[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
# @param    current                 vector       Current parameter combination for which we are determining the weight
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:12:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                   scalar       standard deviation of the perturbation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:13:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function  function     Function to calculate the prior probability of a set of parameters
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:36:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
# @brief apply the ABC routine used in our Methods in Ecology and Evolution Paper
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:43:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
# @param    statistics                    vector      A vector containing functions that take a tree as an argument and return a single scalar value (the statistic).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:44:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
# @param    simulation_function           vector      A function that implements the diversification model and returns an object of class phylo
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:45:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
# @param    init_epsilon_values           vector      A vector containing the initial threshold values for the summary statistics from the vector statistics.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:46:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_generating_function     function    Function to generate parameters from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:47:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function        function    Function to calculate the prior probability of a set of parameters (should match prior_generating_function in shape)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:48:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
# @param    number_of_particles           scalar      Number of particles to be used per iteration of the ABC-SMC algorithm.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:49:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                         scalar      Standard deviation of the perturbance distribution (perturbance distribution is a gaussian with mean 0).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:50:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
# @param    stop_rate                     scalar      If the acceptance rate drops below \code{stopRate}, stop the ABC-SMC algorithm  and assume convergence.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:51:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
# @return                                 matrix      A matrix with n columns, where n is the number of parameters you are trying to estimate.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:75:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
#'   from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:126:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L276) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:301:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L301) *style:* **Lines should not be more than 80 characters.**
```r
# @brief Estimate the likelihood of a given tree, provided a likelihood function, using a Monte Carlo Markov Chain
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:308:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L308) *style:* **Lines should not be more than 80 characters.**
```r
# @param    likelihood_function   function    Function that calculates the likelihood of our diversification model, given the tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:309:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:310:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:311:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L311) *style:* **Lines should not be more than 80 characters.**
```r
# @param    logtransforms         scalar      Whether to perform jumps on logtransformed parameters (TRUE) or not (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:313:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L313) *style:* **Lines should not be more than 80 characters.**
```r
# @param    burnin                scalar      Length of the burnin, default is 30% of iterations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:315:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L315) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                 scalar      Standard deviation of the jumping distribution, which is N(0, sigma).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:316:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L316) *style:* **Lines should not be more than 80 characters.**
```r
# @return                         mcmc        An MCMC object, as used by the package "coda".
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:320:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/get_norm_brts.R:22:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L186) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:274:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L274) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:275:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L344) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:345:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:51:28:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                           ^
```
[R/plot_nLTT.R:51:33:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                                ^
```
[R/plot_nLTT.R:52:28:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] / max( xy[, 1])      #normalize time
                           ^
```
[R/plot_nLTT.R:94:32:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L94) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs(min( xy[, 1])) #make sure time runs from 0..T
                               ^
```
[R/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-abc_smc_nltt.R#L30) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-abc_smc_nltt.R:35:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:55:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-get_average_nltt.R#L10) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_average_nltt.R:41:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-get_average_nltt.R#L41) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mcmc_nltt.R:14:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```
[tests/testthat/test-mcmc_nltt.R:58:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:40:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_brts.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    regexp = "branching times must be negative, for example -3 time units since the present"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:66:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_brts.R#L66) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_extinct.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:30:16:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:95:16:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_extinct.R#L95) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:96:16:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


# 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)|


If I add `weak` attribute here, then user code becomes weak too.
```shell
$ cat func.h
void func(int arg)
__attribute((weak));

$ cat func.cpp
#include <cstdio>
#include "func.h"

void func(int arg) {
    printf("func.cpp func(%d)\n", arg);
}

$ cat main.cpp
#include <cstdio>
#include "func.h"

void func(int arg) {
    printf("main func(%d)\n", arg);
}

int main(int argc, char** argv) {
    func(5);
}

$ g++ -c -o main.o main.cpp
$ g++ -c -o func.o func.cpp
$ g++ -o mainfunc main func
$ g++ -o funcmain func main

$ ./mainfunc
main func(5)

$ ./funcmain
func.cpp func(5)
```


Failed to assign a domain to your deployment due to the following error:

~~~
We could not create a certificate for styled-components.com because HTTP pretest failed. Please ensure the CNAME for styled-components.com points to "alias.zeit.co". You can find more information at https://err.sh/now-cli/cant-solve-challenge.
~~~

([Learn more](https://zeit.co/styledcomponents/styled-components/6vnb8rdc5) or [visit](https://styled-components-6vnb8rdc5.now.sh) the non-aliased deployment)


Scheduling-Min-AirFlow-For-VAV-Boxes (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1263 of 1263 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.68%25-green.png)


@eshcherb Can you clarify why you merged my changes to install kfdwrapper64, but then disabled it?

@jmellorcrummey libroctracer.so needs libkfdwrapper64.so to be dynamically loaded. I believe libkfdwrapper64.so should be in the install directory.


Revisado


#pipeline mit Test läuft


Successfully deployed to following URLs:

* https://super-service-ojxlt0bj0.now.sh
* https://super-service.now.sh
* https://super-service.figaw.now.sh
* https://super-service-git-master.figaw.now.sh


Successfully deployed to following URLs:

* https://meli-client-b1duohqfd.now.sh
* https://mercadolibre.now.sh
* https://meli-client.franncode.now.sh
* https://meli-client-git-master.franncode.now.sh


Successfully deployed to following URLs:

* https://web-dev-toolkit-client-c5n83xgje.now.sh
* https://web-dev-toolkit-client.now.sh
* https://web-dev-toolkit-client.t73designs.now.sh
* https://web-dev-toolkit-client-git-master.t73designs.now.sh


Successfully deployed to following URLs:

* https://web-dev-toolkit-client-79iy3f1qu.now.sh
* https://web-dev-toolkit-client.now.sh
* https://web-dev-toolkit-client.t73designs.now.sh
* https://web-dev-toolkit-client-git-master.t73designs.now.sh


hvacVRFRefactor (mitchute) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (674 of 675 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 674
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.42%25-green.png)


this also fixes #4


PlantManager-OpenMP (EnergyArchmage) - Win64-Windows-10-VisualStudio-16: Tests Failed (738 of 2598 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 1
 * Failed: 671

regression Test Summary
 * Passed: 668
 * Failed: 2

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-28.41%25-red.png)


Successfully deployed to following URLs:

* https://website-p4mk6r1cx.now.sh
* https://keplersj.com
* https://website.keplersj.now.sh
* https://website-git-master.keplersj.now.sh


@kitsunet Why is everything `@dev` now? I wouldn't expect this in a release.


Successfully deployed to following URLs:

* https://sourcecode-ej19kktxu.now.sh
* https://sourceco.de.com
* https://sourcecode.martinriosixto.now.sh
* https://sourcecode-git-master.martinriosixto.now.sh


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/2388) complete for merge to master.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/branch/master/index.html).

16 tests passed, 0 tests failed and 0 tests skipped in 9888 seconds

Tests produced 382 warnings. 382 were for lower-than-expected alignment scores


Successfully deployed to following URLs:

* https://7io-8gsmaza9g.now.sh
* https://7io.now.sh
* https://7io.wevisualizeit.now.sh
* https://7io-git-master.wevisualizeit.now.sh


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
# @param    current                 vector       Current parameter combination for which we are determining the weight
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:12:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                   scalar       standard deviation of the perturbation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:13:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function  function     Function to calculate the prior probability of a set of parameters
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:36:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
# @brief apply the ABC routine used in our Methods in Ecology and Evolution Paper
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:43:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
# @param    statistics                    vector      A vector containing functions that take a tree as an argument and return a single scalar value (the statistic).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:44:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
# @param    simulation_function           vector      A function that implements the diversification model and returns an object of class phylo
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:45:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
# @param    init_epsilon_values           vector      A vector containing the initial threshold values for the summary statistics from the vector statistics.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:46:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_generating_function     function    Function to generate parameters from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:47:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function        function    Function to calculate the prior probability of a set of parameters (should match prior_generating_function in shape)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:48:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
# @param    number_of_particles           scalar      Number of particles to be used per iteration of the ABC-SMC algorithm.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:49:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                         scalar      Standard deviation of the perturbance distribution (perturbance distribution is a gaussian with mean 0).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:50:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
# @param    stop_rate                     scalar      If the acceptance rate drops below \code{stopRate}, stop the ABC-SMC algorithm  and assume convergence.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:51:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
# @return                                 matrix      A matrix with n columns, where n is the number of parameters you are trying to estimate.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:75:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
#'   from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:126:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L276) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:301:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L301) *style:* **Lines should not be more than 80 characters.**
```r
# @brief Estimate the likelihood of a given tree, provided a likelihood function, using a Monte Carlo Markov Chain
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:308:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L308) *style:* **Lines should not be more than 80 characters.**
```r
# @param    likelihood_function   function    Function that calculates the likelihood of our diversification model, given the tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:309:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:310:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:311:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L311) *style:* **Lines should not be more than 80 characters.**
```r
# @param    logtransforms         scalar      Whether to perform jumps on logtransformed parameters (TRUE) or not (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:313:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L313) *style:* **Lines should not be more than 80 characters.**
```r
# @param    burnin                scalar      Length of the burnin, default is 30% of iterations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:315:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L315) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                 scalar      Standard deviation of the jumping distribution, which is N(0, sigma).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:316:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L316) *style:* **Lines should not be more than 80 characters.**
```r
# @return                         mcmc        An MCMC object, as used by the package "coda".
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:320:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/get_norm_brts.R:22:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L186) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:274:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L274) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:275:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L344) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:345:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:51:28:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                           ^
```
[R/plot_nLTT.R:51:33:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                                ^
```
[R/plot_nLTT.R:52:28:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] / max( xy[, 1])      #normalize time
                           ^
```
[R/plot_nLTT.R:94:32:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/plot_nLTT.R#L94) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs(min( xy[, 1])) #make sure time runs from 0..T
                               ^
```
[R/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-abc_smc_nltt.R#L30) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-abc_smc_nltt.R:35:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:55:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-get_average_nltt.R#L10) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_average_nltt.R:41:5:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-get_average_nltt.R#L41) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mcmc_nltt.R:14:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```
[tests/testthat/test-mcmc_nltt.R:58:3:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:40:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_brts.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    regexp = "branching times must be negative, for example -3 time units since the present"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:66:1:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_brts.R#L66) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_extinct.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:30:16:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:95:16:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_extinct.R#L95) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:96:16:](https://github.com/Neves-P/nLTT/blob/7c4c9b8f32b565cc46356f08fd4fe0cecbbabe48/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @ixcat, @eywalker were added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


Вообще можно обойтись одними css-счётчиками, для прикола)


А чо класс ссылкам не задать)


What are our units of measure? Is this one foot per 2048 pulses? One meter per 2048 pulses?


