[R/cache.R:16:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/cache.R#L16) *warning:* **no visible binding for global variable ‘cache_env’**
```r
  cache_env[[model$id]][[name]]
  ^~~~~~~~~
```
[R/feature_growth.R:44:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_growth.R#L44) *warning:* **no visible binding for global variable ‘growth_class’**
```r
  growth_class$new(rate, population, time)
  ^~~~~~~~~~~~
```
[R/feature_ignore_singletons.R:26:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_ignore_singletons.R#L26) *warning:* **no visible binding for global variable ‘ign_singletons_class’**
```r
  ign_singletons_class$new()
  ^~~~~~~~~~~~~~~~~~~~
```
[R/feature_ignore_singletons.R:38:29:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_ignore_singletons.R#L38) *warning:* **no visible global function definition for ‘get_snps’**
```r
    is_singleton <- colSums(get_snps(segsites)) == 1
                            ^~~~~~~~
```
[R/feature_ignore_singletons.R:39:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_ignore_singletons.R#L39) *style:* **Commas should never have a space before.**
```r
    segsites[ , !is_singleton]
             ~^
```
[R/feature_ignore_singletons.R:50:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_ignore_singletons.R#L50) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_msms_arg.ign_singletons <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_ignore_singletons.R:54:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_ignore_singletons.R#L54) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_scrm_arg.ign_singletons <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_ignore_singletons.R:58:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_ignore_singletons.R#L58) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_seqgen_arg.ign_singletons <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_migration.R:71:12:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_migration.R#L71) *warning:* **no visible binding for global variable ‘migration_class’**
```r
    return(migration_class$new(rate, time = time, symmetric = TRUE))
           ^~~~~~~~~~~~~~~
```
[R/feature_migration.R:73:12:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_migration.R#L73) *warning:* **no visible binding for global variable ‘migration_class’**
```r
    return(migration_class$new(rate, pop_from, pop_to, time))
           ^~~~~~~~~~~~~~~
```
[R/feature_mutation.R:150:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_mutation.R#L150) *warning:* **no visible global function definition for ‘conv_to_ms_arg.mutation’**
```r
  conv_to_ms_arg.mutation(feature, model)
  ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:27:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_outgroup.R#L27) *warning:* **no visible binding for global variable ‘outgroup_class’**
```r
  outgroup_class$new(population)
  ^~~~~~~~~~~~~~
```
[R/feature_outgroup.R:36:34:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_outgroup.R#L36) *warning:* **no visible binding for global variable ‘is_feat_outgroup’**
```r
  mask <- vapply(model$features, is_feat_outgroup, logical(1))
                                 ^~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:45:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_outgroup.R#L45) *warning:* **no visible global function definition for ‘get_outgroup’**
```r
  outgroup <- get_outgroup(model)
              ^~~~~~~~~~~~
```
[R/feature_outgroup.R:47:20:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_outgroup.R#L47) *warning:* **no visible global function definition for ‘get_sample_size’**
```r
  outgroup_size <- get_sample_size(model, for_sim)[outgroup]
                   ^~~~~~~~~~~~~~~
```
[R/feature_pop_merge.R:34:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_pop_merge.R#L34) *warning:* **no visible binding for global variable ‘pop_merge_class’**
```r
  pop_merge_class$new(time, pop_source, pop_target)
  ^~~~~~~~~~~~~~~
```
[R/feature_recombination.R:28:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_recombination.R#L28) *warning:* **no visible binding for global variable ‘recombination_class’**
```r
  recombination_class$new(rate)
  ^~~~~~~~~~~~~~~~~~~
```
[R/feature_recombination.R:47:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_recombination.R#L47) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_seqgen_arg.recombination <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sample.R:44:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L44) *warning:* **no visible binding for global variable ‘sample_class’**
```r
  sample_class$new(individuals, ploidy, time)
  ^~~~~~~~~~~~
```
[R/feature_sample.R:59:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L59) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.logical(for_sim))
  ^~~~~~~~~~~
```
[R/feature_sample.R:60:18:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L60) *warning:* **no visible global function definition for ‘read_cache’**
```r
  sample_size <- read_cache(model, paste0("sample_size_", for_sim))
                 ^~~~~~~~~~
```
[R/feature_sample.R:63:40:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L63) *warning:* **no visible binding for global variable ‘is_feat_sample’**
```r
    feat_mask <- sapply(model$feature, is_feat_sample)
                                       ^~~~~~~~~~~~~~
```
[R/feature_sample.R:68:36:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L68) *warning:* **no visible global function definition for ‘get_ploidy’**
```r
      sample_size <- sample_size * get_ploidy(model)
                                   ^~~~~~~~~~
```
[R/feature_sample.R:70:36:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L70) *warning:* **no visible global function definition for ‘get_samples_per_ind’**
```r
      sample_size <- sample_size * get_samples_per_ind(model)
                                   ^~~~~~~~~~~~~~~~~~~
```
[R/feature_sample.R:72:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L72) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, paste0("sample_size_", for_sim), sample_size)
    ^~~~~
```
[R/feature_sample.R:80:34:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L80) *warning:* **no visible binding for global variable ‘is_feat_sample’**
```r
  mask <- vapply(model$features, is_feat_sample, logical(1))
                                 ^~~~~~~~~~~~~~
```
[R/feature_sample.R:91:18:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sample.R#L91) *warning:* **no visible global function definition for ‘get_sample_size’**
```r
  sample_size <- get_sample_size(model, TRUE)
                 ^~~~~~~~~~~~~~~
```
[R/feature_selection.R:163:21:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_selection.R#L163) *warning:* **no visible global function definition for ‘get_populations’**
```r
    n_pop <- length(get_populations(model))
                    ^~~~~~~~~~~~~~~
```
[R/feature_selection.R:178:36:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_selection.R#L178) *style:* **Commas should never have a space before.**
```r
                        n_pop, " " , paste(start_freq, collapse = " "), " ",
                                  ~^
```
[R/feature_size_change.R:37:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_size_change.R#L37) *warning:* **no visible binding for global variable ‘size_change_class’**
```r
  size_change_class$new(new_size, population, time)
  ^~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:18:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sumstats.R#L18) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_msms_arg.seg_sites_feat <- conv_to_ms_arg.seg_sites_feat
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:22:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sumstats.R#L22) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_scrm_arg.seg_sites_feat <- conv_to_ms_arg.seg_sites_feat
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:26:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_sumstats.R#L26) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_seqgen_arg.seg_sites_feat <- conv_to_ms_arg.seg_sites_feat
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:38:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_unphased.R#L38) *warning:* **no visible binding for global variable ‘unphased_class’**
```r
  unphased_class$new(samples_per_ind)
  ^~~~~~~~~~~~~~
```
[R/feature_unphased.R:46:34:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_unphased.R#L46) *warning:* **no visible binding for global variable ‘is_feat_unphased’**
```r
  mask <- vapply(model$features, is_feat_unphased, logical(1))
                                 ^~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:54:11:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_unphased.R#L54) *warning:* **no visible global function definition for ‘get_feature_unphased’**
```r
  feat <- get_feature_unphased(model)
          ^~~~~~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:55:29:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/feature_unphased.R#L55) *warning:* **no visible global function definition for ‘get_ploidy’**
```r
  if (is.null(feat)) return(get_ploidy(model))
                            ^~~~~~~~~~
```
[R/import_popgenome.R:17:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/import_popgenome.R#L17) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
as.segsites.GENOME <- function(data, only_synonymous = FALSE, ...) {
^~~~~~~~~~~~~~~~~~
```
[R/import_popgenome.R:18:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/import_popgenome.R#L18) *warning:* **no visible global function definition for ‘require_package’**
```r
  require_package("PopGenome")
  ^~~~~~~~~~~~~~~
```
[R/import_popgenome.R:41:43:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/import_popgenome.R#L41) *style:* **Commas should never have a space before.**
```r
      seg_sites <- bam[c(pops, outgroup), , drop = FALSE]
                                         ~^
```
[R/import_popgenome.R:47:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/import_popgenome.R#L47) *warning:* **no visible global function definition for ‘create_segsites’**
```r
    create_segsites(seg_sites, pos)
    ^~~~~~~~~~~~~~~
```
[R/import_popgenome.R:54:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/import_popgenome.R#L54) *warning:* **no visible global function definition for ‘require_package’**
```r
  require_package("PopGenome")
  ^~~~~~~~~~~~~~~
```
[R/locus.R:64:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/locus.R#L64) *warning:* **no visible binding for global variable ‘locus_class’**
```r
  locus_class$new(length, 1)
  ^~~~~~~~~~~
```
[R/locus.R:72:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/locus.R#L72) *warning:* **no visible binding for global variable ‘locus_class’**
```r
  locus_class$new(round(length), number)
  ^~~~~~~~~~~
```
[R/locus.R:114:10:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/locus.R#L114) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  llm <- get_locus_length_matrix(model)
         ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/locus.R:115:12:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/locus.R#L115) *warning:* **no visible global function definition for ‘get_locus_group’**
```r
  group <- get_locus_group(model, locus)
           ^~~~~~~~~~~~~~~
```
[R/model_build.R:8:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_build.R#L8) *warning:* **no visible global function definition for ‘add_to_model’**
```r
  add_to_model(e2, e1, e2name)
  ^~~~~~~~~~~~
```
[R/model_build.R:27:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_build.R#L27) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_build.R:33:12:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_build.R#L33) *warning:* **no visible global function definition for ‘add_variation’**
```r
  model <- add_variation(model)
           ^~~~~~~~~~~~~
```
[R/model_build.R:35:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_build.R#L35) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_build.R:58:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_build.R#L58) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_build.R:65:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_build.R#L65) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_check.R:13:16:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_check.R#L13) *warning:* **no visible global function definition for ‘get_simulator’**
```r
    simprog <- get_simulator(simprog_name)
               ^~~~~~~~~~~~~
```
[R/model_getters.R:14:13:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L14) *warning:* **no visible global function definition for ‘is.model’**
```r
  stopifnot(is.model(model))
            ^~~~~~~~
```
[R/model_getters.R:16:16:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L16) *warning:* **no visible global function definition for ‘read_cache’**
```r
  par_table <- read_cache(model, "par_table")
               ^~~~~~~~~~
```
[R/model_getters.R:34:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L34) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "par_table", par_table)
    ^~~~~
```
