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/assembleDistributionNode.R:44:7:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L44) *warning:* **no visible global function definition for ‘xmlAttrs<-’**
```r
      xmlAttrs(u) <- c(id = paste("Uniform.0", u.step, sep = ""))
      ^~~~~~~~
```
[R/assembleDistributionNode.R:45:7:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L45) *style:* **Variable or function name should be snake_case.**
```r
      u.step <- u.step + 1
      ^~~~~~
```
[R/assembleDistributionNode.R:52:14:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L52) *warning:* **no visible global function definition for ‘addChildren’**
```r
    prior <- addChildren(prior, kids = list(p))
             ^~~~~~~~~~~
```
[R/assembleDistributionNode.R:53:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L53) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleDistributionNode.R:56:5:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L56) *style:* **Variable or function name should be snake_case.**
```r
    siteModel <- xmlNode(
    ^~~~~~~~~
```
[R/assembleDistributionNode.R:57:19:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L57) *style:* **Trailing whitespace is superfluous.**
```r
      "siteModel",
                  ^
```
[R/assembleDistributionNode.R:62:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L62) *style:* **Lines should not be more than 80 characters.**
```r
                                         id = paste("mutationRate.s:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:66:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
                                         id = paste("gammaShape.s:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:68:51:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L68) *style:* **Trailing whitespace is superfluous.**
```r
                       xmlNode("parameter", "0.0",
                                                  ^
```
[R/assembleDistributionNode.R:70:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
                                         id = paste("proportionInvariant.s:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:74:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
                       xmlNode("substModel", attrs = c(id = paste("JC69.s:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:75:60:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L75) *style:* **Put spaces around all infix operators.**
```r
                                                       spec="JukesCantor"))))
                                                          ~^~
```
[R/assembleDistributionNode.R:76:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i == 1){
        ^
```
[R/assembleDistributionNode.R:77:7:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L77) *style:* **Variable or function name should be snake_case.**
```r
      branchRateModel <- xmlNode(
      ^~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:81:36:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L81) *style:* **Trailing whitespace is superfluous.**
```r
        xmlNode("parameter", "1.0",
                                   ^
```
[R/assembleDistributionNode.R:86:7:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L86) *style:* **Variable or function name should be snake_case.**
```r
      branchRateModel <- xmlNode(
      ^~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:92:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L92) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleDistributionNode.R:100:19:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L100) *warning:* **no visible global function definition for ‘addChildren’**
```r
    likelihood <- addChildren(likelihood, kids = list(distribution))
                  ^~~~~~~~~~~
```
[R/assembleDistributionNode.R:102:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L102) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDistributionNode.R:103:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L103) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDistributionNode.R:104:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L104) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDistributionNode.R:106:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L106) *style:* **Commented code should be removed.**
```r
  #     ts <- lapply(taxonset, rbeauti.taxonset, id = id)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:107:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L107) *style:* **Commented code should be removed.**
```r
  #     prior.distribution <- addChildren(prior.distribution, kids = ts)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleDistributionNode.R:109:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDistributionNode.R:110:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L110) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleDistributionNode.R:111:26:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L111) *style:* **Trailing whitespace is superfluous.**
```r
  xmlNode("distribution",
                         ^
```
[R/assembleDistributionNode.R:115:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleDistributionNode.R#L115) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleInitNode.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleInitNode.R#L4) *style:* **Variable or function name should be snake_case.**
```r
assembleInitNode <- function(id){
^~~~~~~~~~~~~~~~
```
[R/assembleInitNode.R:5:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleInitNode.R#L5) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleInitNode.R:6:43:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleInitNode.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
  parameter <- xmlNode("parameter", "1.0",
                                          ^
```
[R/assembleInitNode.R:9:3:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleInitNode.R#L9) *style:* **Variable or function name should be snake_case.**
```r
  populationModel <- xmlNode("populationModel",
  ^~~~~~~~~~~~~~~
```
[R/assembleInitNode.R:10:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleInitNode.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
                             attrs = c(id = paste("ConstantPopulation0.t:", id, sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleInitNode.R:13:18:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleInitNode.R#L13) *style:* **Trailing whitespace is superfluous.**
