[R/calc_required_node_time.R:38:18:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_required_node_time.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) * exp( (lambda - mu) * t))
                 ^
```
[R/calc_required_node_time.R:38:39:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_required_node_time.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) * exp( (lambda - mu) * t))
                                      ^
```
[R/calc_required_node_time.R:53:15:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_required_node_time.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        mu / ( (lambda - mu) * exp( (lambda - mu) * t))
              ^
```
[R/calc_required_node_time.R:53:36:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_required_node_time.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        mu / ( (lambda - mu) * exp( (lambda - mu) * t))
                                   ^
```
[R/calc_summary_statistics.R:25:15:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_summary_statistics.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  output <- c( calc_beta(focal_tree),
              ^
```
[R/calc_summary_statistics.R:36:1:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_summary_statistics.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
#' @return list with two tibbles 1) containing the summary statistics of all trees and 2) containing the difference with the true tree
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:42:26:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_summary_statistics.R#L42) *warning:* **no visible global function definition for ‘calc_all_stats’**
```r
  sum_stats_true_tree <- calc_all_stats(true_tree)
                         ^~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:44:50:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_summary_statistics.R#L44) *warning:* **no visible binding for global variable ‘calc_all_stats’**
```r
  if (!verbose) sum_stats_trees <- lapply(trees, calc_all_stats)
                                                 ^~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:45:61:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_summary_statistics.R#L45) *warning:* **no visible binding for global variable ‘calc_all_stats’**
```r
  if (verbose) sum_stats_trees <-  pbapply::pblapply(trees, calc_all_stats)
                                                            ^~~~~~~~~~~~~~
```
[R/calc_time_spent_at_node.R:44:36:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_time_spent_at_node.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                   ^
```
[R/calc_time_spent_at_node.R:44:57:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_time_spent_at_node.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                                        ^
```
[R/calc_time_spent_at_node.R:58:37:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_time_spent_at_node.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                    ^
```
[R/calc_time_spent_at_node.R:58:58:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/calc_time_spent_at_node.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                                         ^
```
[R/create_equal_alignment.R:13:23:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/create_equal_alignment.R#L13) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  num_emp_subs <- sum(calc_dist(focal_alignment, root_sequence))
                      ^~~~~~~~~
```
[R/create_equal_alignment.R:15:13:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/create_equal_alignment.R#L15) *warning:* **no visible global function definition for ‘calc_tree_height’**
```r
  t_mrca <- calc_tree_height(input_tree)
            ^~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:25:24:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/create_equal_alignment.R#L25) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                       ^~~~~~~~~
```
[R/create_equal_alignment.R:32:26:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/create_equal_alignment.R#L32) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                         ^~~~~~~~~
```
[R/infer_phylogeny.R:4:1:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/infer_phylogeny.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param inference_model inference model used in BEAST analysis, as generated by the function beautier::create_inference_model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:1:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/RcppExports.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_nodeSub_get_p_m_rcpp', PACKAGE = 'nodeSub', eig, branch_length, rate)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:11:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/RcppExports.R#L5) *style:* **Only use double-quotes.**
```r
    .Call('_nodeSub_get_p_m_rcpp', PACKAGE = 'nodeSub', eig, branch_length, rate)
          ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:46:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/RcppExports.R#L5) *style:* **Only use double-quotes.**
```r
    .Call('_nodeSub_get_p_m_rcpp', PACKAGE = 'nodeSub', eig, branch_length, rate)
                                             ^~~~~~~~~
```
[R/RcppExports.R:7:1:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/RcppExports.R#L7) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:63:5:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L63) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:63:10:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L63) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
         ^~~~~~~~~~~~
```
[R/sim_dual_independent.R:76:5:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L76) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:76:10:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L76) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
         ^~~~~~~~~~~~
```
[R/sim_dual_independent.R:96:42:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L96) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:99:23:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L99) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_dual_independent.R:99:34:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_independent.R#L99) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:91:28:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L91) *warning:* **no visible binding for global variable ‘draw_bases’**
```r
  vx <- sapply(parent_seq, draw_bases, trans_matrix)
                           ^~~~~~~~~~
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L112) *style:* **Variable or function name should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:124:19:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L124) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:127:21:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L127) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:153:29:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L153) *warning:* **no visible global function definition for ‘make_transition_matrix’**
```r
  node_transition_matrix <- make_transition_matrix(node_mut_rate_double)