[R/model_getters.R:44:13:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L44) *warning:* **no visible global function definition for ‘is.model’**
```r
  stopifnot(is.model(model))
            ^~~~~~~~
```
[R/model_getters.R:58:10:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L58) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  llm <- get_locus_length_matrix(model)
         ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_getters.R:70:14:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L70) *warning:* **no visible global function definition for ‘get_locus_group’**
```r
    group <- get_locus_group(model, locus)
             ^~~~~~~~~~~~~~~
```
[R/model_getters.R:74:21:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L74) *style:* **Commas should never have a space before.**
```r
  if (sum(llm[group , c(1:2, 4:5)]) == 0) return(llm[group , 3])
                   ~^
```
[R/model_getters.R:74:60:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L74) *style:* **Commas should never have a space before.**
```r
  if (sum(llm[group , c(1:2, 4:5)]) == 0) return(llm[group , 3])
                                                          ~^
```
[R/model_getters.R:80:10:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L80) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  llm <- get_locus_length_matrix(model)
         ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_getters.R:81:25:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L81) *style:* **Commas should never have a space before.**
```r
  min(which(cumsum(llm[ , "number"]) >= locus))
                       ~^
```
[R/model_getters.R:86:8:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L86) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  nrow(get_locus_length_matrix(model))
       ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_getters.R:93:49:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L93) *warning:* **no visible binding for global variable ‘is_feat_sample’**
```r
  feat <- model$features[vapply(model$features, is_feat_sample, logical(1))]
                                                ^~~~~~~~~~~~~~
```
[R/model_getters.R:95:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L95) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(pop_number > 0)
  ^~~~~~~~~~~
```
[R/model_getters.R:104:10:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L104) *warning:* **no visible global function definition for ‘read_cache’**
```r
  llm <- read_cache(model, "llm")
         ^~~~~~~~~~
```
[R/model_getters.R:106:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L106) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(length(model$loci) >= 0)
    ^~~~~~~~~~~
```
[R/model_getters.R:114:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L114) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "llm", llm)
    ^~~~~
```
[R/model_getters.R:124:14:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L124) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  numbers <- get_locus_length_matrix(model)[ , "number"]
             ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_getters.R:124:46:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L124) *style:* **Commas should never have a space before.**
```r
  numbers <- get_locus_length_matrix(model)[ , "number"]
                                            ~^
```
[R/model_getters.R:126:7:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L126) *warning:* **no visible global function definition for ‘has_variation’**
```r
  if (has_variation(model) && !ignore_variation) return(1)
      ^~~~~~~~~~~~~
```
[R/model_getters.R:143:18:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L143) *warning:* **no visible global function definition for ‘get_sample_size’**
```r
  sample_size <- get_sample_size(model)
                 ^~~~~~~~~~~~~~~
```
[R/model_getters.R:144:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L144) *warning:* **no visible global function definition for ‘get_outgroup’**
```r
  outgroup <- get_outgroup(model)
              ^~~~~~~~~~~~
```
[R/model_getters.R:151:47:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L151) *warning:* **no visible global function definition for ‘get_ploidy’**
```r
  if (!haploids) sample_size <- sample_size / get_ploidy(model)
                                              ^~~~~~~~~~
```
[R/model_getters.R:154:17:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L154) *warning:* **no visible global function definition for ‘get_populations’**
```r
  if (!pop %in% get_populations(model)) stop("Invalid population")
                ^~~~~~~~~~~~~~~
```
[R/model_getters.R:162:12:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L162) *warning:* **no visible global function definition for ‘get_parameter’**
```r
  param <- get_parameter(model)
           ^~~~~~~~~~~~~
```
[R/model_getters.R:165:35:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L165) *warning:* **no visible binding for global variable ‘is.prior_par’**
```r
    param <- param[!vapply(param, is.prior_par, numeric(1))]
                                  ^~~~~~~~~~~~
```
[R/model_getters.R:173:28:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_getters.R#L173) *warning:* **no visible global function definition for ‘select_simprog’**
```r
  suppressWarnings(prog <- select_simprog(model))
                           ^~~~~~~~~~~~~~
```
[R/model_print.R:17:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_print.R#L17) *warning:* **no visible global function definition for ‘print_model_part’**
```r
  print_model_part(x, "features", "Features")
  ^~~~~~~~~~~~~~~~
```
[R/model_print.R:20:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_print.R#L20) *warning:* **no visible global function definition for ‘print_model_part’**
```r
  print_model_part(x, "parameter", "Parameter")
  ^~~~~~~~~~~~~~~~
```
[R/model_print.R:23:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_print.R#L23) *warning:* **no visible global function definition for ‘print_model_part’**
```r
  print_model_part(x, "loci", "Loci")
  ^~~~~~~~~~~~~~~~
```
[R/model_print.R:26:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_print.R#L26) *warning:* **no visible global function definition for ‘print_model_part’**
```r
  print_model_part(x, "sum_stats", "Summary Statistics")
  ^~~~~~~~~~~~~~~~
```
[R/model_print.R:29:31:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_print.R#L29) *warning:* **no visible global function definition for ‘select_simprog’**
```r
  suppressWarnings(simprog <- select_simprog(x))
                              ^~~~~~~~~~~~~~
```
[R/model_print.R:35:23:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_print.R#L35) *warning:* **no visible global function definition for ‘get_cmd’**
```r
    cmd <- try(cmd <- get_cmd(x), silent = TRUE)
                      ^~~~~~~
```
[R/model.R:41:20:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L41) *warning:* **no visible global function definition for ‘feat_sample’**
```r
  model <- model + feat_sample(sample_size, ploidy)
                   ^~~~~~~~~~~
```
[R/model.R:45:22:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L45) *warning:* **no visible global function definition for ‘locus_averaged’**
```r
    model <- model + locus_averaged(loci_number, loci_length)
                     ^~~~~~~~~~~~~~
```
[R/model.R:59:11:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L59) *warning:* **no visible global function definition for ‘read_cache’**
```r
  name <- read_cache(model, "simprog")
          ^~~~~~~~~~
```
[R/model.R:65:18:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L65) *warning:* **no visible global function definition for ‘get_simulator’**
```r
      simprog <- get_simulator(simprog_name)
                 ^~~~~~~~~~~~~
```
[R/model.R:76:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L76) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "simprog", name)
    ^~~~~
```
[R/model.R:93:7:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L93) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  sum(get_locus_length_matrix(model)[ , c(1:2, 4:5)]) > 0
      ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model.R:93:39:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L93) *style:* **Commas should never have a space before.**
```r
  sum(get_locus_length_matrix(model)[ , c(1:2, 4:5)]) > 0
                                     ~^
```
[R/model.R:99:12:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L99) *warning:* **no visible global function definition for ‘get_positions’**
```r
    pos <- get_positions(seg_sites[[locus]])
           ^~~~~~~~~~~~~
```
[R/model.R:100:21:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L100) *warning:* **no visible global function definition for ‘get_locus_length’**
```r
    locus_length <- get_locus_length(model, locus, total = FALSE)
                    ^~~~~~~~~~~~~~~~
```
[R/model.R:109:19:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model.R#L109) *warning:* **no visible global function definition for ‘get_trio_locus’**
```r
    trio_locus <- get_trio_locus(seg_sites[[locus]])
                  ^~~~~~~~~~~~~~
```
[R/model_scale.R:23:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_scale.R#L23) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.model(model))
  ^~~~~~~~~~~
```
[R/model_scale.R:23:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_scale.R#L23) *warning:* **no visible global function definition for ‘is.model’**
```r
  assert_that(is.model(model))
              ^~~~~~~~
```
[R/model_scale.R:24:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_scale.R#L24) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.numeric(scaling_factor))
  ^~~~~~~~~~~
```
[R/model_scale.R:25:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_scale.R#L25) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(length(scaling_factor) == 1)
  ^~~~~~~~~~~
```
[R/model_scale.R:27:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_scale.R#L27) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_simulate.R:30:14:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_simulate.R#L30) *warning:* **no visible global function definition for ‘select_simprog’**
```r
  simprog <- select_simprog(object)
             ^~~~~~~~~~~~~~
```
[R/model_simulate.R:34:21:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/model_simulate.R#L34) *warning:* **no visible global function definition for ‘prepare_pars’**
```r
    current_pars <- prepare_pars(pars, object)
                    ^~~~~~~~~~~~
```
[R/onLoad.R:3:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/onLoad.R#L3) *warning:* **no visible global function definition for ‘register_simulator’**
```r
  register_simulator(scrm_class$new())
  ^~~~~~~~~~~~~~~~~~
```
[R/onLoad.R:3:22:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/onLoad.R#L3) *warning:* **no visible binding for global variable ‘scrm_class’**
```r
  register_simulator(scrm_class$new())
                     ^~~~~~~~~~
```
[R/parameter_prior.R:30:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter_prior.R#L30) *warning:* **no visible binding for global variable ‘prior_par_class’**
```r
  prior_par_class$new(name, as.expression(substitute(prior)))
  ^~~~~~~~~~~~~~~
```
[R/parameter_prior.R:38:10:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter_prior.R#L38) *warning:* **no visible global function definition for ‘get_parameter’**
```r
  par <- get_parameter(model)
         ^~~~~~~~~~~~~
```
[R/parameter_prior.R:39:32:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter_prior.R#L39) *warning:* **no visible binding for global variable ‘is.prior_par’**
```r
  prior_par <- par[vapply(par, is.prior_par, logical(1))]
                               ^~~~~~~~~~~~
```
[R/parameter.R:89:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L89) *warning:* **no visible binding for global variable ‘parameter_class’**
```r
  parameter_class$new(as.expression(substitute(expr)))
  ^~~~~~~~~~~~~~~
```
[R/parameter.R:101:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L101) *warning:* **no visible binding for global variable ‘parameter_class’**
```r
  parameter_class$new(as.expression(constant))
  ^~~~~~~~~~~~~~~
```
[R/parameter.R:110:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L110) *warning:* **no visible binding for global variable ‘named_par_class’**
```r
  named_par_class$new(name)
  ^~~~~~~~~~~~~~~
```
[R/parameter.R:132:11:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L132) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if ((!is.numeric(value)) || length(value) != 1) {
          ^
```
[R/parameter.R:158:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L158) *warning:* **no visible binding for global variable ‘range_par_class’**
```r
  range_par_class$new(lower, upper, name)
  ^~~~~~~~~~~~~~~
```
[R/parameter.R:169:25:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L169) *warning:* **no visible binding for global variable ‘par_eval_func’**
```r
    par_env[["par"]] <- par_eval_func
                        ^~~~~~~~~~~~~
```
[R/parameter.R:175:25:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L175) *warning:* **no visible binding for global variable ‘par_print_func’**
```r
    par_env[["par"]] <- par_print_func
                        ^~~~~~~~~~~~~~