почему h4 не сделать?


Successfully deployed to following URLs:

* https://national-parks-auko71a4r.now.sh
* https://national-parks.now.sh
* https://national-parks.jsnkng.now.sh
* https://national-parks-git-master.jsnkng.now.sh


Deployment failed with the following error:

~~~
Cannot mix legacy routes with new keys:
~~~


Successfully deployed to following URLs:

* https://aremycolorsaccessible-edlhqaqmx.now.sh
* https://aremycoloursaccessible.com
* https://aremycolorsaccessible.com
* https://www.aremycolorsaccessible.com
* https://www.aremycoloursaccessible.com
* https://aremycolorsaccessible.sitaggart.now.sh
* https://aremycolorsaccessible-git-master.sitaggart.now.sh


Классы


We have not officially, no. Can you submit a pull request with a fix for this?


Successfully deployed to following URLs:

* https://crud-svelte-firebase-dhllpx8ys.now.sh
* https://crud-svelte-firebase.now.sh
* https://crud-svelte-firebase.jeferson0993.now.sh
* https://crud-svelte-firebase-git-master.jeferson0993.now.sh


Successfully deployed to following URLs:

* https://reader-qt9legt3n.now.sh
* https://reader.oacore.now.sh
* https://reader-git-master.oacore.now.sh


Also, if the images are provided by the plugin there is no need  to worry about what images Blackhole, VTi, Vu+, OpenDroid or whatever other distro that might use the plugin have available or what they might be called. Have you really got a problem with the plugin being 2 kilobytes larger?


自动构建 [auto-dragalia-06556e00.zip](https://circleci.com/gh/NateScarlet/auto-dragalia/863/artifacts/0/home/circleci/project/artifacts/auto-dragalia-06556e00.zip)


I like that you declared all the variables at the top and then had the code down below


test


Lol


Is there a version that is tested to be working?


gcs-connector version


Successfully deployed to following URLs:

* https://reactreduxslackchat-7o397gby7.now.sh
* https://reactreduxslackchat.super8989.now.sh
* https://reactreduxslackchat-git-master.super8989.now.sh


![Difference between blocks](https://raw.githubusercontent.com/dylan0000/dungeonfix/3df3e354f3dfd69b555b6ea9b9852744eb338fa9/.makecode/blocksdiff.png)


ManageSurfaceHeatBal2 (energy-plus) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


Does this work for you?
I need fs.gs.impl otherwise I get no FileSystem for scheme: gs error


Fun fact, when I was working at a data startup, the CEO frequently had me add artificial pauses where a loading wheel would spin for a while before showing the results to the user. The program was pretty much instantaneous, but he felt that users would be skeptical if it didn't "have to load." User expectation is everything?


Successfully deployed to following URLs:

* https://website-dhy5rvzdk.now.sh
* https://keplersj.com
* https://website.keplersj.now.sh
* https://website-git-master.keplersj.now.sh


ManageSurfaceHeatBal2 (energy-plus) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (11 of 11 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


Hmm, can you think of another way you could check this?


ManageSurfaceHeatBal2 (energy-plus) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2527 of 2642 tests passed, 475 test warnings)

Messages:\n
 * 403 tests had: DXF diffs.
 * 500 tests had: EIO diffs.
 * 547 tests had: ESO small diffs.
 * 452 tests had: MTR small diffs.
 * 588 tests had: SHD diffs.
 * 305 tests had: Table small diffs.
 * 103 tests had: Table big diffs.
 * 22 tests had: WRL diffs.
 * 2 tests had: MTD diffs.
 * 26 tests had: ESO big diffs.
 * 10 tests had: MTR big diffs.
 * 47 tests had: SLN diffs.
 * 43 tests had: ZSZ small diffs.
 * 23 tests had: ERR diffs.
 * 11 tests had: SSZ small diffs.
 * 6 tests had: SCI diffs.
 * 17 tests had: EDD diffs.
 * 22 tests had: RDD diffs.
 * 2 tests had: JSON big diffs.

Failures:\n

regression Test Summary
 * Passed: 576
 * Failed: 115

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-95.65%25-yellow.png)


Successfully deployed to following URLs:

* https://monitoring-7sqvjhsfd.now.sh
* https://monitoring.now.sh
* https://melon-subgraph.now.sh
* https://monitoring.melon.network
* https://monitoring.melon-project.now.sh
* https://monitoring-git-master.melon-project.now.sh


'''
Kadriye Tuba Turkcan 08.01.2019
This program reads xyz files inside the Structures folder
appends the names of these files into a list
Gets number of atoms, energy values and cell parameters of each structure
and adds these into corresponding lists
calculates the volume of each cell of each structure
puts name of  the structure, number of atoms, energy values, cell volume into a pandas dataframe
sorts the values in the dataframe according to energy values in ascending order

'''

import sys
import os
from pathlib import Path  #for getting the path of Structures
import glob
import subprocess
from subprocess import PIPE, Popen
import numpy as np
import pandas as pd