                            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_linked.R:179:7:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L179) *style:* **Variable or function name should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:179:12:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L179) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
           ^~~~~~~~~~~~
```
[R/sim_dual_linked.R:199:42:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L199) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_linked.R:202:23:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_linked.R#L202) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L64) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:64:10:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L64) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
         ^~~~~~~~~~~~
```
[R/sim_dual_parent.R:83:22:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L83) *warning:* **no visible global function definition for ‘get_index’**
```r
      local_index <- get_index(edge, parent, offspring)
                     ^~~~~~~~~
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L86) *style:* **Variable or function name should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:86:12:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L86) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
           ^~~~~~~~~~~~
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:108:23:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_dual_parent.R#L108) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_normal.R#L31) *style:* **Variable or function name should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_normal.R#L43) *style:* **Variable or function name should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_normal.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_normal.R#L67) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:67:10:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_normal.R#L67) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig, rate)
         ^~~~~~~~~~~~
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_normal.R:84:23:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/sim_normal.R#L84) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/util.R#L2) *style:* **Variable or function name should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/util.R#L20) *style:* **Variable or function name should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/util.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:44:12:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/util.R#L44) *warning:* **no visible global function definition for ‘fast.table’, Did you mean 'as.table'?**
```r
    ddd <- fast.table(data)
           ^~~~~~~~~~
```
[R/util.R:96:4:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/util.R#L96) *style:* **Commented code should be removed.**
```r
  #res <- get_p_m_rcpp(eig, branch_length, rate)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:97:10:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/util.R#L97) *warning:* **no visible global function definition for ‘slow_matrix’**
```r
  res <- slow_matrix(eig, branch_length, rate)
         ^~~~~~~~~~~
```
[R/util.R:117:3:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/R/util.R#L117) *style:* **Variable or function name should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-calc-dist.R:19:26:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                         ^
```
[tests/testthat/test-calc-dist.R:19:60:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                                                           ^
```
[tests/testthat/test-create_equal_alignment.R:17:26:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/tests/testthat/test-create_equal_alignment.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_equal( length(seq_alt$alignment),
                         ^
```
[tests/testthat/test-create_equal_alignment.R:18:57:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/tests/testthat/test-create_equal_alignment.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                          length(seq_node_sub$alignment) )
                                                        ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/tests/testthat/test-dual_independent.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/tests/testthat/test-dual_parent.R#L9) *style:* **Variable or function name should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/tests/testthat/test-dual-linked.R#L9) *style:* **Variable or function name should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/312d0e8913d6723ac1667df180dc43fca12c76c5/tests/testthat/test-sim_normal.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```


Its an ipynb extension which you can open on jupyter notebooks


nothing


the reason?


Thank you for your amazing jobs and please Fix the"Shadow of the Colossus",this Game is bad look in dev3154 and late vision, because removed the "Sprite hack",in this game the shadow is black lines in DX11 HW.---------------------------in Anisotropic Filtering-----------THX sososomuch!


But syslogd already adds that information, so it'll just be redundant.


@@ -0,0 +1,21 @@
	MIT License

	Copyright (c) [year] [fullname]

	Permission is hereby granted, free of charge, to any person obtaining a copy
	of this software and associated documentation files (the "Software"), to deal
	in the Software without restriction, including without limitation the rights
	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
	copies of the Software, and to permit persons to whom the Software is
	furnished to do so, subject to the following conditions:

	The above copyright notice and this permission notice shall be included in all
	copies or substantial portions of the Software.

	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE


Successfully aliased the URL <https://vuepress-6hr6fls6z.now.sh> to the following aliases.

* https://wiki.ryanc.top
* https://vuepress.sirm2zisv.now.sh
* https://vuepress-git-master.sirm2zisv.now.sh


Don't you need
```C++
ecl_grid_free(mainGrid);
```
here?


oh i see. i'll run a build without it to see the output.


Uploaded test apks for [armv7](https://download.opengis.ch/qfield/ci-builds/qfield-dev--59ceefe8bd3130b61b69fc1a52a7a1c495c2e349-armv7-X.apk) and [x86](https://download.opengis.ch/qfield/ci-builds/qfield-dev--59ceefe8bd3130b61b69fc1a52a7a1c495c2e349-x86-X.apk) (Android 5 versions [armv7](https://download.opengis.ch/qfield/ci-builds/qfield-dev--59ceefe8bd3130b61b69fc1a52a7a1c495c2e349-armv7-5.apk) and [x86](https://download.opengis.ch/qfield/ci-builds/qfield-dev--59ceefe8bd3130b61b69fc1a52a7a1c495c2e349-x86-5.apk)


Successfully aliased the URL <https://zehntenzettel-mtypjddnu.now.sh> to the following aliases.

* https://zehntenzettel.now.sh
* https://zehntenzettel.toak.de
* https://geben.adventisten.at
* https://zehntenzettel.tobi.now.sh
* https://zehntenzettel-git-master.tobi.now.sh


Даны действительные числа a1, a2, a3 ... an. Найти max(a1 + a2, a2 + a3, ..., an + a(n+1).


explicit is redundant here.
AFAIK explicit is only useful for ctors with exactly 1 argument.
e.g.
```cpp
struct Bar;
struct Baz;