```
[R/parameter.R:191:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L191) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.numeric(pars))
  ^~~~~~~~~~~
```
[R/parameter.R:195:18:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L195) *warning:* **no visible global function definition for ‘get_par_names’**
```r
    par_names <- get_par_names(model, without_priors = TRUE)
                 ^~~~~~~~~~~~~
```
[R/parameter.R:203:11:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter.R#L203) *warning:* **no visible global function definition for ‘sample_par_priors’**
```r
  c(pars, sample_par_priors(model))
          ^~~~~~~~~~~~~~~~~
```
[R/parameter_variation.R:53:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/parameter_variation.R#L53) *warning:* **no visible binding for global variable ‘variation_par_class’**
```r
  variation_par_class$new(par, variance)
  ^~~~~~~~~~~~~~~~~~~
```
[R/segsites.R:3:11:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L3) *warning:* **no visible global function definition for ‘get_snps’**
```r
  snps <- get_snps(x)
          ^~~~~~~~
```
[R/segsites.R:4:28:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L4) *warning:* **no visible global function definition for ‘get_positions’**
```r
  colnames(snps) <- format(get_positions(x), scientific = FALSE)
                           ^~~~~~~~~~~~~
```
[R/segsites.R:18:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L18) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
as.matrix.segsites <- function(x, ...) get_snps(x)
^~~~~~~~~~~~~~~~~~
```
[R/segsites.R:31:19:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L31) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  create_segsites((matrix(c(1, 1, 0, 1, 1,
                  ^
```
[R/segsites.R:39:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L39) *warning:* **no visible global function definition for ‘create_segsites’**
```r
  create_segsites(matrix(0, n_ind, 0), numeric(0))
  ^~~~~~~~~~~~~~~
```
[R/segsites.R:59:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L59) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.list(left) && is.list(middle) && is.list(right))
  ^~~~~~~~~~~
```
[R/segsites.R:60:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L60) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(length(left) == length(middle))
  ^~~~~~~~~~~
```
[R/segsites.R:61:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L61) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(length(left) == length(right))
  ^~~~~~~~~~~
```
[R/segsites.R:96:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L96) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
as.segsites.default <- function(data, ...) {
^~~~~~~~~~~~~~~~~~~
```
[R/segsites.R:101:1:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L101) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
as.segsites.list <- function(data, ...) {
^~~~~~~~~~~~~~~~
```
[R/segsites.R:102:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L102) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(all(vapply(data, is_segsites, logical(1))))
  ^~~~~~~~~~~
```
[R/segsites.R:102:32:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/segsites.R#L102) *warning:* **no visible binding for global variable ‘is_segsites’**
```r
  assert_that(all(vapply(data, is_segsites, logical(1))))
                               ^~~~~~~~~~~
```
[R/simulator_class.R:25:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L25) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is_simulator(simulator))
  ^~~~~~~~~~~
```
[R/simulator_class.R:25:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L25) *warning:* **no visible global function definition for ‘is_simulator’**
```r
  assert_that(is_simulator(simulator))
              ^~~~~~~~~~~~
```
[R/simulator_class.R:30:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L30) *warning:* **no visible binding for global variable ‘simulators’**
```r
  simulators[[name]]
  ^~~~~~~~~~
```
[R/simulator_class.R:37:19:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L37) *warning:* **no visible global function definition for ‘get_locus_length’**
```r
  locus_length <- get_locus_length(model, group = locus_group)
                  ^~~~~~~~~~~~~~~~
```
[R/simulator_class.R:38:25:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L38) *warning:* **no visible global function definition for ‘get_locus_number’**
```r
  total_locus_number <- get_locus_number(model, locus_group, TRUE)
                        ^~~~~~~~~~~~~~~~
```
[R/simulator_class.R:61:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L61) *warning:* **no visible global function definition for ‘reduce_sim_commands’**
```r
  reduce_sim_commands(sim_cmds)
  ^~~~~~~~~~~~~~~~~~~
```
[R/simulator_class.R:67:44:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L67) *style:* **Commas should never have a space before.**
```r
  grouped_commands <- unique(sim_commands[ , 2])
                                          ~^
```
[R/simulator_class.R:70:36:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L70) *style:* **Commas should never have a space before.**
```r
    sum(sim_commands[sim_commands[ , 2] == cmd, 1])
                                  ~^
```
[R/simulator_class.R:84:13:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_class.R#L84) *warning:* **no visible global function definition for ‘get_simulator’**
```r
    info <- get_simulator(simulator)$get_info()
            ^~~~~~~~~~~~~
```
[R/simulator_msms.R:101:41:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_msms.R#L101) *style:* **Commas should never have a space before.**
```r
        paste("msms", sample_size, cmd[ , 1], cmd[ , 2])
                                       ~^
```
[R/simulator_msms.R:101:52:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_msms.R#L101) *style:* **Commas should never have a space before.**
```r
        paste("msms", sample_size, cmd[ , 1], cmd[ , 2])
                                                  ~^
```
[R/simulator_msms.R:138:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_msms.R#L138) *warning:* **no visible global function definition for ‘register_simulator’**
```r
  register_simulator(msms_class$new(jar, java, priority))
  ^~~~~~~~~~~~~~~~~~
```
[R/simulator_msms.R:138:22:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_msms.R#L138) *warning:* **no visible binding for global variable ‘msms_class’**
```r
  register_simulator(msms_class$new(jar, java, priority))
                     ^~~~~~~~~~
```
[R/simulator_ms.R:86:39:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_ms.R#L86) *style:* **Commas should never have a space before.**
```r
        paste("ms", sample_size, cmd[ , 1], cmd[ , 2])
                                     ~^
```
[R/simulator_ms.R:86:50:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_ms.R#L86) *style:* **Commas should never have a space before.**
```r
        paste("ms", sample_size, cmd[ , 1], cmd[ , 2])
                                                ~^
```
[R/simulator_ms.R:127:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_ms.R#L127) *warning:* **no visible global function definition for ‘register_simulator’**
```r
  register_simulator(ms_class$new(priority))
  ^~~~~~~~~~~~~~~~~~
```
[R/simulator_ms.R:127:22:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_ms.R#L127) *warning:* **no visible binding for global variable ‘ms_class’**
```r
  register_simulator(ms_class$new(priority))
                     ^~~~~~~~
```
[R/simulator_scrm.R:11:10:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_scrm.R#L11) *warning:* **no visible global function definition for ‘read_cache’**
```r
  cmd <- read_cache(model, "scrm_cmd")
         ^~~~~~~~~~
```
[R/simulator_scrm.R:17:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_scrm.R#L17) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "scrm_cmd", cmd)
    ^~~~~
```
[R/simulator_scrm.R:84:41:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_scrm.R#L84) *style:* **Commas should never have a space before.**
```r
        paste("scrm", sample_size, cmd[ , 1], cmd[ , 2])
                                       ~^
```
[R/simulator_scrm.R:84:52:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_scrm.R#L84) *style:* **Commas should never have a space before.**
```r
        paste("scrm", sample_size, cmd[ , 1], cmd[ , 2])
                                                  ~^
```
[R/simulator_seqgen.R:5:17:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L5) *warning:* **no visible global function definition for ‘read_cache’**
```r
  tree_model <- read_cache(model, "tree_model")
                ^~~~~~~~~~
```
[R/simulator_seqgen.R:20:29:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L20) *warning:* **no visible global function definition for ‘create_sumstat_container’**
```r
    tree_model$sum_stats <- create_sumstat_container()
                            ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulator_seqgen.R:21:32:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L21) *warning:* **no visible global function definition for ‘sumstat_sg_trees’**
```r
    tree_model <- tree_model + sumstat_sg_trees()
                               ^~~~~~~~~~~~~~~~
```
[R/simulator_seqgen.R:23:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L23) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "tree_model", tree_model)
    ^~~~~
```
[R/simulator_seqgen.R:47:20:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L47) *warning:* **no visible global function definition for ‘get_locus_length’**
```r
  locus_lengths <- get_locus_length(model, group = locus, total = FALSE)
                   ^~~~~~~~~~~~~~~~
```
[R/simulator_seqgen.R:53:10:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L53) *warning:* **no visible global function definition for ‘sg_generate_opt_cmd’**
```r
  cmd <- sg_generate_opt_cmd(model)
         ^~~~~~~~~~~~~~~~~~~
```
[R/simulator_seqgen.R:67:10:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L67) *warning:* **no visible global function definition for ‘read_cache’**
```r
  cmd <- read_cache(model, "seqgen_cmd")
         ^~~~~~~~~~
```
[R/simulator_seqgen.R:80:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L80) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "seqgen_cmd", cmd)
    ^~~~~
```
[R/simulator_seqgen.R:215:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L215) *warning:* **no visible global function definition for ‘register_simulator’**
```r
  register_simulator(seqgen_class$new(binary, priority))
  ^~~~~~~~~~~~~~~~~~
```
[R/simulator_seqgen.R:215:22:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/simulator_seqgen.R#L215) *warning:* **no visible binding for global variable ‘seqgen_class’**
```r
  register_simulator(seqgen_class$new(binary, priority))
                     ^~~~~~~~~~~~
```
[R/sumstat_dna.R:24:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_dna.R#L24) *warning:* **no visible binding for global variable ‘stat_dna_class’**
```r
  stat_dna_class$new(name, transformation)
  ^~~~~~~~~~~~~~
```
[R/sumstat_file.R:28:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_file.R#L28) *warning:* **no visible binding for global variable ‘stat_file_class’**
```r
  stat_file_class$new(folder)
  ^~~~~~~~~~~~~~~
```
[R/sumstat_four_gamete.R:69:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_four_gamete.R#L69) *warning:* **no visible binding for global variable ‘stat_four_gamete_class’**
```r
  stat_four_gamete_class$new(name, population, transformation)
  ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat_ihh.R:53:45:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_ihh.R#L53) *style:* **Commas should never have a space before.**
```r
                      iHS = data.frame(ihh[ , 1:2], iHS = rep(NA, n_snps))))
                                           ~^
```
[R/sumstat_ihh.R:61:55:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_ihh.R#L61) *style:* **Commas should never have a space before.**
```r
            data.frame(ihh2ihs(ihh, freqbin)$res.ihs[ , -4])
                                                     ~^
```
[R/sumstat_ihh.R:141:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_ihh.R#L141) *warning:* **no visible binding for global variable ‘stat_ihh_class’**
```r
  stat_ihh_class$new(name, population, max_snps, calc_ihs, transformation)
  ^~~~~~~~~~~~~~
```
[R/sumstat_jsfs.R:54:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_jsfs.R#L54) *warning:* **no visible binding for global variable ‘stat_jsfs_class’**
```r
  stat_jsfs_class$new(name, populations, per_locus, transformation)
  ^~~~~~~~~~~~~~~
```
[R/sumstat_mcmf.R:35:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_mcmf.R#L35) *warning:* **no visible binding for global variable ‘stat_mcmf_class’**
```r
  stat_mcmf_class$new(name, population, transformation)
  ^~~~~~~~~~~~~~~
```
[R/sumstat_nucleotide_div.R:45:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_nucleotide_div.R#L45) *warning:* **no visible binding for global variable ‘stat_pi_class’**
```r
  stat_pi_class$new(name, population, transformation)
  ^~~~~~~~~~~~~
```
[R/sumstat_omega.R:146:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_omega.R#L146) *warning:* **no visible binding for global variable ‘stat_omega_class’**
