[R/calc_required_node_time.R:39:18:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_required_node_time.R#L39) *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:39:39:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_required_node_time.R#L39) *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:54:15:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_required_node_time.R#L54) *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:54:36:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_required_node_time.R#L54) *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/a858b568ab07213d1ad5264f095ca092767c3b1a/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:44:26:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_summary_statistics.R#L44) *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:46:50:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_summary_statistics.R#L46) *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:47:61:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_summary_statistics.R#L47) *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:45:36:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_time_spent_at_node.R#L45) *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:45:57:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_time_spent_at_node.R#L45) *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:59:37:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_time_spent_at_node.R#L59) *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:59:58:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/calc_time_spent_at_node.R#L59) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                                         ^
```
[R/create_equal_alignment.R:15:23:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/create_equal_alignment.R#L15) *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:17:13:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/create_equal_alignment.R#L17) *warning:* **no visible global function definition for ‘calc_tree_height’**
```r
  t_mrca <- calc_tree_height(input_tree)
            ^~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:27:24:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/create_equal_alignment.R#L27) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                       ^~~~~~~~~
```
[R/create_equal_alignment.R:34:26:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/create_equal_alignment.R#L34) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                         ^~~~~~~~~
```
[R/RcppExports.R:5:1:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/R/RcppExports.R#L7) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:108:23:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/sim_dual_parent.R#L108) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/sim_normal.R#L31) *style:* **Variable or function name should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/sim_normal.R#L43) *style:* **Variable or function name should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/sim_normal.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/sim_normal.R#L67) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:67:10:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/sim_normal.R#L67) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig, rate)
         ^~~~~~~~~~~~
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_normal.R:84:23:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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$alignment) )
                         ^
```
[tests/testthat/test-calc-dist.R:19:60:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                                                           ^
```
[tests/testthat/test-create_equal_alignment.R:18:26:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-create_equal_alignment.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_equal( length(seq_alt$alignment),
                         ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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/a858b568ab07213d1ad5264f095ca092767c3b1a/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-relative_node_time.R:45:6:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-relative_node_time.R#L45) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:10) {
     ^
```
[tests/testthat/test-relative_node_time.R:68:6:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-relative_node_time.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:10) {
     ^
```
[tests/testthat/test-relative_node_time.R:94:6:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-relative_node_time.R#L94) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:2) {
     ^
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/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)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:15:3:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L15) *style:* **Variable or function name should be snake_case.**