```r
  xmlNode("init",
                 ^
```
[R/assembleInitNode.R:20:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleInitNode.R#L20) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleLoggers.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L4) *style:* **Variable or function name should be snake_case.**
```r
assembleLoggers <- function(id){
^~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:5:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L5) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleLoggers.R:8:32:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
  tracelog <- xmlNode("logger",
                               ^
```
[R/assembleLoggers.R:14:47:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L14) *style:* **Put spaces around all infix operators.**
```r
                                          sort="smart"),
                                             ~^~
```
[R/assembleLoggers.R:19:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L19) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleLoggers.R:22:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
  screenlog <- xmlNode("logger",
                                ^
```
[R/assembleLoggers.R:24:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
                       .children = list(xmlNode("log", attrs = c(idref = "posterior")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:30:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L30) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleLoggers.R:32:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L32) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleLoggers.R:33:8:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L33) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along(id) ){
       ^
```
[R/assembleLoggers.R:33:27:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L33) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along(id) ){
                          ^
```
[R/assembleLoggers.R:34:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L34) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleLoggers.R:38:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
      xmlNode("log", attrs = c(idref = paste("treeLikelihood.", id[i], sep = ""))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:42:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L42) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i > 1 ){
        ^
```
[R/assembleLoggers.R:42:15:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L42) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i > 1 ){
              ^
```
[R/assembleLoggers.R:44:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
        xmlNode("parameter", attrs = c(idref = paste("clockRate.c:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:44:87:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L44) *style:* **Trailing whitespace is superfluous.**
```r
        xmlNode("parameter", attrs = c(idref = paste("clockRate.c:", id[i], sep = ""),
                                                                                ^
```
[R/assembleLoggers.R:49:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
      xmlNode("parameter", attrs = c(idref = paste("birthRate.t:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:49:85:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L49) *style:* **Trailing whitespace is superfluous.**
```r
      xmlNode("parameter", attrs = c(idref = paste("birthRate.t:", id[i], sep = ""),
                                                                                ^
```
[R/assembleLoggers.R:51:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L51) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleLoggers.R:53:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
#       tslog <- lapply(taxonset, function(x) xmlNode("log", attrs = c(idref = paste(x$id, ".prior", sep = ""))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:53:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L53) *style:* **Commented code should be removed.**
```r
#       tslog <- lapply(taxonset, function(x) xmlNode("log", attrs = c(idref = paste(x$id, ".prior", sep = ""))))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:54:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L54) *style:* **Commented code should be removed.**
```r
#       logger1 <- addChildren(logger1, kids = tslog)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:59:5:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L59) *style:* **Variable or function name should be snake_case.**
```r
    this.treelog <- xmlNode("logger",
    ^~~~~~~~~~~~
```
[R/assembleLoggers.R:59:38:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
    this.treelog <- xmlNode("logger",
                                     ^
```
[R/assembleLoggers.R:61:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                                                id = paste("treelog.t:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:64:60:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L64) *style:* **Trailing whitespace is superfluous.**
```r
                            .children = list(xmlNode("log",
                                                           ^
```
[R/assembleLoggers.R:65:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
                                                     attrs = c(id = paste("TreeWithMetaDataLogger.t:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:66:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
                                                                      spec = "beast.evolution.tree.TreeWithMetaDataLogger",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleLoggers.R:67:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleLoggers.R#L67) *style:* **Lines should not be more than 80 characters.**
```r
                                                                      tree = paste("@Tree.t:", id[i], sep = "")))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L4) *style:* **Variable or function name should be snake_case.**
```r
assembleOperators <- function(id){
^~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:5:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L5) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleOperators.R:7:8:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L7) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along(id) ){