```r
  stat_omega_class$new(name, min_win, max_win, grid, binary, transformation)
  ^~~~~~~~~~~~~~~~
```
[R/sumstat_omega.R:150:12:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_omega.R#L150) *warning:* **no visible global function definition for ‘search_executable’**
```r
  !is.null(search_executable("OmegaPlus", envir_var = "OMEGAPLUS"))
           ^~~~~~~~~~~~~~~~~
```
[R/sumstat.R:69:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L69) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/sumstat.R:85:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L85) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.model(model))
  ^~~~~~~~~~~
```
[R/sumstat.R:85:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L85) *warning:* **no visible global function definition for ‘is.model’**
```r
  assert_that(is.model(model))
              ^~~~~~~~
```
[R/sumstat.R:87:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L87) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(!is.null(segsites_list))
    ^~~~~~~~~~~
```
[R/sumstat.R:88:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L88) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(all(vapply(segsites_list, is_segsites, logical(1))))
    ^~~~~~~~~~~
```
[R/sumstat.R:88:43:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L88) *warning:* **no visible binding for global variable ‘is_segsites’**
```r
    assert_that(all(vapply(segsites_list, is_segsites, logical(1))))
                                          ^~~~~~~~~~~
```
[R/sumstat.R:91:24:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L91) *warning:* **no visible global function definition for ‘remove_singletons’**
```r
      segsites_list <- remove_singletons(segsites_list)
                       ^~~~~~~~~~~~~~~~~
```
[R/sumstat.R:94:7:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L94) *warning:* **no visible global function definition for ‘requires_trees’**
```r
  if (requires_trees(model)) assert_that(!is.null(trees))
      ^~~~~~~~~~~~~~
```
[R/sumstat.R:94:30:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L94) *warning:* **no visible global function definition for ‘assert_that’**
```r
  if (requires_trees(model)) assert_that(!is.null(trees))
                             ^~~~~~~~~~~
```
[R/sumstat.R:95:7:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L95) *warning:* **no visible global function definition for ‘requires_files’**
```r
  if (requires_files(model)) assert_that(!is.null(files))
      ^~~~~~~~~~~~~~
```
[R/sumstat.R:95:30:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L95) *warning:* **no visible global function definition for ‘assert_that’**
```r
  if (requires_files(model)) assert_that(!is.null(files))
                             ^~~~~~~~~~~
```
[R/sumstat.R:109:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L109) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.model(model))
  ^~~~~~~~~~~
```
[R/sumstat.R:109:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L109) *warning:* **no visible global function definition for ‘is.model’**
```r
  assert_that(is.model(model))
              ^~~~~~~~
```
[R/sumstat.R:118:20:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L118) *warning:* **no visible global function definition for ‘conv_for_trios’**
```r
      seg_sites <- conv_for_trios(seg_sites, model)
                   ^~~~~~~~~~~~~~
```
[R/sumstat.R:163:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L163) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.model(model))
  ^~~~~~~~~~~
```
[R/sumstat.R:163:15:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L163) *warning:* **no visible global function definition for ‘is.model’**
```r
  assert_that(is.model(model))
              ^~~~~~~~
```
[R/sumstat.R:166:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L166) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is.list(trios))
    ^~~~~~~~~~~
```
[R/sumstat.R:167:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L167) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(!is.null(segsites_list))
    ^~~~~~~~~~~
```
[R/sumstat.R:173:7:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L173) *warning:* **no visible global function definition for ‘assert_that’**
```r
      assert_that(is.numeric(trio))
      ^~~~~~~~~~~
```
[R/sumstat.R:175:7:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L175) *warning:* **no visible global function definition for ‘assert_that’**
```r
      assert_that(length(trio) == 3)
      ^~~~~~~~~~~
```
[R/sumstat.R:183:22:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L183) *warning:* **no visible global function definition for ‘as.segsites’**
```r
    segsites_list <- as.segsites(segsites_list, ...)
                     ^~~~~~~~~~~
```
[R/sumstat.R:187:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L187) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(length(segsites_list) == get_locus_number(model))
    ^~~~~~~~~~~
```
[R/sumstat.R:187:42:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L187) *warning:* **no visible global function definition for ‘get_locus_number’**
```r
    assert_that(length(segsites_list) == get_locus_number(model))
                                         ^~~~~~~~~~~~~~~~
```
[R/sumstat.R:196:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L196) *warning:* **no visible global function definition for ‘calc_sumstats’**
```r
  calc_sumstats(model, segsites_list, tree_list)
  ^~~~~~~~~~~~~
```
[R/sumstat.R:201:14:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L201) *warning:* **no visible global function definition for ‘get_summary_statistics’**
```r
  any(sapply(get_summary_statistics(model), function(x) x$requires_segsites()))
             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat.R:206:14:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L206) *warning:* **no visible global function definition for ‘get_summary_statistics’**
```r
  any(sapply(get_summary_statistics(model), function(x) x$requires_trees()))
             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat.R:211:14:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat.R#L211) *warning:* **no visible global function definition for ‘get_summary_statistics’**
```r
  any(sapply(get_summary_statistics(model), function(x) x$requires_files()))
             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat_seg_sites.R:20:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_seg_sites.R#L20) *warning:* **no visible binding for global variable ‘stat_segsites_class’**
```r
  stat_segsites_class$new(name, transformation)
  ^~~~~~~~~~~~~~~~~~~
```
[R/sumstat_seg_sites.R:26:21:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_seg_sites.R#L26) *warning:* **no visible global function definition for ‘get_locus_length’**
```r
    locus_length <- get_locus_length(model, i, total = FALSE)
                    ^~~~~~~~~~~~~~~~
```
[R/sumstat_seg_sites.R:32:12:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_seg_sites.R#L32) *warning:* **no visible global function definition for ‘get_positions’**
```r
    pos <- get_positions(seg_sites[[i]])
           ^~~~~~~~~~~~~
```
[R/sumstat_seg_sites.R:41:38:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_seg_sites.R#L41) *style:* **Commas should never have a space before.**
```r
    trio_segsites <- seg_sites[[i]][ , left | middle | right]
                                    ~^
```
[R/sumstat_seg_sites.R:50:5:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_seg_sites.R#L50) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(nrow(seg_sites[[i]]) > 0)
    ^~~~~~~~~~~
```
[R/sumstat_sfs.R:35:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_sfs.R#L35) *warning:* **no visible binding for global variable ‘stat_sfs_class’**
```r
  stat_sfs_class$new(name, population, transformation)
  ^~~~~~~~~~~~~~
```
[R/sumstat_tajimas_d.R:56:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_tajimas_d.R#L56) *warning:* **no visible binding for global variable ‘stat_tajimas_d_class’**
```r
  stat_tajimas_d_class$new(name, population, transformation)
  ^~~~~~~~~~~~~~~~~~~~
```
[R/sumstat_trees.R:20:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_trees.R#L20) *warning:* **no visible binding for global variable ‘stat_trees_class’**
```r
  stat_trees_class$new(name, identity)
  ^~~~~~~~~~~~~~~~
```
[R/sumstat_trees.R:49:3:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/R/sumstat_trees.R#L49) *warning:* **no visible binding for global variable ‘stat_sg_trees_class’**
```r
  stat_sg_trees_class$new("trees", identity)
  ^~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-feature-ign-singletons.R:13:45:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-feature-ign-singletons.R#L13) *style:* **Commas should never have a space before.**
```r
               list(create_test_segsites()[ , -c(1, 3)],
                                           ~^
```
[tests/testthat/test-feature-ign-singletons.R:14:45:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-feature-ign-singletons.R#L14) *style:* **Commas should never have a space before.**
```r
                    create_test_segsites()[ , -c(1, 3)]))
                                           ~^
```
[tests/testthat/test-model-class.R:241:44:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-model-class.R#L241) *style:* **Commas should always have a space after.**
```r
               data.frame(name = c("theta","tau"),
                                           ^
```
[tests/testthat/test-segsites-class.R:30:31:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-segsites-class.R#L30) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  segsites <- create_segsites((matrix(c(1, 1, 0, 1, 1,
                              ^
```
[tests/testthat/test-segsites-class.R:36:26:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-segsites-class.R#L36) *style:* **Commas should never have a space before.**
```r
  ss_subset <- segsites[ , 1:2]
                        ~^
```
[tests/testthat/test-segsites-class.R:38:64:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-segsites-class.R#L38) *style:* **Commas should never have a space before.**
```r
  expect_equivalent(as.matrix(ss_subset), as.matrix(segsites)[ , 1:2])
                                                              ~^
```
[tests/testthat/test-segsites-class.R:41:30:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-segsites-class.R#L41) *style:* **Commas should never have a space before.**
```r
  expect_equal(dim(segsites[ , 1]), c(3, 1))
                            ~^
```
[tests/testthat/test-segsites-class.R:42:33:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-segsites-class.R#L42) *style:* **Commas should never have a space before.**
```r
  expect_equal(dim(segsites[1:2 , ]), c(2, 3))
                               ~^
```
[tests/testthat/test-segsites-class.R:43:32:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-segsites-class.R#L43) *style:* **Commas should never have a space before.**
```r
  expect_equal(dim(segsites[-2 , 1:3]), c(2, 2))
                              ~^
```
[tests/testthat/test-simulator-seqgen.R:274:27:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-simulator-seqgen.R#L274) *style:* **Commas should always have a space after.**
```r
  model <- coal_model(c(5,5,2), 1, 100) +
                          ^
```
[tests/testthat/test-simulator-seqgen.R:274:29:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-simulator-seqgen.R#L274) *style:* **Commas should always have a space after.**
```r
  model <- coal_model(c(5,5,2), 1, 100) +
                            ^
```
[tests/testthat/test-sumstat-jsfs.R:10:60:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-sumstat-jsfs.R#L10) *style:* **Commas should never have a space before.**
```r
                                                   1, 0, 1 ,0 ),
                                                          ~^
```
[tests/testthat/test-sumstat-jsfs.R:10:61:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-sumstat-jsfs.R#L10) *style:* **Commas should always have a space after.**
```r
                                                   1, 0, 1 ,0 ),
                                                            ^
```
[tests/testthat/test-sumstat-jsfs.R:11:54:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-sumstat-jsfs.R#L11) *style:* **Put spaces around all infix operators.**
```r
                                                 nrow=7, ncol=4, byrow = TRUE),
                                                    ~^~
```
[tests/testthat/test-sumstat-jsfs.R:11:62:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-sumstat-jsfs.R#L11) *style:* **Put spaces around all infix operators.**
```r
                                                 nrow=7, ncol=4, byrow = TRUE),
                                                            ~^~
```
[tests/testthat/test-sumstat-jsfs.R:19:42:](https://github.com/statgenlmu/coala/blob/379703864fbb42a0223f6113730d22d2c77ff56c/tests/testthat/test-sumstat-jsfs.R#L19) *style:* **Put spaces around all infix operators.**
```r
                                      dim=c(2, 2, 3) + 1))
                                        ~^~
```