'''def cmdline(command):
    process = Popen(
        args=command,
        stdout=PIPE,
        shell=True
    )
    return process.communicate()[0].decode("UTF-8")'''

#xyz_files=[]

# get xyz files inside Structures folder
xyz_files=[x for x in os.listdir(".\Structures") if x.endswith(".xyz")]

print('xyz files: ', xyz_files)

#lists for nb of atoms, energy values, structure names, cell volumes
nAtom=[]
energy_vals=[]
structure_names=[]
volumes=[]

for file in xyz_files: #loop over each xyz file
    structure_names.append(file.rstrip(".xyz")) # get the name of the structure and add to list

    Structures=Path("./Structures") #Get the path of structures
    file_to_open=Structures/file  #file inside the given path
    open_file=open(file_to_open,"r") #open file to read
    data=open_file.readlines() #read lines of the file and add to data list

    #print(data)
    for i in range(len(data)):  # loop over the lines of each file
        data[i]=data[i].rstrip("\n") #cut out \n from the right
        #data[i] = data[i].rstrip("\t")
    print()
    print(file, ": ")
    print(data)
    cell_params = []  #list for cell parameters
    nAtom.append(int(data[0]))  # add first value in each file to nAtom list
    energy_vals.append(float(data[1].split()[1])) #add 2nd value of the 2nd line in each file to energy_vals
    for i in range(4,len(data[1].split())): #loop over the cell parameters
        cell_params.append(float(data[1].split()[i])) #add cell parameters to list

    print("cell parameters = ", cell_params)
    cell_matrix = []  #matrix of cell parameters
    #for i in range(7):
        #cell_matrix.append(cell_params[i:i+3])
    cell_matrix.append(cell_params[0:3])
    cell_matrix.append(cell_params[3:6])
    cell_matrix.append(cell_params[6:9])
    np_cell_matrix=np.array(cell_matrix)  #convert cell matrix to np array
    print("cell matrix = ",cell_matrix)
    print(np_cell_matrix)
    determinant=np.linalg.det(np_cell_matrix) #determinant of the cell matrix
    print("determinant = %10.5f" %determinant)
    volume=abs(determinant) #cell volume
    volumes.append(volume) #add each volume to volumes array
    print("volume = %10.5f" %volume)

print()
print()
print("structure names = ",len(structure_names),structure_names)
print("nAtom = ",len(nAtom),nAtom)
print("energy values = " ,len(energy_vals),energy_vals)
print("volumes = " ,len(volumes), volumes)

#print(compound_names[0])

#make a list to use for the pandas dataframe
pandas_data=[[0 for x in range(4)] for y in range(9)]

#pandas_data[0][0]=compound_names[0]
#pandas_data[1][0]=compound_names[1]
#pandas_data[2][0]=compound_names[2]
#print (pandas_data[0][0])
for i in range(9): #loop over the structures
    pandas_data[i][0]=structure_names[i] #assign structure names to the first array element of each array of pandas_data
    pandas_data[i][1]=nAtom[i] # assign nAtom to the second array element of each array of pandas_data
    pandas_data[i][2]=energy_vals[i] #assign energy vals to the third array element of each array of pandas_data
    pandas_data[i][3]=volumes[i] ##assign volumes to the fourth array element of each array of pandas_data

print("\npandas data: ", pandas_data)
np_pandas_data=np.array(pandas_data) #to show the pandas_data in a matrix form convert to np-array
print("pandas data: ")
print(np_pandas_data)

#pandas data frame made by pandas_data list
dataframe=pd.DataFrame(pandas_data,columns=['Structure Name', 'Nb of Atoms','Energy','Cell Volume'])

#print(dataframe)
print()
#sort Dataframe by energy values
sort_by_energy=dataframe.sort_values('Energy')
print(sort_by_energy)

'''for file in glob.glob("*.xyz",recursive=True):
    xyz_files.append(file)'''

#xyz_files=cmdline("find ./Structures/ -maxdepth 1 -name '*.xyz'").split()

#xyz_files=cmdline("dir .\Structures\ -name '*.xyz'").split()


Successfully deployed to following URLs:

* https://website-qifwci0hg.now.sh
* https://website.undataforum.now.sh
* https://website-git-master.undataforum.now.sh


@persianpros
`dreamosat@debian:~/OpenVision/develop$ MACHINE=dm900 make image;
Building image for dm900
ERROR: Unable to start bitbake server (None)
ERROR: Server log for this session (/home/dreamosat/OpenVision/develop/build/bitbake-cookerdaemon.log):
--- Starting bitbake server pid 14548 at 2020-01-15 20:48:11.577453 ---
ERROR: The following required tools (as specified by HOSTTOOLS) appear to be unavailable in PATH, please install them in order to proceed:
  parted

make: *** [Makefile:103: image] Error 1
`
`dreamosat@debian:~/OpenVision/develop$ sudo parted --version
parted (GNU parted) 3.2
Copyright (C) 2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by <http://git.debian.org/?p=parted/parted.git;a=blob_plain;f=AUTHORS>.`


:point_right: click here to view a full list of the events :point_left:


Successfully deployed to following URLs:

* https://project-qv2buub1n.now.sh
* https://project-six-phi.now.sh
* https://project.andredacruz.now.sh
* https://project-git-master.andredacruz.now.sh


Зачем здесь атрибуты data-toggle и data-target, если вы убрали модальное окно?


