[R/cache.R:16:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/cache.R#L16) *warning:* **no visible binding for global variable ‘cache_env’**
```r
  cache_env[[model$id]][[name]]
  ^~~~~~~~~
```
[R/feature_growth.R:44:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_growth.R#L44) *warning:* **no visible binding for global variable ‘growth_class’**
```r
  growth_class$new(rate, population, time)
  ^~~~~~~~~~~~
```
[R/feature_ignore_singletons.R:28:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_ignore_singletons.R#L28) *warning:* **no visible binding for global variable ‘ign_singletons_class’**
```r
  ign_singletons_class$new()
  ^~~~~~~~~~~~~~~~~~~~
```
[R/feature_ignore_singletons.R:40:29:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_ignore_singletons.R#L40) *warning:* **no visible global function definition for ‘get_snps’**
```r
    is_singleton <- colSums(get_snps(segsites)) == 1
                            ^~~~~~~~
```
[R/feature_ignore_singletons.R:41:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_ignore_singletons.R#L41) *style:* **Commas should never have a space before.**
```r
    segsites[ , !is_singleton]
             ~^
```
[R/feature_ignore_singletons.R:52:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_ignore_singletons.R#L52) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_msms_arg.ign_singletons <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_ignore_singletons.R:56:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_ignore_singletons.R#L56) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_scrm_arg.ign_singletons <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_ignore_singletons.R:60:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_ignore_singletons.R#L60) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_seqgen_arg.ign_singletons <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_migration.R:72:12:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_migration.R#L72) *warning:* **no visible binding for global variable ‘migration_class’**
```r
    return(migration_class$new(rate, time = time, symmetric = TRUE))
           ^~~~~~~~~~~~~~~
```
[R/feature_migration.R:74:12:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_migration.R#L74) *warning:* **no visible binding for global variable ‘migration_class’**
```r
    return(migration_class$new(rate, pop_from, pop_to, time))
           ^~~~~~~~~~~~~~~
```
[R/feature_mutation.R:178:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_mutation.R#L178) *warning:* **no visible global function definition for ‘conv_to_ms_arg.mutation’**
```r
  conv_to_ms_arg.mutation(feature, model)
  ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:31:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_outgroup.R#L31) *warning:* **no visible binding for global variable ‘outgroup_class’**
```r
  outgroup_class$new(population)
  ^~~~~~~~~~~~~~
```
[R/feature_outgroup.R:40:34:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_outgroup.R#L40) *warning:* **no visible binding for global variable ‘is_feat_outgroup’**
```r
  mask <- vapply(model$features, is_feat_outgroup, logical(1))
                                 ^~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:49:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_outgroup.R#L49) *warning:* **no visible global function definition for ‘get_outgroup’**
```r
  outgroup <- get_outgroup(model)
              ^~~~~~~~~~~~
```
[R/feature_outgroup.R:51:20:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_outgroup.R#L51) *warning:* **no visible global function definition for ‘get_sample_size’**
```r
  outgroup_size <- get_sample_size(model, for_sim)[outgroup]
                   ^~~~~~~~~~~~~~~
```
[R/feature_pop_merge.R:47:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_pop_merge.R#L47) *warning:* **no visible binding for global variable ‘pop_merge_class’**
```r
  pop_merge_class$new(time, pop_source, pop_target)
  ^~~~~~~~~~~~~~~
```
[R/feature_recombination.R:35:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_recombination.R#L35) *warning:* **no visible binding for global variable ‘recombination_class’**
```r
  recombination_class$new(rate)
  ^~~~~~~~~~~~~~~~~~~
```
[R/feature_recombination.R:54:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_recombination.R#L54) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_seqgen_arg.recombination <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sample.R:44:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sample.R#L44) *warning:* **no visible binding for global variable ‘sample_class’**
```r
  sample_class$new(individuals, ploidy, time)
  ^~~~~~~~~~~~
```
[R/feature_sample.R:59:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sample.R#L63) *warning:* **no visible binding for global variable ‘is_feat_sample’**
```r
    feat_mask <- sapply(model$feature, is_feat_sample)
                                       ^~~~~~~~~~~~~~
```
[R/feature_sample.R:68:36:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sample.R#L68) *warning:* **no visible global function definition for ‘get_ploidy’**
```r
      sample_size <- sample_size * get_ploidy(model)
                                   ^~~~~~~~~~
```
[R/feature_sample.R:70:36:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sample.R#L70) *warning:* **no visible global function definition for ‘get_samples_per_ind’**
```r
      sample_size <- sample_size * get_samples_per_ind(model)
                                   ^~~~~~~~~~~~~~~~~~~
```
[R/feature_sample.R:72:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sample.R#L72) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, paste0("sample_size_", for_sim), sample_size)
    ^~~~~
```
[R/feature_sample.R:80:34:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sample.R#L80) *warning:* **no visible binding for global variable ‘is_feat_sample’**
```r
  mask <- vapply(model$features, is_feat_sample, logical(1))
                                 ^~~~~~~~~~~~~~
```
[R/feature_sample.R:91:18:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/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:176:21:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_selection.R#L176) *warning:* **no visible global function definition for ‘get_populations’**
```r
    n_pop <- length(get_populations(model))
                    ^~~~~~~~~~~~~~~
```