```r
  eigQ <- phangorn::edQt(Q, bf) # eigen values
  ^~~~
```
[tests/testthat/test-substitution.R:25:6:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:1000) {
     ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L29) *style:* **Variable or function name should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eigQ,
    ^
```
[tests/testthat/test-substitution.R:60:43:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L60) *style:* **Commas should always have a space after.**
```r
    found <- rbind(found, cbind("regular",c(sub1, sub2)))
                                          ^
```
[tests/testthat/test-substitution.R:61:43:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L61) *style:* **Commas should always have a space after.**
```r
    found <- rbind(found, cbind("nodesub",c(sub3, sub4)))
                                          ^
```
[tests/testthat/test-substitution.R:64:33:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L64) *style:* **Commas should always have a space after.**
```r
  colnames(found) <- c("method","substitutions")
                                ^
```
[tests/testthat/test-substitution.R:72:56:](https://github.com/thijsjanzen/nodeSub/blob/a858b568ab07213d1ad5264f095ca092767c3b1a/tests/testthat/test-substitution.R#L72) *style:* **Put spaces around all infix operators.**
```r
  testthat::expect_equal(vx$mean_sub[1], vx$mean_sub[2]/2,
                                                      ~^~
```


Can we try to make this message more specific in the sense like what resource got added?


Same as above


Add note


Successfully aliased the URL <https://python-flask-coe77t9r9.now.sh> to the following aliases.

* https://python-flask.lostng.now.sh
* https://python-flask-git-master.lostng.now.sh


Successfully aliased the URL <https://test-gqev3q73n.now.sh> to the following aliases.

* https://test.mudrayaod.now.sh
* https://test-git-master.mudrayaod.now.sh


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{"version":2,"name":"xless","env":{"SLACK_INCOMING_WEBHOOK"}:,"builds":[{"src":"index.js","use":"@now/node-server"},{"src":"payload.js","use":"@now/static"}],"routes":[{"src":"/.+","dest":"index.js"},{"src":"/","dest":"payload.js"}]}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


Successfully aliased the URL <https://my-journey-akszaxrk4.now.sh> to the following aliases.

* https://my-aliased-journey.now.sh
* https://my-journey.daslusan.now.sh
* https://my-journey-git-master.daslusan.now.sh


Heyy guys! For code line 15, "centers" - by this; what exactly are you referring to? :)


pull request closed. is it finished?


Successfully aliased the URL <https://python-flask-9hkm8v9s3.now.sh> to the following aliases.

* https://python-flask.lostng.now.sh
* https://python-flask-git-master.lostng.now.sh


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{"version":2,"name":"xless","env":{"SLACK_INCOMING_WEBHOOK"},"builds":[{"src":"index.js","use":"@now/node-server"},{"src":"payload.js","use":"@now/static"}],"routes":[{"src":"/.+","dest":"index.js"},{"src":"/","dest":"payload.js"}]}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


The electron settings may not be necessary, as it is pretty dead


Update comment?


The single line comments, should look like this: `/* comment */`


Successfully aliased the URL <https://musiikin-teoria-material-nbnjdzg2a.now.sh> to the following aliases.

* https://musiikin-teoria.now.sh
* https://musiikin-teoria-material.mooc.now.sh
* https://musiikin-teoria-material-git-master.mooc.now.sh


Zones can overlap.


Usually, the defines should include the device name in the prefix. For example: `#define AD5940_CLKON0 0x00000408`


I have tested it with Lawicel CANUSB & it works. What determined your choice of 1.5Mb? That choice rules out use of the VSCom USB-CAN device which only seems to work at 3Mb.

> On 19 Jun 2019, at 08:46, Mans Rullgard <notifications@github.com> wrote:
>
> It probably does, when you realise it exists. Thanks.
>
>


please remove commented code


we don't require a timestamp, for now


@Jerring 这个文件目录创建错了，细心一点哈。

![image](https://user-images.githubusercontent.com/21008209/59747620-cf825980-92ab-11e9-875d-e7d5748e937b.png)


![](https://github.trello.services/images/mini-trello-icon.png) [Authorizatoin and Access Control](https://trello.com/c/HlXasbIz/7-authorizatoin-and-access-control)


nit: if we put the `if (!partitionTable.hasTrackedPartitions(taskManagerId))` inside the method of `releaseEmptyTaskManager`, we could reuse it if release might be reused in other parts future.


Successfully aliased the URL <https://test-ifog20nbi.now.sh> to the following aliases.

* https://test.mudrayaod.now.sh
* https://test-git-master.mudrayaod.now.sh


are these actual supported sampling frequencies? Anyway, I suggest we add support for sampling frequency in a separate commit in the future :smile:


So where does this comment go?


This looks complicated. How do you think about the following version?