Для ссылки, необходимо сделать отдельный блок, т.к. когда пользователь будет залогинен, будет отображаться другое содержимое (в теории). Ну и капс соответственно.


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 13173](https://teamcity.mesosphere.io/viewLog.html?buildId=115509&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 216 Build time: 00:09:09


v(Danilo) = DAMN FAST


godoc, I need to look in the code to know what that bool in return means.


Shall I remove this commit in general? Because it has no use?


Ich find, daß Beleuchtungsrichtung nicht korrekt ist, weil ein Punktlicht 360 Grad strahlt, da gibt es keine Richtung. Die Betrachungsrichtung spielt auch keine Rolle, wenn die Kamera die Position nicht verändert.
Der erste Satz ist zwar trocken, aber nicht falsch, oder? Daher fand ich den zweiten Satz als Ergänzung OK.


dhhghfgh


Part of the reason it is async currently is that the next chunk to add is a Logger that then takes the fixed chains and logs them to one of the CT logs.  It reads the fixed chains from the chains channel, so it can begin logging chains as soon as the first ones have been fixed and put on the channel, rather than having to wait until all of the chains have been fixed by the Fixer before beginning its work.  Similarly for the ErrorHandler piece.

The caller would then do something like,

f := NewFixer(... chains chan ...)
l := NewLogger(... chains chan ...)
f.QueueChains(chains)  // Admittedly this function could have a better name for the API
f.Wait()
l.Wait()


@saper actually this looks unrelated. Even rebuilding the previous release does not produce the artefacts. Something may have changed on appveyors side.


well you don't want to do other versions yourself since Git does it for you. If you just keep the file the same name then every commit becomes its own version and you can go back and view it or revert back to it.


Bad function name. Use please Google Coding Style.


This would match "Afternoon" which is a legitimate type of tea, so I can't accept this as is, sorry.


Compass is effectively EOL at this point While i am/was one of the core maintainers its up to @chriseppstein  ultimently what happens with a release. I highly suggest moving to the eyeglass-sass project if you can.


Yes, LGTM.  (Though honestly, why are we rewriting this in go instead of binding `sd_journal_sendv`?  Since this was written `memfd()` has been introduced, which is more secure and faster than tmpfiles for example...)


Ah, I hadn't spotted the /i.


Can be const here.


May be const?


No camel case? :/


Actually, I feel this was a very sloppy implementation. I'll try to get
together something better for the weekend.

On Thursday, 28 January 2016, Dave Doolin <notifications@github.com> wrote:

> Good idea!
>
> I'll take a look at it this weekend, super swamped at work right now.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/chamini2/latexcolor.com/commit/31759e572a852f90715592fa798833730ed41e4a#commitcomment-15733313>
> .
>


How about merging the two methods (`HasTag...` and `SetTag...`) in such a way that it sets it when it doesn't find one?