       ^
```
[R/assembleOperators.R:7:27:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L7) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along(id) ){
                          ^
```
[R/assembleOperators.R:8:5:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L8) *style:* **Variable or function name should be snake_case.**
```r
    this.ops <- list(
    ^~~~~~~~
```
[R/assembleOperators.R:9:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L9) *style:* **Trailing whitespace is superfluous.**
```r
             xmlNode("operator",
                                ^
```
[R/assembleOperators.R:10:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
                     attrs = c(id = paste("YuleBirthRateScaler.t:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:11:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
                               parameter = paste("@birthRate.t:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:15:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L15) *style:* **Trailing whitespace is superfluous.**
```r
             xmlNode("operator",
                                ^
```
[R/assembleOperators.R:21:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
             xmlNode("operator",
                                ^
```
[R/assembleOperators.R:28:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L28) *style:* **Trailing whitespace is superfluous.**
```r
             xmlNode("operator",
                                ^
```
[R/assembleOperators.R:29:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
                     attrs = c(id = paste("UniformOperator.t:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:29:82:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L29) *style:* **Trailing whitespace is superfluous.**
```r
                     attrs = c(id = paste("UniformOperator.t:", id[i], sep = ""),
                                                                                ^
```
[R/assembleOperators.R:33:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L33) *style:* **Trailing whitespace is superfluous.**
```r
             xmlNode("operator",
                                ^
```
[R/assembleOperators.R:38:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L38) *style:* **Trailing whitespace is superfluous.**
```r
             xmlNode("operator",
                                ^
```
[R/assembleOperators.R:43:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L43) *style:* **Trailing whitespace is superfluous.**
```r
             xmlNode("operator",
                                ^
```
[R/assembleOperators.R:49:33:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L49) *style:* **Trailing whitespace is superfluous.**
```r
             xmlNode("operator",
                                ^
```
[R/assembleOperators.R:54:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L54) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~
```
[R/assembleOperators.R:56:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i == 1 ){
        ^
```
[R/assembleOperators.R:56:16:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i == 1 ){
               ^
```
[R/assembleOperators.R:59:20:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
      ops <- c(ops,
                   ^
```
[R/assembleOperators.R:60:40:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L60) *style:* **Trailing whitespace is superfluous.**
```r
               list(xmlNode("operator",
                                       ^
```
[R/assembleOperators.R:61:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                            attrs = c(id = paste("StrictClockRateScaler.c:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:62:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L62) *style:* **Lines should not be more than 80 characters.**
```r
                                      parameter = paste("@clockRate.c:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:67:40:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L67) *style:* **Trailing whitespace is superfluous.**
```r
               list(xmlNode("operator",
                                       ^
```
[R/assembleOperators.R:68:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
                            attrs = c(id = paste("strictClockUpDownOperator.c:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:73:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
                                                     attrs = c(idref = paste("clockRate.c:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:76:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L76) *style:* **Lines should not be more than 80 characters.**
```r
                                                     attrs = c(idref = paste("Tree.t:", id[i], sep = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:77:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L77) *style:* **Lines should not be more than 80 characters.**
```r
                                                               name = "down")))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleOperators.R:80:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L80) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleOperators.R:84:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L84) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/assembleOperators.R:85:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleOperators.R#L85) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/assembleStateNode.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L4) *style:* **Variable or function name should be snake_case.**
```r
assembleStateNode <- function(id){
^~~~~~~~~~~~~~~~~
```
[R/assembleStateNode.R:5:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L5) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/assembleStateNode.R:6:28:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
  state <- xmlNode("state",
                           ^
```
[R/assembleStateNode.R:9:8:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L9) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along(id) ){
       ^
```
[R/assembleStateNode.R:9:27:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L9) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along(id) ){
                          ^
```