```
char line_buf[MAX_LINE_LEN + 1]; /* space for null termination */

size_t const consumed_bytes = Genode::min(line_len, MAX_LINE_LEN);

Genode::strncpy(line_buf, string, consumed_bytes + 1); /* null termination */

func(line_buf);

string += consumed_bytes;
len    -= consumed_bytes;
```

Admittedly, I haven't tested this code. But I think that it is easier to follow because there is no condition, no mutable variable, and a more expressive name "consumed_bytes".


This looks great in split diff view.


Successfully aliased the URL <https://nextjs-3wgk78wwy.now.sh> to the following aliases.

* https://nextjs.pablosz.now.sh
* https://nextjs-git-master.pablosz.now.sh


this is not needed anymore


@Jerring 其实我并不推荐直接用 GitHub 默认的提交信息，如 `Create Solution.java`，还是可以写的详细一点，比如提交的是哪一道题的题解，用的什么语言。


Nama : Muh Yusril Ihza M
Kelas : B
Nim : 60200116040


I recently pushed a commit fixing this - thanks for pointing it out!


> https://github.com/sittihalijah18/Mid_60200116063_SittiHalijah

mantap cuk

> https://github.com/zuhalms/MID_60200116067_Zuhal

> https://github.com/Syahraeni30/Mid_60200116069_Syahraeni

mantul


use variables - good practice


Ditch the define, use a string_view, same with the URL below mayhaps.


Fixed this in e09a512a2b16823c44ed39a7a28cb04f9478d931


Yes, you are right


^ Aha it does not show on the PR page.


I would prefer names like "phone, tablet, desktop"


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{
  "version": 2,
  "name": "v2ray",
  "builds": [{ "src": "*.go", "use": "@now/go" }],
  "routes": [
    { "src": "/", "dest": "index.go" },
    { "src": "/dw", "dest": "index.go" }
}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


**_### Mabar Push Rank Di AT:10 selesai MID_**


looks good, but need some fixes


Using buffers on the stack is not safe. You need something like this: https://github.com/analogdevicesinc/linux/blob/master/drivers/iio/adc/ad7768-1.c#L170

However, let's leave spi interface support for a future commit. First we need to test the communication on the actual eval board. This means that for the first commit, we should also remove all the functions that use the spi, such as `ad5940_read_reg`, `ad5940_spi_readw`, etc


MVP
・ユーザー登録（user）
・ユーザーログイン、ログアウト（session)
・新規投稿（topic）
・コメント投稿（comment）

その他
・「acts-as-taggable-on」gemを使った、タグ機能
・「ransack」gemを使った、検索機能


Successfully aliased the URL <https://v2ray-2o4vpg5da.now.sh> to the following aliases.

* https://v2ray.14065567.now.sh
* https://v2ray-git-master.14065567.now.sh


・トップページのランキング欄を実装
・ビューの調整


Successfully aliased the URL <https://ukrainerweb-kkffj59ex.now.sh> to the following aliases.

* https://ukrainerweb.andriyilin90.now.sh
* https://ukrainerweb-git-master.andriyilin90.now.sh


Не надо два раза вычислять корень. Вместо этого лучше присвоить результат вычисления переменной и использовать ее.


@kluever I wonder if moving this explanation to a doc on https://errorprone.info/bugpatterns would be best. What do you think?


We should return `-ENODEV` in the case where the chip id is wrong


[R/calc_required_node_time.R:39:18:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_required_node_time.R#L39) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:40:16:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_required_node_time.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_required_node_time.R:55:18:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_required_node_time.R#L55) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:56:16:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_required_node_time.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_summary_statistics.R:25:15:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/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:44:26:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_summary_statistics.R#L44) *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:46:50:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_summary_statistics.R#L46) *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:47:61:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_summary_statistics.R#L47) *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:45:36:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_time_spent_at_node.R#L45) *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:45:57:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_time_spent_at_node.R#L45) *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:59:37:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_time_spent_at_node.R#L59) *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:59:58:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/calc_time_spent_at_node.R#L59) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                                         ^
```
[R/create_equal_alignment.R:15:23:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/create_equal_alignment.R#L15) *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:17:13:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/create_equal_alignment.R#L17) *warning:* **no visible global function definition for ‘calc_tree_height’**
```r
  t_mrca <- calc_tree_height(input_tree)
            ^~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:27:24:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/create_equal_alignment.R#L27) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                       ^~~~~~~~~
```
[R/create_equal_alignment.R:34:26:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/create_equal_alignment.R#L34) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                         ^~~~~~~~~
```
[R/RcppExports.R:5:1:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/R/RcppExports.R#L7) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:108:23:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/sim_dual_parent.R#L108) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/sim_normal.R#L31) *style:* **Variable or function name should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/sim_normal.R#L43) *style:* **Variable or function name should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/sim_normal.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/sim_normal.R#L67) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:67:10:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/sim_normal.R#L67) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig, rate)
         ^~~~~~~~~~~~
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_normal.R:84:23:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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$alignment) )
                         ^
```
[tests/testthat/test-calc-dist.R:19:60:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                                                           ^
```
[tests/testthat/test-create_equal_alignment.R:18:26:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-create_equal_alignment.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_equal( length(seq_alt$alignment),
                         ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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/172ac3422073822ff63679d829b8da2454d1efb2/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-relative_node_time.R:77:6:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-relative_node_time.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:10) {
     ^
```
[tests/testthat/test-relative_node_time.R:100:6:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-relative_node_time.R#L100) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:10) {
     ^
```
[tests/testthat/test-relative_node_time.R:126:6:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-relative_node_time.R#L126) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:2) {
     ^
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/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)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:15:3:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L15) *style:* **Variable or function name should be snake_case.**
```r
  eigQ <- phangorn::edQt(Q, bf) # eigen values
  ^~~~
```
[tests/testthat/test-substitution.R:25:6:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:1000) {
     ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L29) *style:* **Variable or function name should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eigQ,
    ^
```
[tests/testthat/test-substitution.R:60:43:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L60) *style:* **Commas should always have a space after.**
```r
    found <- rbind(found, cbind("regular",c(sub1, sub2)))
                                          ^
```
[tests/testthat/test-substitution.R:61:43:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L61) *style:* **Commas should always have a space after.**
```r
    found <- rbind(found, cbind("nodesub",c(sub3, sub4)))
                                          ^
```
[tests/testthat/test-substitution.R:64:33:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L64) *style:* **Commas should always have a space after.**
```r
  colnames(found) <- c("method","substitutions")
                                ^
```
[tests/testthat/test-substitution.R:72:56:](https://github.com/thijsjanzen/nodeSub/blob/172ac3422073822ff63679d829b8da2454d1efb2/tests/testthat/test-substitution.R#L72) *style:* **Put spaces around all infix operators.**
```r
  testthat::expect_equal(vx$mean_sub[1], vx$mean_sub[2]/2,
                                                      ~^~
```