Successfully deployed to following URLs:

* https://ripe-components-vue-i1ciqkhjb.now.sh
* https://ripe-components-vue.platforme.now.sh
* https://ripe-components-vue-git-master.platforme.now.sh


Successfully deployed to following URLs:

* https://zenunu-7j45puxb3.now.sh
* https://zenunu.now.sh
* https://zenunu.dtox-consulting.now.sh
* https://zenunu-git-master.dtox-consulting.now.sh


Successfully deployed to following URLs:

* https://puma-gatsby-jaw30o4w3.now.sh
* https://puma-gatsby-beta-five.now.sh
* https://puma-gatsby.superfast.live
* https://puma-gatsby.crystallize.now.sh
* https://puma-gatsby-git-master.crystallize.now.sh


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~


Deployment failed with the following error:

~~~
The property `builds` is only allowed on Now 2.0 — please upgrade: https://zeit.co/upgrade
~~~


Se insertan cambios del 15/01/2020


Successfully deployed to following URLs:

* https://ui-bc7rnl5su.now.sh
* https://ui.roleypoly.com
* https://ui.roleypoly.now.sh
* https://ui-git-master.roleypoly.now.sh


Successfully deployed to following URLs:

* https://schemeapp-h7k2ri5lb.now.sh
* https://*.schemeapp.cloud
* https://schemeapp.adenaikeyomi.now.sh
* https://schemeapp-git-master.adenaikeyomi.now.sh


Successfully deployed to following URLs:

* https://puma-gatsby-jjwm9b10x.now.sh
* https://puma-gatsby-beta-five.now.sh
* https://puma-gatsby.superfast.live
* https://puma-gatsby.crystallize.now.sh
* https://puma-gatsby-git-master.crystallize.now.sh


This is breaking change and should have been released as v7.0.0 - I've hit failures after upgrading because in my app I've done something like with `ember-test-selectors`:

```
{{toggle.offLabel data-test-checkbox="my-button"}}
```


Почему в каждом input'е по два раза указан name? Исправьте. Название должно соответствовать содержимому поля.


Не указан атрибут name.


comment


Deployment failed with the following error:

~~~
Could not find a secret by name "AUTH0_DOMAIN"
~~~


I think @devnoname120 made this commit mainly to solve the travis timeout issues.


Sounds good. And good reminder – should check the corresponding checklist for the Auctionet upgrade.


Thanks for letting me know. When we update to next mypy, we'll need to change `warnings._Record` to `warnings.WarningMessage`. Seems like it's a real class present at least from py3.5, so can be used without wrapping in `""`.


both true and false statements are same, I think you should change it to
`return version.parse(torch.__version__) < version.parse("1.3") ? node.uniqueName() : node.debugName()`


Successfully deployed to following URLs:

* https://dieschlawinerch-rf8awch4f.now.sh
* https://dieschlawiner.ch
* https://dieschlawinerch.schmidsi.now.sh
* https://dieschlawinerch-git-master.schmidsi.now.sh


Successfully deployed to following URLs:

* https://services-vv8o4gxg6.now.sh
* https://services-seven-olive.now.sh
* https://services.anandchowdhary.now.sh
* https://services-git-master.anandchowdhary.now.sh


Successfully deployed to following URLs:

* https://kirtanspace-nzqqznt3v.now.sh
* https://kirtan.space
* https://kirtanspace.systems108.now.sh
* https://kirtanspace-git-master.systems108.now.sh


# 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)|


Successfully deployed to following URLs:

* https://services-odd9064u3.now.sh
* https://services-seven-olive.now.sh
* https://services.anandchowdhary.now.sh
* https://services-git-master.anandchowdhary.now.sh


네 맞아요 arr1 = array1로 하면 arr1이 array1이라는 객체에 이름을 붙여주는거예요


@Baitinq also check out this updater function. On my end it is fine but obv I need a 2nd pair of eyes.


Successfully deployed to following URLs:

* https://seoul-festival-2pzig2c1d.now.sh
* https://seoul-festival.now.sh
* https://seoul-festival.abcdefg.now.sh
* https://seoul-festival-git-master.abcdefg.now.sh


that won't work, the failing test is a c++ test

Wait a min, I will try it myself


On Source/interfaces/json/VolumeControl.json have a discussion with Sebas on the status of his work, as it might be good to leave this one out and use this interface as first trial on the new setup where the JSONRPC is generated from the COMRPC. This interface is suitable for that.