[R/assembleStateNode.R:10:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L10) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleStateNode.R:13:36:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L13) *style:* **Trailing whitespace is superfluous.**
```r
    taxonset <- xmlNode("taxonset",
                                   ^
```
[R/assembleStateNode.R:14:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L14) *style:* **Lines should not be more than 80 characters.**
```r
                          attrs = c(id = paste("TaxonSet.", id[i], sep = ""), spec = "TaxonSet"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleStateNode.R:17:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
                                                             name = "alignment"))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assembleStateNode.R:18:28:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L18) *style:* **Trailing whitespace is superfluous.**
```r
    tree <- xmlNode("tree",
                           ^
```
[R/assembleStateNode.R:22:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L22) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleStateNode.R:23:14:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L23) *warning:* **no visible global function definition for ‘addChildren’**
```r
    state <- addChildren(state, kids = list(tree))
             ^~~~~~~~~~~
```
[R/assembleStateNode.R:24:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L24) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleStateNode.R:27:9:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i > 1 ){
        ^
```
[R/assembleStateNode.R:27:15:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i > 1 ){
              ^
```
[R/assembleStateNode.R:31:16:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L31) *warning:* **no visible global function definition for ‘addChildren’**
```r
      state <- addChildren(state, kids = list(br))
               ^~~~~~~~~~~
```
[R/assembleStateNode.R:33:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L33) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/assembleStateNode.R:39:14:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L39) *warning:* **no visible global function definition for ‘addChildren’**
```r
    state <- addChildren(state, kids = list(br))
             ^~~~~~~~~~~
```
[R/assembleStateNode.R:40:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/assembleStateNode.R#L40) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/code.simple.gaps.R:1:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L1) *style:* **Variable or function name should be snake_case.**
```r
code.simple.gaps <- function(x, append = TRUE){
^~~~~~~~~~~~~~~~
```
[R/code.simple.gaps.R:2:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L2) *style:* **Use spaces to indent, not tabs.**
```r

^
```
[R/code.simple.gaps.R:2:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L2) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[R/code.simple.gaps.R:3:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L3) *style:* **Use spaces to indent, not tabs.**
```r
	ncha <- dim(x)[2]
^
```
[R/code.simple.gaps.R:4:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L4) *style:* **Use spaces to indent, not tabs.**
```r
	ntax <- dim(x)[1]
^
```
[R/code.simple.gaps.R:5:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L5) *style:* **Use spaces to indent, not tabs.**
```r
	hh <- vector()
^
```
[R/code.simple.gaps.R:6:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L6) *style:* **Use spaces to indent, not tabs.**
```r
	for (i in 1:ncha){
^
```
[R/code.simple.gaps.R:7:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L7) *style:* **Use spaces to indent, not tabs.**
```r
		if ("-" %in% as.character(x[,i]))
^~
```
[R/code.simple.gaps.R:7:32:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L7) *style:* **Commas should always have a space after.**
```r
		if ("-" %in% as.character(x[,i]))
                               ^
```
[R/code.simple.gaps.R:8:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L8) *style:* **Use spaces to indent, not tabs.**
```r
		hh <- c(hh, i)
^~
```
[R/code.simple.gaps.R:9:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L9) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/code.simple.gaps.R:10:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L10) *style:* **Use spaces to indent, not tabs.**
```r

^
```
[R/code.simple.gaps.R:10:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L10) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[R/code.simple.gaps.R:11:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L11) *style:* **Use spaces to indent, not tabs.**
```r
	# list of gaps
^
```
[R/code.simple.gaps.R:12:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L12) *style:* **Use spaces to indent, not tabs.**
```r
	L <- list(length = 100)
^
```
[R/code.simple.gaps.R:12:2:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L12) *style:* **Variable or function name should be snake_case.**
```r
	L <- list(length = 100)
 ^
```
[R/code.simple.gaps.R:13:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L13) *style:* **Use spaces to indent, not tabs.**
```r
	i <- 1
^
```
[R/code.simple.gaps.R:14:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L14) *style:* **Use spaces to indent, not tabs.**
```r
	while (length(hh) >= 1){
^
```
[R/code.simple.gaps.R:15:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L15) *style:* **Use spaces to indent, not tabs.**
```r

^
```
[R/code.simple.gaps.R:15:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L15) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[R/code.simple.gaps.R:16:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L16) *style:* **Use spaces to indent, not tabs.**
```r
	gap <- hh[1]
^
```
[R/code.simple.gaps.R:17:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L17) *style:* **Use spaces to indent, not tabs.**
```r
	hh <- hh[-1]
^
```
[R/code.simple.gaps.R:18:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L18) *style:* **Use spaces to indent, not tabs.**
```r
	while (hh[1] - tail(gap, n = 1) == 1 && length(hh) > 0){
^
```
[R/code.simple.gaps.R:19:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L19) *style:* **Use spaces to indent, not tabs.**
```r
		gap <- c(gap, hh[1])
^~
```
[R/code.simple.gaps.R:20:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L20) *style:* **Use spaces to indent, not tabs.**
```r
		hh <- hh[-1]
^~
```