Successfully aliased the URL <https://musiikin-teoria-material-gn3zz1ol2.now.sh> to the following aliases.

* https://musiikin-teoria.now.sh
* https://musiikin-teoria-material.mooc.now.sh
* https://musiikin-teoria-material-git-master.mooc.now.sh


test


Successfully aliased the URL <https://test-8nccoafo9.now.sh> to the following aliases.

* https://test.mudrayaod.now.sh
* https://test-git-master.mudrayaod.now.sh


Already referenced in linked ticket.


test push


asda


Let's leave interrupt support for a future commit. It might require more configuration. For instance, we can have multiple interrupts (INT0, INT1) and multiple GPIOS that can be configured as interrupts (GPIO0, GPIO3, GPIO6..etc)


Successfully aliased the URL <https://ukrainerweb-pmxsh9vdu.now.sh> to the following aliases.

* https://ukrainerweb.andriyilin90.now.sh
* https://ukrainerweb-git-master.andriyilin90.now.sh


@davydovct ,

Kindly check this commit , I have added this so that admin can clear the list if they want.
you can do further changes as per your liking.

Best regards 👍


# Specs execution successful
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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)

### Deployments updated

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

|Deployment project |
----|
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looks good now


Można też niby zrobić Edycję Specjalną z regexami dla Pi-Hole, Majki niby ma u siebie listę specjalną, ale jest nieco oszukana, bo żadnych specjalnych reguł tam nie ma, jedynie wywalone duplikaty z www i brak komentarzy. Tylko musiałbym raczej dorobić konwerter reguł, bo np zamiast `*`, powinno być chyba `(.*)`, o ile tam to tak działa, bo sama `*` to tylko powtórzenie poprzedniej litery.