[R/feature_selection.R:191:36:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_selection.R#L191) *style:* **Commas should never have a space before.**
```r
                        n_pop, " " , paste(start_freq, collapse = " "), " ",
                                  ~^
```
[R/feature_size_change.R:47:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_size_change.R#L47) *warning:* **no visible binding for global variable ‘size_change_class’**
```r
  size_change_class$new(new_size, population, time)
  ^~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:18:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sumstats.R#L18) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_msms_arg.seg_sites_feat <- conv_to_ms_arg.seg_sites_feat
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:22:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sumstats.R#L22) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_scrm_arg.seg_sites_feat <- conv_to_ms_arg.seg_sites_feat
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:26:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_sumstats.R#L26) *style:* **Variable and function names should not be longer than 30 characters.**
```r
conv_to_seqgen_arg.seg_sites_feat <- conv_to_ms_arg.seg_sites_feat
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:52:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_unphased.R#L52) *warning:* **no visible binding for global variable ‘unphased_class’**
```r
  unphased_class$new(samples_per_ind)
  ^~~~~~~~~~~~~~
```
[R/feature_unphased.R:60:34:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_unphased.R#L60) *warning:* **no visible binding for global variable ‘is_feat_unphased’**
```r
  mask <- vapply(model$features, is_feat_unphased, logical(1))
                                 ^~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:68:11:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_unphased.R#L68) *warning:* **no visible global function definition for ‘get_feature_unphased’**
```r
  feat <- get_feature_unphased(model)
          ^~~~~~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:69:29:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/feature_unphased.R#L69) *warning:* **no visible global function definition for ‘get_ploidy’**
```r
  if (is.null(feat)) return(get_ploidy(model))
                            ^~~~~~~~~~
```
[R/import_popgenome.R:19:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/import_popgenome.R#L19) *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:20:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/import_popgenome.R#L20) *warning:* **no visible global function definition for ‘require_package’**
```r
  require_package("PopGenome")
  ^~~~~~~~~~~~~~~
```
[R/import_popgenome.R:43:43:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/import_popgenome.R#L43) *style:* **Commas should never have a space before.**
```r
      seg_sites <- bam[c(pops, outgroup), , drop = FALSE]
                                         ~^
```
[R/import_popgenome.R:49:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/import_popgenome.R#L49) *warning:* **no visible global function definition for ‘create_segsites’**
```r
    create_segsites(seg_sites, pos)
    ^~~~~~~~~~~~~~~
```
[R/import_popgenome.R:56:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/import_popgenome.R#L56) *warning:* **no visible global function definition for ‘require_package’**
```r
  require_package("PopGenome")
  ^~~~~~~~~~~~~~~
```
[R/interface_abc.R:80:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/interface_abc.R#L80) *warning:* **no visible global function definition for ‘get_summary_statistics’**
```r
  sumstats <- get_summary_statistics(model)
              ^~~~~~~~~~~~~~~~~~~~~~
```
[R/interface_abc.R:84:7:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/interface_abc.R#L84) *warning:* **no visible global function definition for ‘assert_that’**
```r
      assert_that(is.numeric(value))
      ^~~~~~~~~~~
```
[R/interface_abc.R:86:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/interface_abc.R#L86) *style:* **lines should not be more than 80 characters.**
```r
        warning("Value of the ", stat$get_name(), " statistic is not a vector. ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/locus.R:84:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/locus.R#L84) *warning:* **no visible binding for global variable ‘locus_class’**
```r
  locus_class$new(length, 1)
  ^~~~~~~~~~~
```
[R/locus.R:92:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/locus.R#L92) *warning:* **no visible binding for global variable ‘locus_class’**
```r
  locus_class$new(round(length), number)
  ^~~~~~~~~~~
```
[R/locus.R:151:10:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/locus.R#L151) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  llm <- get_locus_length_matrix(model)
         ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/locus.R:152:12:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/locus.R#L152) *warning:* **no visible global function definition for ‘get_locus_group’**
```r
  group <- get_locus_group(model, locus)
           ^~~~~~~~~~~~~~~
```
[R/model_build.R:10:7:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_build.R#L10) *warning:* **no visible global function definition for ‘is.model’**
```r
  if (is.model(e1)) return(add_to_model(e2, e1, e2name))
      ^~~~~~~~
```
[R/model_build.R:10:28:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_build.R#L10) *warning:* **no visible global function definition for ‘add_to_model’**
```r
  if (is.model(e1)) return(add_to_model(e2, e1, e2name))
                           ^~~~~~~~~~~~
```
[R/model_build.R:48:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_build.R#L48) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_build.R:54:12:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_build.R#L54) *warning:* **no visible global function definition for ‘add_variation’**
```r
  model <- add_variation(model)
           ^~~~~~~~~~~~~
```
[R/model_build.R:56:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_build.R#L56) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_build.R:79:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_build.R#L79) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_build.R:86:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_build.R#L86) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/model_check.R:18:16:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_check.R#L18) *warning:* **no visible global function definition for ‘get_simulator’**