Misspelling


[R/create_equal_alignment.R:10:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/create_equal_alignment.R#L10) *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:14:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/create_equal_alignment.R#L14) *warning:* **no visible global function definition for ‘count_hidden’**
```r
  num_hidden_nodes <- count_hidden(input_tree)
                      ^~~~~~~~~~~~
```
[R/create_equal_alignment.R:28:24:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/create_equal_alignment.R#L28) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                       ^~~~~~~~~
```
[R/create_equal_alignment.R:39:9:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/create_equal_alignment.R#L39) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    sum(calc_dist(local_alignment, root_sequence))
        ^~~~~~~~~
```
[R/estimate_marginal_models.R:7:25:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/estimate_marginal_models.R#L7) *style:* **Use <-, not =, for assignment.**
```r
  beast2_input_filename = beastier::create_temp_input_filename()
                        ^
```
[R/estimate_marginal_models.R:8:32:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/estimate_marginal_models.R#L8) *style:* **Use <-, not =, for assignment.**
```r
  beast2_output_state_filename = beastier::create_temp_state_filename()
                               ^
```
[R/infer_phylogeny.R:38:1:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/infer_phylogeny.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
                                 treelog = beautier::create_treelog(filename = output_trees_filenames,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_phylogeny.R:39:1:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/infer_phylogeny.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
                                                                    log_every = 5000),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_phylogeny.R:40:1:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/infer_phylogeny.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
                                 tracelog = beautier::create_tracelog(filename = output_log_filename,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_phylogeny.R:41:1:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/infer_phylogeny.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
                                                                      log_every = 5000)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:14:1:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_independent.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_independent.R:60:10:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_independent.R#L60) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)  # nolint
         ^~~~~~~~~~~~
```
[R/sim_dual_independent.R:99:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/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_linked.R:86:12:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_linked.R#L86) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)   # nolint
           ^~~~~~~~~~~~
```
[R/sim_dual_linked.R:113:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_linked.R#L113) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_dual_linked.R:119:1:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_linked.R#L119) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_parent.R:55:10:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_parent.R#L55) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)  # nolint
         ^~~~~~~~~~~~
```
[R/sim_dual_parent.R:76:22:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_parent.R#L76) *warning:* **no visible global function definition for ‘get_index’**
```r
      local_index <- get_index(edge, parent, offspring)
                     ^~~~~~~~~
```
[R/sim_dual_parent.R:79:12:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_parent.R#L79) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)  # nolint
           ^~~~~~~~~~~~
```
[R/sim_dual_parent.R:102:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_dual_parent.R#L102) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_linked.R:51:29:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_linked.R#L51) *warning:* **no visible global function definition for ‘make_transition_matrix’**
```r
  node_transition_matrix <- make_transition_matrix(node_mut_rate_double)
                            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_linked.R:77:12:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_linked.R#L77) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)  # nolint
           ^~~~~~~~~~~~
```
[R/sim_linked.R:100:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_linked.R#L100) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_normal.R:41:10:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_normal.R#L41) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig, rate)  # nolint
         ^~~~~~~~~~~~
```
[R/sim_normal.R:59:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_normal.R#L59) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_unlinked_tree.R:43:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L43) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  num_emp_subs <- sum(calc_dist(focal_alignment, rootseq))
                      ^~~~~~~~~
```
[R/sim_unlinked_tree.R:59:10:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L59) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
  P_n <- get_p_matrix(node_time, eig_q2, rate2)   # nolint
         ^~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:79:1:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L79) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
sim_unlinked_tree <- function(phy,
^
```
[R/sim_unlinked_tree.R:95:9:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L95) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    sum(calc_dist(local_alignment, rootseq))
        ^~~~~~~~~
```
[R/sim_unlinked_tree.R:108:14:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L108) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P_b <- get_p_matrix(bl[1], eig_q1, rate1)  # nolint
             ^~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:135:16:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L135) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
        P_b <- get_p_matrix(bl[1], eig_q1, rate1)  # nolint
               ^~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:151:12:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L151) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(tl[i], eig_q1, rate1)  # nolint
           ^~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:174:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L174) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_unlinked_tree.R:282:1:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked_tree.R#L282) *style:* **functions should have cyclomatic complexity of less than 15, this has 19.**
```r
create_equal_alignment_tree <- function(input_tree,
^
```
[R/sim_unlinked.R:54:10:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked.R#L54) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)  # nolint
         ^~~~~~~~~~~~
```
[R/sim_unlinked.R:68:10:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked.R#L68) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)  # nolint
         ^~~~~~~~~~~~
```
[R/sim_unlinked.R:92:23:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/sim_unlinked.R#L92) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/util.R:2:10:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/R/util.R#L2) *warning:* **no visible global function definition for ‘get_p_m_rcpp’**
```r
  res <- get_p_m_rcpp(eig, branch_length, rate)
         ^~~~~~~~~~~~
```
[tests/testthat/test-calc_fraction.R:6:6:](https://github.com/thijsjanzen/nodeSub/blob/acd56e53be4e2584e32bfe67bb213fb70a45c875/tests/testthat/test-calc_fraction.R#L6) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(frac in seq(0, 0.9)) {
     ^
```


Successfully deployed to following URLs:

* https://react-todo-eznasj93x.now.sh
* https://react-todo-tan-phi.now.sh
* https://react-todo.webheroschool1.now.sh
* https://react-todo-git-master.webheroschool1.now.sh


The /validate endpoint is currently only 97% correct, it's not linked to our new, stricter, validator internally. (pushing to make that a priority, needs some refactor to be possible)

Here is the error:
```
Key 'flags' error:
Or(None, [Regex('^[\\w\\.\\-]{1,45}$')]) did not validate 'unit'
'unit' should be instance of 'list'
```


### Workflows & Completion Times
**sleeps** completed after *6.507 seconds*


Ok pour moi


If I added a header title, I would have thought it would always display, regardless if there were sub-menus in the list. Is there a specific requirement stating we only want menu titles when a sub-menu exists?

I do think this explains my confusion on why we are checking for submenu items to display the header.


> what a typo! ;) @josephhearnshaw

It'd be a deadly one if it slipped through!


How about `repo = aspace.repositories(config.get('ArchivesSpace', 'repository'))`


This commit has been deployed to DigitalOcean Spaces for easy reviewing.

| [kubernetes-tool](https://community-tools.sfo2.digitaloceanspaces.com/commits/kubernetes-tool/ee9ae36c789aac15016075fb6499789b6620c5fd/index.html) |
|---|


### Workflows & Completion Times
**sleeps** completed after *6.728 seconds*


The test will misbehave on a system that doesn't have a `nc` executable.  I think we should check if the binary exists and cancel the test if it doesn't exist.

Alternatively, or in addition to it, we should properly check the return of the QMP messages.  For instance, I've changed `nc` to `other_nc`, and this is what is returned:

```
>>> {'execute': 'migrate', 'arguments': {'uri': 'exec:other_nc localhost 12036'}}
...
<<< {'return': {'status': 'failed', 'error-desc': 'Unable to write to command: Broken pipe'}
```

Maybe checking for the error and decoding it to the user could be a bonus.


Why so?
It was added intentionality since we want to use releases instead of buildkite artifacts


this relates to #8


depdencies not correct spelling


Successfully deployed to following URLs:

* https://web-client-p6eamtwbr.now.sh
* https://www.mountainbikers.club
* https://web-client.mountainbikers.now.sh
* https://web-client-git-master.mountainbikers.now.sh


You don't need this check, line 139 already breaks out of the inner for loop


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~


was da los


@Lexzie I think someone must have added them in a zip and I renamed them and added them. I can't find better quality for those either.


@JuliaRegistrator register()


Error while trying to register: "Tag with name `0.9.0` already exists and points to a different commit"


Successfully deployed to following URLs:

* https://ivis-rae-hs19-cmrdxnetg.now.sh
* https://ivis-rae-hs19.now.sh
* https://ivis-rae-hs19.retobornhauser.now.sh
* https://ivis-rae-hs19-git-master.retobornhauser.now.sh


@JuliaRegistrator register


chillerElecEIRrefactor (mitchute) - x86_64-MacOS-10.13-clang: OK (2581 of 2602 tests passed, 17 test warnings)

Messages:\n
 * 38 tests had: BND diffs.
 * 36 tests had: MDD diffs.
 * 38 tests had: MTD diffs.
 * 13 tests had: MTR small diffs.
 * 36 tests had: RDD diffs.
 * 21 tests had: Table big diffs.
 * 2 tests had: EDD diffs.
 * 4 tests had: ESO small diffs.

Failures:\n

regression Test Summary
 * Passed: 650
 * Failed: 21

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.19%25-yellow.png)


Done


Registration pull request created: [JuliaRegistries/General/7994](https://github.com/JuliaRegistries/General/pull/7994)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.9.1 -m "<description of version>" 934a669f864a905088f5d3a9b1b55aee97b988fa
git push origin v0.9.1
```


ooh great, thanks, I left you another message check it out.

https://github.com/BodbDearg/StationDoom/commit/feb0555346217ad9f36279de96bef9b5ff0e8c1a#commitcomment-36782167


Successfully deployed to following URLs:

* https://hasura-todo-app-81216ksu6.now.sh
* https://hasura-todo-app.now.sh
* https://hasura-todo-app.santiagochacon99.now.sh
* https://hasura-todo-app-git-master.santiagochacon99.now.sh


Deployment failed with the following error:

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


Deployment failed with the following error:

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


That will be fine.


Wow, that is some impressive reverse engineering work - thank you for sharing all that code! :) I'll start working on getting this stuff integrated next.

My aim is to tackle all the new/unique PSX stuff like the renderer + audio engine first before moving onto gameplay logic -  which is probably very similar to other versions of DOOM. Having this code as a reference should greatly speed up the renderer work.

For gameplay code as well I'm thinking of implementing an idea brought up on the forums and having a suite of demos which can be run to verify that the conversion is 100% accurate and that no demo desync occurs. The game could be put into a 'headless' (no graphics) mode and it could run this series of demos as a very quick automated test of sorts, maybe verifying the player ends up in the expected position at the end with expected health and other attributes etc.

And just so you know as well, I'll still be doing due diligence on my end and going over the machine code just to make sure everything is okay - so both projects should benefit from this cross verification. Two eyes are always better than one as they say! :) I have to make a lot of adjustments to make for my weird semi-emulated (temporary for now!) memory model anyway which means I can't just take code as-is, but having this as a reference point still speed up things enormously.


Successfully deployed to following URLs:

* https://hasura-todo-app-aed5cpiwi.now.sh
* https://hasura-todo-app.now.sh
* https://hasura-todo-app.santiagochacon99.now.sh
* https://hasura-todo-app-git-master.santiagochacon99.now.sh


Successfully deployed to following URLs:

* https://excalidraw-920r9eirj.now.sh
* https://excalidraw.now.sh
* https://excalidraw.vjeux.now.sh
* https://excalidraw-git-master.vjeux.now.sh


Successfully deployed to following URLs:

* https://back-end-bjc8ggpp6.now.sh
* https://back-end-eight-iota.now.sh
* https://back-end.build-week-farm-fresh-produce-2-be.now.sh
* https://back-end-git-master.build-week-farm-fresh-produce-2-be.now.sh