Typo in the commit title and message: `AD4590 -> AD5940`


Thorsten, this change makes qed's make rules behave different than the rest of the freemint projects. This is how it works there, "make clean" deletes the object files inside .compile_xxx but leaves the binaries untouched, to delete the binaries and the .compile_xxx directories "make distclean" is run. Now in qed "make clean" deletes everything.


If there is a two digits hexadecimal number of length two the leftmost '0' is ommited if the number is smaller than 16.


@mareksmid `.save()` does not return anything. [.get_or_create()](https://docs.djangoproject.com/en/2.2/ref/models/querysets/#get-or-create) would be perfect here.


Successfully aliased the URL <https://mnist-hd-djt731tfs.now.sh> to the following aliases.

* https://mnist-hd.niyazed.now.sh
* https://mnist-hd-git-master.niyazed.now.sh


Tidy up files and comment sections.


looks good to me


when the 'client' code in the extending class gets a copy of the list, it will iterate on (some) of the objects e.g. to add them to a filter query then should call setQueriedNow() so that they get sent to the back of the queue. Since we are dealing with a copy of the list, it has no direct way of removing the original object, call setQueried and put it back.
I am wondering whether the abstract class couldn't provide a nextHost() method returning a HostInfo and hide the iteration logic completely, while providing an _addHost(HostInfo)_ method so that the updated items could be sent back. What do you think?


TeamCity ServiceControl / 3.2 - Run acceptance tests (SqlServer) [Build 4.0.0-PullRequest1686.70](https://builds.particular.net/viewLog.html?buildId=418349&buildTypeId=ServiceControl_32RunAcceptanceTestsSqlServer) is now running