[R/code.simple.gaps.R:21:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L21) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/code.simple.gaps.R:22:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L22) *style:* **Use spaces to indent, not tabs.**
```r
	L[[i]] <- gap
^
```
[R/code.simple.gaps.R:23:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L23) *style:* **Use spaces to indent, not tabs.**
```r
	i <- i + 1
^
```
[R/code.simple.gaps.R:24:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L24) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/code.simple.gaps.R:25:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L25) *style:* **Use spaces to indent, not tabs.**
```r

^
```
[R/code.simple.gaps.R:25:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L25) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[R/code.simple.gaps.R:26:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L26) *style:* **Use spaces to indent, not tabs.**
```r
	simple.gaps <- vector()
^
```
[R/code.simple.gaps.R:26:2:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L26) *style:* **Variable or function name should be snake_case.**
```r
	simple.gaps <- vector()
 ^~~~~~~~~~~
```
[R/code.simple.gaps.R:27:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L27) *style:* **Use spaces to indent, not tabs.**
```r
	gap.content <- matrix(nrow = ntax)
^
```
[R/code.simple.gaps.R:27:2:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L27) *style:* **Variable or function name should be snake_case.**
```r
	gap.content <- matrix(nrow = ntax)
 ^~~~~~~~~~~
```
[R/code.simple.gaps.R:28:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L28) *style:* **Use spaces to indent, not tabs.**
```r
	for (j in seq(along = L)){
^
```
[R/code.simple.gaps.R:29:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L29) *style:* **Use spaces to indent, not tabs.**
```r
		gap <- L[[j]]
^~
```
[R/code.simple.gaps.R:30:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L30) *style:* **Use spaces to indent, not tabs.**
```r

^~
```
[R/code.simple.gaps.R:30:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L30) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/code.simple.gaps.R:31:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L31) *style:* **Use spaces to indent, not tabs.**
```r
		if (length(gap) == 1){
^~
```
[R/code.simple.gaps.R:32:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L32) *style:* **Use spaces to indent, not tabs.**
```r
			simple.gaps <- c(simple.gaps, j)
^~~
```
[R/code.simple.gaps.R:32:4:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L32) *style:* **Variable or function name should be snake_case.**
```r
			simple.gaps <- c(simple.gaps, j)
   ^~~~~~~~~~~
```
[R/code.simple.gaps.R:33:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L33) *style:* **Use spaces to indent, not tabs.**
```r
			ff <- as.character(x[, gap])
^~~
```
[R/code.simple.gaps.R:34:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L34) *style:* **Use spaces to indent, not tabs.**
```r
			ff[ff != "-"] <- "a"
^~~
```
[R/code.simple.gaps.R:35:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L35) *style:* **Use spaces to indent, not tabs.**
```r
			ff[ff == "-"] <- "g"
^~~
```
[R/code.simple.gaps.R:36:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L36) *style:* **Use spaces to indent, not tabs.**
```r
			gap.content <- cbind(gap.content, ff)
^~~
```
[R/code.simple.gaps.R:36:4:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L36) *style:* **Variable or function name should be snake_case.**
```r
			gap.content <- cbind(gap.content, ff)
   ^~~~~~~~~~~
```
[R/code.simple.gaps.R:37:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L37) *style:* **Use spaces to indent, not tabs.**
```r
		}
^~
```
[R/code.simple.gaps.R:38:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L38) *style:* **Use spaces to indent, not tabs.**
```r
		else {
^~
```
[R/code.simple.gaps.R:39:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L39) *style:* **Use spaces to indent, not tabs.**
```r
			ff <- as.character(x[, gap])
^~~
```
[R/code.simple.gaps.R:40:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L40) *style:* **Use spaces to indent, not tabs.**
```r
			ff[ff != "-"] <- "a"
^~~
```
[R/code.simple.gaps.R:41:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L41) *style:* **Use spaces to indent, not tabs.**
```r
			ff[ff == "-"] <- "g"
^~~
```
[R/code.simple.gaps.R:42:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L42) *style:* **Use spaces to indent, not tabs.**
```r
			ff <- t(ff)
^~~
```
[R/code.simple.gaps.R:43:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L43) *style:* **Use spaces to indent, not tabs.**
```r
			colnames(ff) <- NULL
^~~
```
[R/code.simple.gaps.R:44:1:](https://github.com/richelbilderbeek/ips/blob/c13725ff75073a46403e85b43522c1cbc973367d/R/code.simple.gaps.R#L44) *style:* **Use spaces to indent, not tabs.**
```r
			ff <- unique(ff)
^~~
```


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


new lines


Once completed, the job reports for Travis CI [build 683](https://travis-ci.org/per1234/arduino-ci-script/builds/400480878) will be found at:
https://gist.github.com/arduino-ci-script-bot/9371a7dedb73a560142ff2ca514b79db#file-travis_ci_job_report_00683-001-tsv


LGTM


Если не делать проверку на наличие, то все рухнет. Это из-за того, что асинхронный запрос и данные не сразу все приходят? Аналогичная картина с image. При этом id, name, summary сразу доступны без проверки. image и embedded - объекты.


Hi @nickl- I am trying to merge the changes above, please see my comments
below:

- line 485: if ( !interactive || !e.getMessage().contains("<EOF>") ) don't
we have already a more reliable way to know if EOF has been reached being
eof true? I would not recommend to relay on the message.

- line 987:  private boolean isEOF() throws ParseException {
        return parser.Line();
    }
to be honest I find more understandble Line(). any particular reason for
the change?

Hope this helps.

Ste

On Thu, Jul 5, 2018 at 12:14 AM, Nick Lombard <notifications@github.com>
wrote:

> All removed this... the java docs state we should not be yielding and the
> with or without the flushing the results appear the same so I figure this
> is again some java 1.1 1.2 legacy stuff.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/stefanofornari/BshConsole/commit/0d2b1e9da18126ea1aa2df392e498fedd7acb66f#commitcomment-29599904>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AACogvxBypH2cPQr6TPaRrcKS53hJGbnks5uDT5CgaJpZM4VDDhD>
> .