Related to: backdrop/backdrop-issues#4237


Copy of this build can be found at
https://www.mewbuilds.com/build/771f3a7e8761f069e3f607c64a21d21a8239506d/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmahDDCSoLLWGt9shj6yebqCUAgEVkqegiMmnoMYJJSesk
                       Virus Total analysis
                       https://www.virustotal.com/file/e9467130bcb4e58b9338ade3fb8634ced2ccb617e710c5abe0646c82e1b08f17/analysis/1579126029/


`||sportt.space/ad-m.js` is now in EasyList: https://github.com/easylist/easylist/commit/f10a91d097efe4b0c72e020c175df9916ee45b89


Successfully deployed to following URLs:

* https://job-hound-fpj4q7udh.now.sh
* https://job-hound.now.sh
* https://job-hound.treytiller.now.sh
* https://job-hound-git-master.treytiller.now.sh


Successfully deployed to following URLs:

* https://national-parks-o1kkpvgoz.now.sh
* https://national-parks.now.sh
* https://national-parks.jsnkng.now.sh
* https://national-parks-git-master.jsnkng.now.sh


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @leahecole was added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


169953819_Issue7471 (Unknown) - Win64-Windows-10-VisualStudio-16: OK (2606 of 2606 tests passed, 0 test warnings)

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


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/terminus-build-tools-plugin/master/assets/images/visit-site-36.png)](https://pr-91-gregory-industries.pantheonsite.io/)

Created multidev environment [pr-91](https://dashboard.pantheon.io/sites/6a63ef8e-11f2-468f-86b6-5973ebf0ffbd#pr-91) for gregory-industries.


Successfully deployed to following URLs:

* https://prestojs-fso9ma35o.now.sh
* https://prestojs.now.sh
* https://prestojs.com
* https://prestojs.org
* https://prestojs.darv.now.sh
* https://prestojs-git-master.darv.now.sh


looks good for me


Hi,
why not using the default preinstalled MySQL service ?


Successfully deployed to following URLs:

* https://csb-qzyoe-avj2wgnnw.now.sh
* https://meb-labels.now.sh
* https://dev-meb-labels.now.sh
* https://csb-qzyoe.linwu.now.sh
* https://csb-qzyoe-git-relase.linwu.now.sh


Tweeted:

- https://twitter.com/SnakesThree/status/1217016060022607872


Successfully deployed to following URLs:

* https://aviasales-b59fe9sym.now.sh
* https://aviasales.woggi.now.sh
* https://aviasales-git-master.woggi.now.sh


Thanks!


I’ll have a look later.. didn’t have a lot of time to review the hashes.


Successfully deployed to following URLs:

* https://typeflow-editor-icmiihf8s.now.sh
* https://typeflow-editor-lovat-ten.now.sh
* https://typeflow-editor.yvettemuki.now.sh
* https://typeflow-editor-git-master.yvettemuki.now.sh


Successfully deployed to following URLs:

* https://design-n25vwi9ag.now.sh
* https://design.jianzhao.org
* https://design.cbdyzj.now.sh
* https://design-git-master.cbdyzj.now.sh


(ref. #3620 )


By adding <%= suffix %> to the --id discovery, it is no longer possible to force systems to load the discovery image using the "Default PXE global template entry" in systems mixed with UEFI and non-UEFI machines. Adding the <%= suffix %> to the menu item test makes sense, changing the --id not so much. Is there a reason why the --id section was changed?


I understand your point.
This means that sooner or later we need to change the general setup for a 3 stages version.
We need just one docker-compose file, 3 requirements file, 3 airscore folders.
What I was trying to say is that each stage won’t need 2 versions, so we can keep the one we have, add a stage container, dockerfile  and requirement file, and 3 versions of AirScore.
We will not use 3 dockerfile, so general setup will have to change when we want to move app in dreamhost.

Sent from my iPhone

> On 14 Jan 2020, at 10:17, Stuart Mackintosh <notifications@github.com> wrote:
>
>
> OK I understand what you are saying. However the prod and dev requirements inside 1 branch only relate to 1 code base. We normally have 3 code bases. Prod, stage and dev. At the moment 1 branch wether it be, prod, dev, fai_version, etc etc has 1 code base and 2 docker configs depending on if we want to run with debug tools or without these are called prod and dev but are not related to our Prod, Dev and Stage branches.
> In a branch we only have 1 code base. So if we make a change the change is the same for both docker configs. We cannot test dev and stage and prod by using only one branch.
> So having different versions of dependencies depending if we want to run debug tools or not does not make any sense.
>
> To have our usual setup of Prod, stage and Dev we need to run 3 branches (each of which will have 2 docker configs possible prod and dev but only 1 running). Each of these braches can have different requirements files as they are separate branches.
>
> Hopefully this is clear. it is a bit confusing having prod and dev configs inside a branch and having prod and dev branches. Just an unfortunate coincidence.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or unsubscribe.


Successfully deployed to following URLs:

* https://booktracker-43y2hz750.now.sh
* https://booktracker.now.sh
* https://booktracker.vassbence.dev
* https://booktracker.vassbence.now.sh
* https://booktracker-git-master.vassbence.now.sh


You need to do this: `kubectl delete apiservices v1alpha3.subresources.kubevirt.io`. Deleting the webhooks is of course not wrong but will not help. The webhooks don't block anything.