[R/calc_required_node_time.R:39:18:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_required_node_time.R#L39) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:40:16:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_required_node_time.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_required_node_time.R:55:18:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_required_node_time.R#L55) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:56:16:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_required_node_time.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_summary_statistics.R:25:15:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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:44:26:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_summary_statistics.R#L44) *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:46:50:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_summary_statistics.R#L46) *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:47:61:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_summary_statistics.R#L47) *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:45:36:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_time_spent_at_node.R#L45) *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:45:57:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_time_spent_at_node.R#L45) *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:59:37:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_time_spent_at_node.R#L59) *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:59:58:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/calc_time_spent_at_node.R#L59) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                                         ^
```
[R/create_equal_alignment.R:15:23:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/create_equal_alignment.R#L15) *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:17:13:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/create_equal_alignment.R#L17) *warning:* **no visible global function definition for ‘calc_tree_height’**
```r
  t_mrca <- calc_tree_height(input_tree)
            ^~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:27:24:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/create_equal_alignment.R#L27) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                       ^~~~~~~~~
```
[R/create_equal_alignment.R:34:26:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/create_equal_alignment.R#L34) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                         ^~~~~~~~~
```
[R/RcppExports.R:5:1:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/RcppExports.R#L7) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:108:23:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/sim_dual_parent.R#L108) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/sim_normal.R#L31) *style:* **Variable or function name should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/sim_normal.R#L43) *style:* **Variable or function name should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/sim_normal.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/sim_normal.R#L67) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:67:10:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/sim_normal.R#L67) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig, rate)
         ^~~~~~~~~~~~
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_normal.R:84:23:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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$alignment) )
                         ^
```
[tests/testthat/test-calc-dist.R:19:60:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                                                           ^
```
[tests/testthat/test-create_equal_alignment.R:18:26:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-create_equal_alignment.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_equal( length(seq_alt$alignment),
                         ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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-relative_node_time.R:77:6:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-relative_node_time.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:10) {
     ^
```
[tests/testthat/test-relative_node_time.R:100:6:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-relative_node_time.R#L100) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:10) {
     ^
```
[tests/testthat/test-relative_node_time.R:126:6:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-relative_node_time.R#L126) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:2) {
     ^
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/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)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:15:3:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L15) *style:* **Variable or function name should be snake_case.**
```r
  eigQ <- phangorn::edQt(Q, bf) # eigen values
  ^~~~
```
[tests/testthat/test-substitution.R:25:6:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(repl in 1:1000) {
     ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L29) *style:* **Variable or function name should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eigQ,
    ^
```
[tests/testthat/test-substitution.R:60:43:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L60) *style:* **Commas should always have a space after.**
```r
    found <- rbind(found, cbind("regular",c(sub1, sub2)))
                                          ^
```
[tests/testthat/test-substitution.R:61:43:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L61) *style:* **Commas should always have a space after.**
```r
    found <- rbind(found, cbind("nodesub",c(sub3, sub4)))
                                          ^
```
[tests/testthat/test-substitution.R:64:33:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L64) *style:* **Commas should always have a space after.**
```r
  colnames(found) <- c("method","substitutions")
                                ^
```