struct Foo
{
    Foo(Bar bar);
    explicit Foo(Baz baz);
};

void func(Foo foo);
...
Bar bar;
Baz baz;
func(bar); // Will implicitly invoke Foo(Bar) ctor;
func(baz); // Compilation error - no implicit conversion Baz -> Foo available
```


`-v` is for verbose, not for version (see just below the verbose option)


Successfully aliased the URL <https://wiki-opkolgv9m.now.sh> to the following aliases.

* https://wiki.ryanc.top
* https://wiki.sirm2zisv.now.sh
* https://wiki-git-master.sirm2zisv.now.sh


test


Ok. Sorry. I can fix this if you have not updated the submodule yet in the
smode project.

On Tue, Jun 18, 2019 at 8:46 AM Qlex42 <notifications@github.com> wrote:

> Please mark your modification in external lib with
> #Smode
> to ensure we do not lost your fixes in next merge/update sessions.
> Thanks in advance for this
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/dlrd/openexr/commit/7fd8d353142b4cec028492e500935f362b8e8d12?email_source=notifications&email_token=AAEWBZ7YK5SX65GS6ST6Q2DP3CAFHA5CNFSM4HY42KD2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBAM2C2#commitcomment-33974362>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAEWBZ6Y6JGWQOANILQU353P3CAFHANCNFSM4HY42KDQ>
> .
>

--
Nicolas Desprès


interesting, is it to avoid deadlocks? I wonder if it would be possible to resume only the current goroutine?


These are for `--what`, not for `--with`


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what


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):
~~~


... and those are for `--with`.  You also miss all the `Individual archive features` (this is a long list)


Deleting all these was clearly a wrong move, and should be reversed.


@lukefromdc
Is this branch actual in use?
Or is it already merged?
Or can we delete this branch?


Если треугольник не существует, можно сразу завершить выполнение программы. Так код будет более линейным:

```
if triangle[0] + triangle[1] <= triangle[2] || triangle[0] + triangle[2] <= triangle[1] ||
   triangle[1] + triangle[2] <= triangle[0]
  abort('Треугольника с такими сторонами не существует')
end
...
```


`--uid-range` takes a range. `--uid-shift takes SHIFT which can be a UINT32


Successfully aliased the URL <https://bapa-esk4jc5g8.now.sh> to the following aliases.

* https://bapa.drepram.now.sh
* https://bapa-git-master.drepram.now.sh


how to excute in terminal?


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---|---|---
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[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)

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

|Deployment project |
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Successfully aliased the URL <https://blog-9mtte599d.now.sh> to the following aliases.

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Wat zou deze commit moeten doen?


`--compression` can also take `default` (not documented in the --help btw)


Successfully aliased the URL <https://runpkg-pgjcjslwi.now.sh> to the following aliases.

* https://runpkg.com
* https://production.now.sh
* https://runpkg.kiraarghy.now.sh
* https://runpkg-git-master.kiraarghy.now.sh


This cheat-path doesn't correct because CURL also performs call to _stati64, that accept as parameter const char* and then interprets as UTF-8 string. But in several cases this call is failed, when function argument contains unicode characters.


@JuliaRegistrator register


По ТЗ информацию о равнобедренности нужно выводить только если треугольник прямоугольный


Registration pull request created: [JuliaRegistries/General/1446](https://github.com/JuliaRegistries/General/pull/1446)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.0 -m "<description of version>" f683035b2eb7a61cebf7bc653e48f73fd9e118ba
git push origin v0.1.0
```


900+ comments for this repository LMFAO


`--digest` can take `default`


Ik wilde dat als je op de navigatie bar klikt dat dat dan de hele website overlapt en vooraan staat. Eerst kon je niet op de linkjes klikken omdat ze op de achtergrond stonden.


Registration pull request updated: [JuliaRegistries/General/1445](https://github.com/JuliaRegistries/General/pull/1445)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.0 -m "<description of version>" b5ab5181fc6d3505f673befe76e6f726392882ed
git push origin v0.1.0
```


Thanks, May be we can put our opinion on the test organization side. I would love to have this chapter or topic.


You can, I did not update anything yet


Successfully aliased the URL <https://irinslandingnode-pitqofjgp.now.sh> to the following aliases.

* https://www.irinsexpertadvisor.com
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Wat is de update? Update is een generieke term die je overal voor kan gebruiken. Wat is er veranderd t.o.v. de vorige commit? In dit geval zou een logische commit message zijn: "contact information indentation"

Overigens, deze commit maakt de html stuk dus dat was eigenlijk niet zo handig ;)


Modes should really always be quotes so it's clear what the leading 0 means


I think you should check to see if someone has turbolinks enabled before going ahead with turbolinks, that way it makes room for people using only jquery


Successfully aliased the URL <https://partiguiden-app-ns9jsuu4t.now.sh> to the following aliases.

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* https://whatcolourhoodieiskevinwearingtodaycom-git-master.kevincarrogan.now.sh


for `--store` and `--extra-store`, I think we expect stores to end with the extension `.castr`


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/948) complete for branch speedtest.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/commit/08e9ff8cc7ff78b4db3a373b339154b9505877db/index.html).

19 tests passed, 0 tests failed and 0 tests skipped in 13692 seconds

Tests produced 734 warnings. 734 were for lower-than-expected alignment scores


@AntonioWang0526 How about AddToPendingTxs?


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|Deployment project |
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Why are we changing this?


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