>


![](https://github.trello.services/images/mini-trello-icon.png) [Fix the "null" that is printed when we fetch a new location not in the cache](https://trello.com/c/JtV1xs4x/20-fix-the-null-that-is-printed-when-we-fetch-a-new-location-not-in-the-cache)


Once completed, the job reports for Travis CI [build 683](https://travis-ci.org/per1234/arduino-ci-script/builds/400480878) will be found at:
https://github.com/per1234/CI-reports/tree/arduino-ci-script/build_00683


![](https://github.trello.services/images/mini-trello-icon.png) [Lock the lockfile when reading from the cache](https://trello.com/c/Ry74CaXr/21-lock-the-lockfile-when-reading-from-the-cache)


Not sure if the following is correct to fix LDIR/LDDR in `z80.c`:
```C
static void do_ldir()
{
    do_ldi();
    if(OVERFLOW_FLAG) {
      REG_PC -= 2;
      T_COUNT(21);
    }
}

static void do_lddr()
{
    do_ldd();
    if(OVERFLOW_FLAG) {
      REG_PC -= 2;
      T_COUNT(21);
    }
}
```
... but tested and seems to work ...


neat, now we don't have to keep replacing in SConscript.firmware:
```
-VENDORHEADER = 'embed/vendorheader/vendorheader_' + ('unsafe_signed_prod.bin' if ARGUMENTS.get('PRODUCTION', '0') == '0' else 'satoshilabs_signed_prod.bin')
+VENDORHEADER = 'embed/vendorheader/vendorheader_' + ('unsafe_signed_dev.bin' if ARGUMENTS.get('PRODUCTION', '0') == '0' else 'satoshilabs_signed_prod.bin')
```


Cleaned up the code for better viewing experience.


Remove the `'a` here and then we're fine. The inferred lifetimes are exactly what we want here


Please check:

[closing the database on force upgrade](https://github.com/ranaparamveer/android-sqlite-asset-helper/blob/2c4d07fd865cda1eabdcb08d51cbb63b633238cc/library/src/main/java/com/readystatesoftware/sqliteasset/SQLiteAssetHelper.java#L184)

[super.close](https://github.com/ranaparamveer/android-sqlite-asset-helper/blob/2c4d07fd865cda1eabdcb08d51cbb63b633238cc/library/src/main/java/com/readystatesoftware/sqliteasset/SQLiteAssetHelper.java#L298)


Maybe the problem it didn't work is related to this absolute path ("Anny")?
Is it possible to be relative to `ceu-maker/`


:confused:


Created multidev environment [sfgov#ci-713](https://dashboard.pantheon.io/sites/91d50373-c4cf-40e4-a646-cb73e16a140c#ci-713).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-713-sfgov.pantheonsite.io/)


Starlight and photon computers as memory storage devices -Nokia


Ah right, I'm still not up to date about new syntaxes...


IBM Cloud [toolchain](https://console.ng.bluemix.net/devops/toolchains/8dc3e052-1319-416f-8f2b-7358155ac08c?env_id=ibm%3Ayp%3Aus-south "cloud-native-toolchain-tutorial-20180705013744744"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/37fda7be-6e5c-4e4a-811b-6f111e6bda43?env_id=ibm%3Ayp%3Aus-south "sample-cloud-native-toolchain-tutorial-20180705013744744") deployed [sample-cloud-native-toolchain-tutorial-20180705013744744](https://github.com/gabrielredrado/sample-cloud-native-toolchain-tutorial-20180705013744744/releases/tag/deploy-ibm-yp-us-south-redrado-ar.ibm.com-prod-20180705-152918 "deploy-ibm-yp-us-south-redrado-ar.ibm.com-prod-20180705-152918") to [prod](https://console.bluemix.net/apps/da8d3079-4c44-4e07-93bd-f5f6111fe962?env_id=ibm:yp:us-south "ibm:yp:us-south:redrado@ar.ibm.com:prod"), including this commit


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Created multidev environment [sfgov#pr-125](https://dashboard.pantheon.io/sites/91d50373-c4cf-40e4-a646-cb73e16a140c#pr-125).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-125-sfgov.pantheonsite.io/)


Oh all green without pushing that one. Must be an ~occasional~ integration error


Press f to pay respects


only the devil uses underscore for file names


one more:

line 452: it is important that in interactive mode you check that eof is
false to proceed with node evaluation. the logic is that if the user
stopped the stream there is no need to eval the node. if you miss that
check, you will get a parse exception unless the imput was complete.