No. I mean that any npm-script that is executing `node <js-script>` could be changed to simply `<js-script>` if the node shebang were added to the js-script.

Example:
```json
"build:fp": "node lib/fp/build-dist.js"
```

If the node shebang were added to `lib/fp/build-dist.js` like so:

```
#! /usr/bin/env node
'use strict';

var _ = require('lodash'),
    async = require('async'),
    path = require('path'),
    webpack = require('webpack');

var minify = require('../common/minify.js');
// ...
```

This would allow the `lib/fp/build-dist.js` script to be executed directly, without needing to invoke node. It would slightly simplify the npm-scripts. But more importantly, it makes it easier to invoke executable scripts from the command line and follows standard practice whereby executable scripts can be executed directly (ala binaries).

Taken a step further, the executable js scripts could be added to `bin` so that consumers of lodash can execute them (since they would be given a symlink into `./node_modules/.bin`) but that depends on which, if any, of the scripts would make sense to be executed by a user.


it would probably be easier to use a locale, perhaps?


OK, done.


No problem. Mistakes happen


Those lines are not even necessary, because this is already the Horde\ManageSieve\Exception namespace.


But it's a really nice feature, in priniciple :)


May be use MakeShared?


I didn't realize you've done this already.


Ich find, daß Beleuchtungsrichtung nicht korrekt ist, weil ein Punktlicht 360 Grad strahlt, da gibt es keine Richtung. Die Betrachungsrichtung spielt auch keine Rolle, wenn die Kamera die Position nicht verändert.
Der erste Satz ist zwar trocken, aber nicht falsch, oder? Daher fand ich den zweiten Satz als Ergänzung OK


Быстро, круто, дорого - не заголовки, так как не несут смысловой нагрузки.
в вебинаре про это говорилось. как вариант - <b></b>


That missing `@` is probably on every active branch.


I've noticed that some of these were hanging so I'm happy for this increase to be made.


I dunno about this one, I think I need a second Thumbs Up on this.  :P


выноси input


Это ссылки, по которым осуществляется переход на детализацию новости. Так же их можно обернуть в заголовок, к примеру

.


# Assignment 3 Grading Rubric (15 points total)

## Task Set 1

- [ ] Regex matches entire dinucleotide repeat (AT)5 and only the repeat (1 pt)
- [ ] Regex matches entire dinucleotide repeat (AT)5, only the repeat, and is different from above (1 pt)
- [ ] Regex matches entire dinucleotide repeat (AT)5, only the repeat, and is different both above (1 pt)
- [ ] Regex correctly matches all instances of `R` or `S` (1 pt)
- [ ] Regex (find and replace) matches all instances of `R` or `S` and replaces them with `N` (1 pt)

## Task Set 2

- [ ] Regex (find and replace) correctly reverses the order of the columns from 1,2,3,4 (as you see them) to 4,3,2,1 (1 pt)
- [ ] Regex (find and replace) correctly reverses the order of the columns from 1,2,3,4 (as you see them) to 1,2,4,3 (1 pt)
- [ ] Regex (find and replace) correctly replaces commas with tabs (1 pt)
- [ ] Regex (find and replace) correctly gives us the horrible format requested (1 pt)

## Task Set 3

- [ ] Regex (find and replace) correctly parses out only the lane number from the header (1 pt)
- [ ] Regex (find and replace) correctly parses out only the flowcell ID from the header (1 pt)
- [ ] Regex (find and replace) correctly parses any flowcell ID from the header (1 pt)

## Task Set 4

- [ ] Regex (find and replace) correctly extracts only the serial number from the fastq sequence (1 pt)
- [ ] Regex (find and replace) correctly turns the fastq into a fasta having the requested format (2 pt)

## Task Set 5

- [ ] Regex (find and replace) correctly extracts the (AT)5 repeat (Regex bliss)


это одна форма


Потерялись контролы
![2016-01-28 03-36-47 nerds-catalog-1000 jpg 1000x1872](https://cloud.githubusercontent.com/assets/8250032/12646764/2769906c-c5fc-11e5-8b58-77482174b275.png)


endl; 뉴라인 안해도 되남 ㅎㅎㅎ


```expect(response).to redirect_to article_path(I18N.t('baby-costs-calculator'), locale: locale)```

```
#config/locales/en.yml
en:
    baby_cost_calculator:
        title: baby-costs-calculator
```

```
#config/locales/cy.yml
cy:
    baby_cost_calculator:
        title: cyfrifiannell-costau-babi
```


Maybe add a test for object as well?


= null for $name and $route is missing


:+1: ;-)


Please use your real name


все заголовки лучше объединить в отдельный класс, с заданными стилями отображения.
чтобы не привязываться каждый раз каскадом к тегу <h2>, который кстати может им и не быть, как в случае "Быстро круто дорого"


Thanks!


There's quite a bit of logic in this file but not even a single test, which worries me a lot if any changes will be needed here.


это не картинки, тут целый блок, который состоит из картинки, а при наведении будет показываться блок, в котором есть название, описание и цена.


@fazibear I think it would be good to keep a ref to the original lib for both credits and documentation (btw inesita is great!)


Const?


this is dicom parse class


Remove the constructor if nothing happens here


Using QGIS 2.12.3 (Win64bit) with contextual WMS-legends doesn't work!
The WMS-Counterpart is a patched UMNMapserver 7.0 - Examples:

Standard-Legend:
http://geodaten.metropoleruhr.de/spw/spw_web?language=ger&SERVICE=WMS&VERSION=1.3.0&SLD_VERSION=1.1.0&REQUEST=GetLegendGraphic&FORMAT=image/png&LAYER=oepnv_linien&STYLE=

Contextual-Legend (working):
http://geodaten.metropoleruhr.de/spw/spw_web?language=ger&SERVICE=WMS&VERSION=1.3.0&SLD_VERSION=1.1.0&REQUEST=GetLegendGraphic&FORMAT=image/png&LAYER=oepnv_linien&STYLE=&BBOX=361299.31917663925560191,5701245.71691642235964537,362276.95459430309711024,5701856.90441704634577036&CRS=EPSG:25832&WIDTH=148&HEIGHT=925

QGIS sends following Request with Contextual-Legends checked (grabbed from Apache-log) - non-working:
http://geodaten.metropoleruhr.de/spw/spw_web?language=ger&&SERVICE=WMS&VERSION=1.3.0&SLD_VERSION=1.1.0&REQUEST=GetLegendGraphic&FORMAT=image/png&LAYER=oepnv_linien&STYLE=&BBOX=300000,5620000,440000,5770000&CRS=EPSG:25832

In order to work well in UMN-mapserver-logic, QGIS needs to send one more parameter-set (WIDTH and HEIGHT of the mapcanvas in px).

http://www.mapserver.org/de/development/rfc/ms-rfc-101.html

Moreover the BBOX seems to be wrong, IMHO this should be an dynamic parameter in getlegend-requests, whether the one QGIS seems to be static! In my last example the requests BBOX is the mapextent from the service.
Please Review the function. THX


куда ссылки потерялись?


Good call


h1 заголовок на странице должен быть один.


Please rename to $message


Wow, I didn't know Safari was crashing :(

I just pushed a fix. Basically I stop the element as in `someAudioElement.pause()` and I also disconnect the source `source.disconnect()`.

It seems to have stopped crashing. Pushed it live to vertexshaderart.com if you want to test it


ju is retarded
now ju is abe to report mi coment


Hey @josephsavona what was the exact conflict?


@Volpey check this out, bitch!


It makes no difference since packagist ignores the state of any aliases in tags and exclusively looks at the current "default" branch for alias information.


I think this was never used


Please take out my email address from the travis notifications. Thanks.


Yes, of course it would be really simpler if everybody in python's community would have switched to Python 3 now :p ! But we still have to maintain support for Python 2, and I've make the choice to use only native string in guessit and rebulk codebase.

If user doesn't provide native str type to guessit api, it will be converted for guessit internals, but response will also be converted back for the user to retrieve the same type as the input.

So from guessit point of view, we always deal with native strings, and for user point of view, input type is always the same as output type. (give unicode, it will reply unicode, give str it will reply str)


Why we need to add **id** to this element?  Where we can use it?
Can we use  `ng-init="showIDE=false"`   instead of `angular.element('#codenvyleftmenu').hide();`  in LoadFactoryCtrl  constructor?


Newline between @param and @return


может логичнее назвать "gallery-img/gallery-picture"


Here's the change. Probably not helpful but you can at least see what I did

https://github.com/greggman/vertexshaderart/commit/edde8c892612be5d8959623ea1bc4b0cfbec7ad6


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 13179](https://teamcity.mesosphere.io/viewLog.html?buildId=115532&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 174 Build time: 00:06:56


トールハンマー！


Revert this -.-


Please use single quote over double quote all over the place


s/background/peridicalController


MCPE has differrent network ID!!!


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 13178](https://teamcity.mesosphere.io/viewLog.html?buildId=115525&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 214 Build time: 00:08:06


Ignore the stylesheet changes for the count types, was starting to change the colors but did not complete this task. Still need to find a workable color palette.


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 13175](https://teamcity.mesosphere.io/viewLog.html?buildId=115523&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 216 Build time: 00:08:10


True does nothing. Please remove it.


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 13177](https://teamcity.mesosphere.io/viewLog.html?buildId=115526&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 216 Build time: 00:08:20


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 13174](https://teamcity.mesosphere.io/viewLog.html?buildId=115524&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 214 Build time: 00:08:25


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 13176](https://teamcity.mesosphere.io/viewLog.html?buildId=115531&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 216 Build time: 00:08:24


Please use a /* html element */ comment block similar to other classes


Why?


initializeConnections() may call shutdown() pls guard houseKeepingExecutorService there


Please lowercase comments


Updated. Added a unit test to confirm we can associate comments with a child of a heredoc.


Please use tabs over spaces all over the place


@unho right, I don't know why I wrote it like that.


That's basically what I was looking for :)


Again not scheduled, it's periodical or whatever else you choose. Scheduled implies a schedule which is not provided here.


@roccomuso why the onClose event can't work with htmlAllowed = true?


.travis.yml file grew too big. Create shell script files to name stuff and call them from here.


Just check for if ($title)


Thanks for the additional clarification.


Cherry-picking with manual conflict resolution should preserve authorship, I think. Anyway, I suppose it's just a nitpick (as there's no evidence of you doing it regularly :).


Rename to messengerStart and messengerEnd


Не нашёл, где ещё к вам обратиться. Ишью-трекера у вас нет на репозитории. При нажатии на "dt-show_skill_tree" в консоль падает ошибка "TypeError: duo[jl[725]] is not a function(…)" и ничего не происходит


Based on my research it could work but I'm not sure


Ok, should be in a new commit: _Introduce ObjectMapperFactory_


That would be cool.

I'm not personally a big fan of tabs, and I do like tests, but I'm not enough of a js person to make a big deal about it if everything works.


container - это класс с клеарфиксом я так понимаю?


Beta v0.1 complete


title не указал


I used a website to find the way to get a file writter


лучше избегать магических чисел типа 1,2,3 и использовать Enum или String в таких случаях.


Think about returning const reference instead of value. Within tests context it will be ok.


At this point I ask myself why we need $this->_message and $this->_title etc. because there is not need to pass it to another method for later use


- [ ] 書くステップに `<!-- (4) -->` と各のは冗長なので、`<entry>` タグの上に一つ書くようにしましょう。


#17 closed


So Logger would read and Fixer would write, to this chains chan?

Is the problem with:

```
f := NewFixer()
for t := range inputs {
  t := t
  go func() {
    r, err := f.Fix(t)
    …
    Log(r)
  }()
}

```
that it would create too many goroutines?

If it's goroutine management then that should be broken out, e.g.:

```
var wg sync.WaitGroup
for i := 0; i < 10; i++ {
  wg.Add(1)
  go func() {
    defer wg.Done()
    for order := range inCh {
      res, err := f.Fix(in)
      …
      Log(res)
    }
  }()
}
… add orders to inCh …
wg.Wait()
```

Mixing concurrency management and application logic makes it harder to test and reason about.


-I want to leave a response to a few things on Task 4.  Appears Amie is correct on Task 4 Part 1. Somehow when I copied it over I added an extra ) before the .{6}  so it reads """@().{6})(:.*)([^\n]*\n+)+(\d*)([^\n]*\n+)+(.*)""" instead of """@(.{6})(:.*)([^\n]*\n+)+(\d*)([^\n]*\n+)+(.*)""" like it should. If that ) is removed then it works perfectly.
- Task 4 Part 2 however works just fine for me.  I checked again this morning. I will attach to screen shots showing that it works. Not sure if its just that we have different computers?
![proof of task 4 part 2 1](https://cloud.githubusercontent.com/assets/16652287/12647089/1a974c0c-c599-11e5-8e55-cd00f58aba23.PNG)
![proof of task 4 part 2 2](https://cloud.githubusercontent.com/assets/16652287/12647088/1a961ed6-c599-11e5-92b5-56e8b281b616.PNG)


@n1k0 @almet @natim @leplatrem : is this the correct way to do it?


XDDDDDDDDDDDDDDDDDDDDDDDDD


Some comment


что за имя переменной ru?


Yeah, would be nice. Think I won't spend more time on this since it seems we may stop using this in a matter of months.


I don’t think it would add any additional coverage, and we don’t want to test `ops.get` here.


`READREGISTER` => `READ`


You should probably `append` here also!


Looks good :)


Did this give you more information?


I'd probably check this error with `os.IsNotExist` before printing that the file doesn't exist. If it's not a "not exist" error, I'd log it with `log.Printf`. Also, I'd probably not log anything if the file doesn't exist since it will get noisy.


This shouldnt be needed provided CMake is in path it should already find all other components.


@fredgibbs @jacobwgreene  I fixed some errors that were causing the site to fail. There's now a live preview of this lesson:

http://programminghistorian.github.io/ph-submissions/lessons/intro-to-ar-development

You should be ready to create an issue for the lesson now, including that link so reviewers can easily find it. I changed the lesson slug to make it shorter, but feel free to change back.


What is your problem with barry_allen? I may be able to assist you


This explanation needs improvement


используй локализацию, никакого голого текста в коде


While working adding unit test, I came across a difference in water reference temperature used to calculated hot water density.  In the Unit Heater parent object, the design hot water vol flow rate is calculated at 60.0C, just like the hot water Cp, but ReportSizingOutput uses , 5.05 C as the reference water temperature.  And this difference in temperature leads to slight change of water mass flow rate and design coil capacity.  This brings about 1.7% difference between the Design Coil Load and the Design Coil Capacity.  Shouldn't we use consistent reference temperature for sizing calculation? I went ahead checked FanCoil and Unit Ventilator objects and found out the same issue.

I am assuming that 5.05C is the reference temperature for water volume flow rate calculation. Shall I change reference water temperature used to calculated water density from 60.0C to 5.05C in the UnitHeater parent object design hot water vol flow rate calculation? @mjwitte @rraustad @Myoldmopar


`up_vote.js.erb` and `down_vote.js.erb` are identical. What changes would you make so that you can use only one file?


- [ ] CSRFトークンチェックエラー時**の**遷移先を制御したい場合は、以下のような設定を行う。（以下の定義例は、ブランクプロジェクトからの抜粋である）


I have this in my Onyx repo


Use sandbox


`expensiveCheckFn.assign = expensiveChecksInterceptor(fn.assign)` is done so `.assign` has the `try...catch`. The execution of the function is fine


Take a look at `bufio.ScanLines`


Please retain authorship on your commits


also, better would be to move fillpool() **from** initializeConnections() **after** initializing houseKeepingExecutorService now.
and probably rename initializeConnections() to failFast() or something.


используй logger  для таких целей


Shouldn’t, `exec` returns buffers and not streams as I initially expected…

```js
var child = exec('....', (err) => { /* ... */ });

child.stderr.pipe(process.stderr);
child.stdout.pipe(process.stdout);
```


- Make this user definable
- use to compute sensitivity?


For what is that patch? For me is sound also working without this...


yeah, I was about to change that, I was trying some other stuff on the Gradle side for a change... with no luck :(


или выноси в именованные переменные


Yeah mostly as an FYI in case you hadn't noticed or were using some
automated process that lost authorship more often
On Thu, Jan 28, 2016 at 09:26 Vladimír Čunát <notifications@github.com>
wrote:

> Cherry-picking with manual conflict resolution should preserve authorship,
> I think. Anyway, I suppose it's just a nitpick (as there's no evidence of
> you doing it regularly :).
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/NixOS/nixpkgs/commit/109ba4c86166f9b7aa31ba45869ee93b0eecb2e0#commitcomment-15733946>
> .
>


@yoojinkimhong DWMR. Good good. Keep pressing ahead!


#181还是不能访问谷歌！请检查！


If you're going to use regexes here, how about a regex matches the whole line and captures the submatch with `regexp.FindSubmatchIndex`.

Also, my cgroup file has `/docker/<CONTAINER ID>`, so I'm not sure that `/docker-` will match correctly in all cases.

Here's the format I see:

```


@unho : https://github.com/asyschikov/translate/commit/38240ac0fd0355c7e143e61dfacba223311d0801


And weirdly if I look up I think Task 4 part 1 may have been an accidental change because it was added in my last commit. You can see where the original I had was changed in this photo. Green is added, red is deleted. Not sure what happened here! So complicated.
![task 4 info](https://cloud.githubusercontent.com/assets/16652287/12647239/d6244b46-c599-11e5-8c42-f1d05183d6f9.PNG)


**[unitTests_php_branches run failed](http://qa-s2.wikia-prod:8080/job/unitTests_php_branches/26730/testReport/) for this commit**


:ok:


**[unitTests_php_branches run failed](http://qa-s2.wikia-prod:8080/job/unitTests_php_branches/26729/testReport/) for this commit**


OK


Thanks for your quick repsonse. I'm out of office right know. But disconnect() makes totally sense, I guess.
I'll have a look it when I'm back.


Assignment 1 Files


Copy-pasta: replace with appropriate data sheet links


Ok, will do in following tests.


@almet: this is the full code for the calendar application- that is functional


I should shut up, anyway. The `ChildProcess` returned by `exec` doesn’t have `stdout` and `stderr`.

Can you post the output of the whole `npm install`?


What about `makeblastdb`?