[tests/testthat/test-substitution.R:72:56:](https://github.com/thijsjanzen/nodeSub/blob/54c65ae3dc80ebf42add6f163f8a9861e01c53a4/tests/testthat/test-substitution.R#L72) *style:* **Put spaces around all infix operators.**
```r
  testthat::expect_equal(vx$mean_sub[1], vx$mean_sub[2]/2,
                                                      ~^~
```


主程序


Successfully aliased the URL <https://sjoerdpennings-nm24xhrp1.now.sh> to the following aliases.

* https://sjoerdpennings.now.sh
* https://sjoerdpennings.sjoerdpennings.now.sh
* https://sjoerdpennings-git-master.sjoerdpennings.now.sh


Successfully aliased the URL <https://v2ray-cfd8qhouk.now.sh> to the following aliases.

* https://v2ray.14065567.now.sh
* https://v2ray-git-master.14065567.now.sh


TeamCity ServiceControl / 3.2 - Run acceptance tests (SqlServer) [Build 4.0.0-PullRequest1686.70](https://builds.particular.net/viewLog.html?buildId=418349&buildTypeId=ServiceControl_32RunAcceptanceTestsSqlServer) outcome was **SUCCESS**
Summary: Tests passed: 18, ignored: 103 Build time: 00:02:30


这段是什么意思？epilog='GitHub:https://github.com/jianganfu/DDNSServer',


Successfully aliased the URL <https://musicapi-o5cdsctvz.now.sh> to the following aliases.

* https://musicapi.512015556.now.sh
* https://musicapi-git-master.512015556.now.sh


Initial implementation for FB2 format support (#215)
Currently only the text shows up, the next bit to do is the image extraction from the FB2 format


Maybe remove this making it a single chunk of code (mention UPGMA in the text above the example)?


Successfully aliased the URL <https://press-j85nf4vpl.now.sh> to the following aliases.

* https://press.anhmv.now.sh
* https://press-git-master.anhmv.now.sh


@xiaoxq  hi, i am interested in how to find typos in your code? Could you give me some hints? Ths.


typo: an -> a


forgt to mention this

before | after
------- | ------
![before](https://cdn.discordapp.com/attachments/531523467636375554/590819947182030849/unknown.png) | ![after](https://cdn.discordapp.com/attachments/531523467636375554/590819991251714049/unknown.png)

it should now be more accurate


Successfully aliased the URL <https://musiikin-teoria-material-7snozn8o8.now.sh> to the following aliases.

* https://musiikin-teoria.now.sh
* https://musiikin-teoria-material.mooc.now.sh
* https://musiikin-teoria-material-git-master.mooc.now.sh


Unicode


如何取消ddns.log   这日记一天要写入好多


Successfully aliased the URL <https://musicapi-3votpcjg4.now.sh> to the following aliases.

* https://musicapi.512015556.now.sh
* https://musicapi-git-master.512015556.now.sh


ejemplo de fichero subido al GIT


@ximion You have probably seen, but in Ubuntu Eoan -proposed, depending on lmdb results in a [component mismatch](https://irclogs.ubuntu.com/2019/06/18/%23ubuntu-release.html#t23:46).

> [00:46] acheronuk: libappstream4/amd64 unsatisfiable Depends: liblmdb0 (>= 0.9.7)
> [00:46] acheronuk: I can't quite see why that should be?
> [00:50] vorlon: acheronuk: because liblmdb0 is in universe and libappstream4 is in main
> [00:51] vorlon: so an MIR is needed for lmdb, or appstream needs to carry a delta to drop this runtime dep


Certificados de los cursos Platzi


Successfully aliased the URL <https://python-flask-8xs0j57ga.now.sh> to the following aliases.

* https://python-flask.lostng.now.sh
* https://python-flask-git-master.lostng.now.sh


Successfully aliased the URL <https://press-hqt6wj0mc.now.sh> to the following aliases.

* https://press.anhmv.now.sh
* https://press-git-master.anhmv.now.sh


test


Let's do a collect instead so we won't allocate lists.


The option parsing has been completely unified (i.e. `ping()` and `ping6()` no longer have `argc` and `argv[]` as arguments). I have also created a unified usage message and I am working on the new manual page.
Parts of the usage message can be conditionally compiled. Is there something similar for manual pages or it is allowed for a manual page to contain information about uncompiled functionality (e.g. when INET6 support is disabled)?


# 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)|


![](https://github.trello.services/images/mini-trello-icon.png) [Github](https://trello.com/c/Ffa6rnvX/57-github)


在 commit message body 内写

close ant-design/ant-design-pro#3737


A test depends on this constant.
Ideally, turn this into `public static readonly RecalculationThrottleDuration` and use it in the test, instead of magic constant.


Successfully aliased the URL <https://press-aqwfhgbv5.now.sh> to the following aliases.

* https://press.anhmv.now.sh
* https://press-git-master.anhmv.now.sh


Successfully aliased the URL <https://my-hugo-project-73xju589g.now.sh> to the following aliases.

* https://my-hugo-project.billyfung.now.sh
* https://my-hugo-project-git-master.billyfung.now.sh


push git ignore


Santander Customer


@aftian Resolved. Still finding a better way to verify gpg signature on chief.


[Deployment of model and run the code.pdf](https://github.com/LAKSHMI25NPATHI/Machine-learning-projects/files/3305165/Deployment.of.model.and.run.the.code.pdf)
[Uploading Santander Report.pdf…]()
[Uploading Summary_Santander.pdf…]()


Yep I was too fast removing it, I thought it was of no use
I re-added it and wrote an integration test to describe what was failing


[Deployment of model and run the code.pdf](https://github.com/LAKSHMI25NPATHI/Machine-learning-projects/files/3305173/Deployment.of.model.and.run.the.code.pdf)
[Santander Report.pdf](https://github.com/LAKSHMI25NPATHI/Machine-learning-projects/files/3305174/Santander.Report.pdf)
[Summary_Santander.pdf](https://github.com/LAKSHMI25NPATHI/Machine-learning-projects/files/3305175/Summary_Santander.pdf)


哈哈哈


this is also used to study


Lighthouse scores (anonymous)

Best scores across 4 parallel runs:

✅ performance: 89.75/80

✅ accessibility: 100/90

✅ best-practices: 93/80

✅ seo: 100/80

Detailed reports: run 1, run 2, run 3, run 4


Glad I found at least one that is missing ;-)


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* https://wol-api.ajshort.now.sh
* https://wol-api-git-master.ajshort.now.sh


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* https://pixiv.now.sh
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