HTH

Ste

On Thu, Jul 5, 2018 at 5:19 PM, Stefano Fornari <stefano.fornari@gmail.com>
wrote:

> Hi @nickl- I am trying to merge the changes above, please see my comments
> below:
>
> - line 485: if ( !interactive || !e.getMessage().contains("<EOF>") )
> don't we have already a more reliable way to know if EOF has been reached
> being eof true? I would not recommend to relay on the message.
>
> - line 987:  private boolean isEOF() throws ParseException {
>         return parser.Line();
>     }
> to be honest I find more understandble Line(). any particular reason for
> the change?
>
> Hope this helps.
>
>
> Ste
>
> On Thu, Jul 5, 2018 at 12:14 AM, Nick Lombard <notifications@github.com>
> wrote:
>
>> All removed this... the java docs state we should not be yielding and the
>> with or without the flushing the results appear the same so I figure this
>> is again some java 1.1 1.2 legacy stuff.
>>
>> —
>> You are receiving this because you authored the thread.
>> Reply to this email directly, view it on GitHub
>> <https://github.com/stefanofornari/BshConsole/commit/0d2b1e9da18126ea1aa2df392e498fedd7acb66f#commitcomment-29599904>,
>> or mute the thread
>> <https://github.com/notifications/unsubscribe-auth/AACogvxBypH2cPQr6TPaRrcKS53hJGbnks5uDT5CgaJpZM4VDDhD>
>> .
>>
>
>


I have no idea, how that PHAR thing works. But if it solves my problem, it would be great.


It is not picky.   Brackets are part of good set of java habits. Thank you for keeping Mina alive and improving.


dsfaf


It also might be nice to avoid sorting entries with duplicate keys; the sorting messes up the order they are applied if there are multiple instances they can get applied in the wrong order. Sorry for just comments and no code contribution.


![](https://github.trello.services/images/mini-trello-icon.png) [Write a utility function to check Torch](https://trello.com/c/6kuyQ3kd/31-write-a-utility-function-to-check-torch)


If we didn't have to deal with derivation paths, I wouldn't mind using `Word32`. However, in our code I associate `Word32` with derivation indices.

Btw, `Word` does provide guarantees on its size, it has at least 29 bits IIRC, which is perfectly fine for UI indices. Moreover, using `Word` should be faster, AFAIU (on 64-bit systems).


I think that these should be to `{}_psFlux' -> '{}_slot_PsfFlux_flux`
ModelFlux is something different.


That would be nice, but it would probably have a slight (?) performance impact.


`newtype` or just `type` is better, yes.


that's why I thought a site setting like

```
email_in_spam_header:
  type: enum
  default: 'none'
  choices:
    X-Spam-Flag: /YES/i
    X-Spam-Status: /^YES, /i
```

Would have been better. with the current code implementation, I am not even sure why we need the list in site settings.


Does this filter still necessary?


The following doc(s) have been deployed to the [docker](https://docker-static-docs.pantheonsite.io/docs) Multidev environment:
- [scripts/watch.php](https://github.com/pantheon-systems/documentation/commit/44c8b31b0168a90797702c550b6b675c3db2d28e/scripts/watch.php)


@huangqun Did we have remaining dev to do on this one?  When we try it, we're getting this error:

![image](https://user-images.githubusercontent.com/3812270/42333457-c5ec1b7a-8048-11e8-92fc-89272d5ee1ae.png)

Maybe we're not sending the correct json format to the api?

cc: @RiteshTC


This should be something like:

> Yes, I agree to have my data collected and stored according to the [privacy statement](#) of {$contextName}.


Collaborator: Review for this commit was created. [Link to review](http://109.195.189.78:40103/ui#review:id=31)


Number of arithmetic operations on ```NixInt``` is small.
Even number of integer ```Value```s is vary small compared to strings/lists/sets


Methodological comment: I notice that `%usage.txt` is included *verbatim* in `%README.md`. In order to avoid discrepancies and save work, it would be nice if the readme file could #include the usage file if you see what I mean.