Also if you say that it's the same for all of them, let's set it in the `AnyBlastCommand` trait (for now), to reduce copy-paste risks


I would rather do:

authenticate()
   .then(function(headers) {
      return fetch(url, headers);
   });


This looks good to me. I'd probably try to add a test or two somehow. Perhaps split the parsing part into its own function and pass it a filename of a fixture file (or make the `func` take the file contents instead of a filename and test it by passing the expected contents).


@jtimon thoughts?
I wanted to play with local policy, but the `AcceptToMempool` function is **huge**,  figured this makes it more easily configurable.

I'll probably extract these to `policy/policy.*`,  but just as an idea,  think this could be merged?
Ping @luke-jr?

Should be mostly move-only.


It is instantiated in the FeatureSet class.


There's no notion of output record for `makeblastdb`.


I wondered the same, and I imagine what's passed in is some transformed version of the accept attribute value, but trying to set it directly resulted in a system dialogue saying something along the lines of "There are no applications servicing the requested type."


ack, lgtm


It will especially get noisy when `docker-gen` is run outside a container.


#1245

cicleci is faster than gitmate


This might cause this object to fail if somebody uses a custom executioner. In that case they'll receive your `mooseError()` so I guess we'll deal with it at that time, if that happens.


Are you referring to the README sentence: The onClose callback is not available using the HTML syntax.? or did you noticed any bug when htmlAllowed = true?


LGTM, thanks for catching & fixing! :+1:


обертку для попапа стоит сделать, иначе что ты будешь вызывать скриптом чтобы показать)


Could we use here the same message ?
"Change journal output mode (short, short-iso, short-precise, short-monotonic, verbose, export, json, json-pretty, json-sse, cat)"

We should output supported.formats


@leonardodistasio yay, c'est mieux ainsi avec `root "home#nomnomnom"`. Prenez juste un moment pour configurer votre éditeur pour avoir **2 espaces** partout et aucune tabulation.


@Natim : at each place where fetch is called?


why's that needed?


Ow :s I understand... But all the modules have an option in admin activate/desactivate...
that's what makes it "modular".
But on the external libraires point, I agree with you... why maintain it if it is done by others...
so sad it can't merge...


There's a little inconsistency between how `Add` and `Remove` works. Looking at this line I read: when adding new `key` remove *all* keys and only then add new one. But `Remove` specifically says: remove the key iff it has the same value. Why?


You and/or @carloslima might also want to look into [power_assert](https://github.com/ma2gedev/power_assert_ex).

Here's the output from a failing test:

```
 1) test single kelly (PainStakingTest)
     test/painstaking_test.exs:6
     Small bets for small edges

     kelly([small_edge]) == {:ok, [{"small edge", 1.01}]}
     |      |
     |      {"small edge", [prob: 0.55], [us: -120]}
     {:ok, [{"small edge", 1.0}]}
     stacktrace:
       test/painstaking_test.exs:13
```

Much more usable than the standard `ExUnit` version, in my opinion.

Also, sorry if dropping in like this is annoying.. just trying to help!


The it should have empty `ValidOutputFields`, no? When you write an expression you have to provide an output record for `makeblastdb` as well.


same as lines 139ff


OK


I think this should be called `CurrentContainerID` since is the the ID, not the name. The function below should be named accordingly.


обертка для попапа(здесь впринципы ей может быть "login-fom" с классом "Popup".


This hard reference is causing failure when running the runner on machine having only VS 2015


really?


тогда уж не login-form-container, а login-form-inner


= default


If this is for testing only, create a helper in tests and not a public method here.


Consistent with other methods.


Did github update the file on the pull request after I pushed it to my repository or do I have to do that manually?


@jtimon thoughts?
I wanted to play with local policy, but the `AcceptToMempool` function is **huge**,  figured this makes it more easily modifiable*.

I'll probably extract these to `policy/policy.*`,  but just as an idea,  think this could be merged?
Ping @luke-jr?

Should be equivalent to ~MOVE-ONLY.


Ahh, that's what custom means :-)

On Thu, Jan 28, 2016, 7:37 AM Cody Permann <notifications@github.com> wrote:

> This might cause this object to fail if somebody uses a custom
> executioner. In that case they'll receive your mooseError() so I guess
> we'll deal with it at that time, if that happens.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/dschwen/moose/commit/b0306ec28a314038318118d468187c9ecd5cf1da#commitcomment-15734233>
> .
>


# Assignment 3 Grading Rubric (15 points total)

## Task Set 1

- [ ] Regex matches entire dinucleotide repeat (AT)5 and only the repeat (1 pt)
- [ ] Regex matches entire dinucleotide repeat (AT)5, only the repeat, and is different from above (1 pt)
- [ ] Regex matches entire dinucleotide repeat (AT)5, only the repeat, and is different both above (1 pt)
- [ ] Regex correctly matches all instances of `R` or `S` (1 pt)
- [ ] Regex (find and replace) matches all instances of `R` or `S` and replaces them with `N` (1 pt)

## Task Set 2

- [ ] Regex (find and replace) correctly reverses the order of the columns from 1,2,3,4 (as you see them) to 4,3,2,1 (1 pt)
- [ ] Regex (find and replace) correctly reverses the order of the columns from 1,2,3,4 (as you see them) to 1,2,4,3 (1 pt)
- [ ] Regex (find and replace) correctly replaces commas with tabs (1 pt)
- [ ] Regex (find and replace) correctly gives us the horrible format requested (1 pt)

## Task Set 3

- [ ] Regex (find and replace) correctly parses out only the lane number from the header (1 pt)
- [ ] Regex (find and replace) correctly parses out only the flowcell ID from the header (1 pt)
- [ ] Regex (find and replace) correctly parses any flowcell ID from the header (1 pt)

## Task Set 4

- [ ] Regex (find and replace) correctly extracts only the serial number from the fastq sequence (1 pt)
- [ ] Regex (find and replace) correctly turns the fastq into a fasta having the requested format (2 pt)

## Task Set 5

- [ ] Regex (find and replace) correctly extracts the (AT)5 repeat (Regex bliss)


Ok


Shouldn't this be `>> 3`?


:bomb:


:ok:


I keep seeing this on my feature branches as well. Is it time to finally merge this to master? I have no idea what this is from.


See https://github.com/dcousens/bitcoin/commit/0f231a925c522bdb29627d2910ee59086b02599f instead


@aembler I needed this in order to be able to add a stack under a specific stack folder


PaperSpigotConfig?


Very good finally coming to an end!


@yihui It looks like the problem Jenny is observing originates somewhere in the generation of markdown by knitr. I can reproduce what she is seeing (an additional `<!-- -->` appended to the plot image) if I just do this:

```r
library(knitr)
opts_knit$set(rmarkdown.pandoc.to = "markdown_github")
knit("README.Rmd")
```


wouldn't it be simpler to just loop through the whole thing with a generator in the end removing empty lines?


Question:  Since this is dependent upon hash table...what size should this be tested with?  Is the default value 64, suitable?


I find the function name with no parameter for show and false for hide a bit confusing. Could we make two methods for `showToolbar()` and `hideToolbar()`?


Well not quite, at least not literally. You can ask the warehouse for the EXECUTE_ON group "custom" then do what you want with that group (like execute them at a special location). Yaqi uses that quite a bit in his Eigenvalue Executioner.


I think it would interfere. I know it's not good that services are using this in production, but I'm not convinced a message like that would help - and it's not that many services compared to the number of people using this for prototyping.

An alternative could be to have a splash page hidden by cookie, or something in `index.html`


- [ ] 「`<sec:access-denied-handler>` タグの`ref`属性に、Exception毎に遷移先を切り替える`AccessDeniedHandler`のBean名を指定する。」といった感じの方がよい。＋ ここでは `error-page`属性の話題は不要。


不能转发UDP吗？


I think the convention we've been using in Swift has been captial-cased like MaxNumberOfWebViews instead of the C-style MAX_NUMBER_OF_WEB_VIEWS.


[Glanzlicht und die Veränderung der Position](https://vid.me/fiPX)


`at` is wrong here, it suggests something happening *at* this position, whereas as you're actually doing increment/advancement. Only looking at parameter name you can know what's happening.


Ah ok sorry I misunderstood the message, I thought it was referring to the htmlAllowed feature, instead it's about the inability to assign a JS function trough HTML.

Nevermind then :)


I think we should raise this as a problem statement and discuss that.


You might want to just make this a mixin that uses a `collection` attribute from implementing classes.


Advance will be better, since you're using it in both directions +1 and -1 as well.


not sure...

If somebody passes the file content as lines without line breaks, all empty lines will be `""`. So I kinda wanted to remove them all in this case.


Since we're always setting the height to 0, even if we set the toolbar to visible, won't it still be hidden?


:shipit:


= default


=default


What is the meaning of returned values, explain in godoc, especially the bool at the end.


currently the selector buttons don't do anything - Show All, Lightning Talks, Large Demo
I'm pretty sure you already knew that but just checking. Let me know if you want me to merge it or if you want to hook those up first.


This would be better implemented as a mixin as well.


*nods* That's about the direction I'm heading; DRY cleanup needs doing.

Do you have any thoughts on how to get collection name automatically from the associated model? For the adapters it's not so bad, but getting the model name automatically would be especially useful for, eg, the serializer.