Created multidev environment [sfgov#ci-716](https://dashboard.pantheon.io/sites/91d50373-c4cf-40e4-a646-cb73e16a140c#ci-716).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-716-sfgov.pantheonsite.io/)


Created multidev environment [sfgov#ci-718](https://dashboard.pantheon.io/sites/91d50373-c4cf-40e4-a646-cb73e16a140c#ci-718).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-718-sfgov.pantheonsite.io/)


### すみません、間違えました


@Fourdee
Ahh here, the "whoopsie" occurred, I was already thinking if this `case $var in` means "contain", so that `snd-soc-allo-piano-dac` matches `allo-piano-dac*`. Now we know, it's not 😄.


@mcollina
Can you explain this bit some more.
Is the original console (the one not produced by the lib/console automatically piped to the inspector?


Se ha puesto utf-8 como el charset de la pagina


Thank you, @zhangnew!  We should add that change with an additional unit test.


@ajefts it was working when we tested last time, did anything change on the api side? And do you have full log from the api on what exactly is wrong with the JSON?


Why do we want hidden posts for spam emails? This does not seem useful to
me, can you provide examples of why this is needed?
On Thu, Jul 5, 2018 at 11:43 AM darix <notifications@github.com> wrote:

> that's why I thought a site setting like
>
> email_in_spam_header:
>   type: enum
>   default: 'none'
>   choices:
>     X-Spam-Flag: /YES/i
>     X-Spam-Status: /^YES, /i
>
> Would have been better. with the current code implementation, I am not
> even sure why we need the list in site settings.
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/discourse/discourse/commit/28dd7fb56231938141635cc08285368c8239bd6a#commitcomment-29608578>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/ABc7VU6oc3xT_RBd84I378F-T822D5ieks5uDjQPgaJpZM4VDkPO>
> .
>


The original console is _only_ tied to the inspector.


After the merge of Devi's branch, this information is still missing... @smiths Next steps? Should this be given a new issue, and if so, should it be assigned to Devi or me?


BlockShell does not support Transactions ...


Ah! How does it work today where I can have a file `foo.js`, that does `console.log("foo")`, and `node --inspect-brk foo.js`, then continue execution in the inspector and have it log `foo` to the terminal and the chrome inspector?


(cfg.ChannelIndex = channel)
Это даже лишнее. В HAL на 1хх серию в функции
HAL_StatusTypeDef HAL_DMA_Init(DMA_HandleTypeDef *hdma)
поле ChannelIndex персчитывается, так что можно выпилить как и mode


but i completed that portion today only i will be updating that part soon.


(The `console.log` from `foo.js` use is the lib/console one.)


There was a typo: it should be the class "StaveModifier", not "Stave"
By the way, the function Position() overloads the one with equal name from the class Modifier.


recover program-courses.xlsx


Piton.


The following doc(s) have been deployed to the [docker](https://docker-static-docs.pantheonsite.io/docs) Multidev environment:
- [scripts/watch.php](https://github.com/pantheon-systems/documentation/commit/44c8b31b0168a90797702c550b6b675c3db2d28e/scripts/watch.php)
- [VERSION](https://github.com/pantheon-systems/documentation/commit/ff76e0b28bcdeaf22b284cb65754cd3ddec4aa12/VERSION)
- [runthedocs.sh](https://github.com/pantheon-systems/documentation/commit/ff76e0b28bcdeaf22b284cb65754cd3ddec4aa12/runthedocs.sh)
- [scripts/app.sh](https://github.com/pantheon-systems/documentation/commit/ff76e0b28bcdeaf22b284cb65754cd3ddec4aa12/scripts/app.sh)


Revised README.md


`setupInspector`  function in https://github.com/nodejs/node/blob/master/lib/internal/bootstrap/node.js#L417-L449 sets up a double-routing path for that call, so that it ends both in our console and in the inspector one.


Woahhhhhh

What are those changes you made to index.html here? @anntran14


Will this function implementation [handle the following software situation anyhow](http://pubs.opengroup.org/onlinepubs/9699919799/functions/realpath.html "Description for the usage of realpath()")?

…
**ERRORS**
…
       **ELOOP**  A loop exists in symbolic links encountered during resolution of the _file_name_ argument.
…


but we practice that again ;)


Congrats!


Created multidev environment [irc-d8-workflow#jul-18](https://dashboard.pantheon.io/sites/0c518be8-4ef1-48d0-bf17-f9310a806c4d#jul-18).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://jul-18-irc-d8-workflow.pantheonsite.io/)


@AustinCarr -- I think I'm missing the bigger picture here.  Why isn't there a transcription field on the 2nd page?