```r
    simprog <- get_simulator(simprog_name)
               ^~~~~~~~~~~~~
```
[R/model_getters.R:15:13:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L15) *warning:* **no visible global function definition for ‘is.model’**
```r
  stopifnot(is.model(model))
            ^~~~~~~~
```
[R/model_getters.R:17:16:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L17) *warning:* **no visible global function definition for ‘read_cache’**
```r
  par_table <- read_cache(model, "par_table")
               ^~~~~~~~~~
```
[R/model_getters.R:35:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L35) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "par_table", par_table)
    ^~~~~
```
[R/model_getters.R:45:13:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L45) *warning:* **no visible global function definition for ‘is.model’**
```r
  stopifnot(is.model(model))
            ^~~~~~~~
```
[R/model_getters.R:59:10:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L59) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  llm <- get_locus_length_matrix(model)
         ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_getters.R:71:14:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L71) *warning:* **no visible global function definition for ‘get_locus_group’**
```r
    group <- get_locus_group(model, locus)
             ^~~~~~~~~~~~~~~
```
[R/model_getters.R:75:21:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L75) *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:75:60:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L75) *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:81:10:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L81) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  llm <- get_locus_length_matrix(model)
         ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_getters.R:82:25:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L82) *style:* **Commas should never have a space before.**
```r
  min(which(cumsum(llm[ , "number"]) >= locus))
                       ~^
```
[R/model_getters.R:87:8:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L87) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  nrow(get_locus_length_matrix(model))
       ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_getters.R:94:49:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L94) *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:96:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L96) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(pop_number > 0)
  ^~~~~~~~~~~
```
[R/model_getters.R:105:10:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L105) *warning:* **no visible global function definition for ‘read_cache’**
```r
  llm <- read_cache(model, "llm")
         ^~~~~~~~~~
```
[R/model_getters.R:107:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L107) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(length(model$loci) >= 0)
    ^~~~~~~~~~~
```
[R/model_getters.R:115:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L115) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "llm", llm)
    ^~~~~
```
[R/model_getters.R:125:14:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L125) *warning:* **no visible global function definition for ‘get_locus_length_matrix’**
```r
  numbers <- get_locus_length_matrix(model)[ , "number"]
             ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_getters.R:125:46:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L125) *style:* **Commas should never have a space before.**
```r
  numbers <- get_locus_length_matrix(model)[ , "number"]
                                            ~^
```
[R/model_getters.R:127:7:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L127) *warning:* **no visible global function definition for ‘has_variation’**
```r
  if (has_variation(model) && !ignore_variation) return(1)
      ^~~~~~~~~~~~~
```
[R/model_getters.R:144:18:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L144) *warning:* **no visible global function definition for ‘get_sample_size’**
```r
  sample_size <- get_sample_size(model)
                 ^~~~~~~~~~~~~~~
```
[R/model_getters.R:145:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L145) *warning:* **no visible global function definition for ‘get_outgroup’**
```r
  outgroup <- get_outgroup(model)
              ^~~~~~~~~~~~
```
[R/model_getters.R:152:47:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L152) *warning:* **no visible global function definition for ‘get_ploidy’**
```r
  if (!haploids) sample_size <- sample_size / get_ploidy(model)
                                              ^~~~~~~~~~
```
[R/model_getters.R:155:17:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L155) *warning:* **no visible global function definition for ‘get_populations’**
```r
  if (!pop %in% get_populations(model)) stop("Invalid population")
                ^~~~~~~~~~~~~~~
```
[R/model_getters.R:163:12:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L163) *warning:* **no visible global function definition for ‘get_parameter’**
```r
  param <- get_parameter(model)
           ^~~~~~~~~~~~~
```
[R/model_getters.R:166:35:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L166) *warning:* **no visible binding for global variable ‘is.prior_par’**
```r
    param <- param[!vapply(param, is.prior_par, numeric(1))]
                                  ^~~~~~~~~~~~
```
[R/model_getters.R:174:28:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_getters.R#L174) *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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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_scale.R:23:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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:40:14:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_simulate.R#L40) *warning:* **no visible global function definition for ‘select_simprog’**
```r
  simprog <- select_simprog(object)
             ^~~~~~~~~~~~~~
```
[R/model_simulate.R:44:21:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model_simulate.R#L44) *warning:* **no visible global function definition for ‘prepare_pars’**
```r
    current_pars <- prepare_pars(pars, object)
                    ^~~~~~~~~~~~
```
[R/model.R:72:20:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L72) *warning:* **no visible global function definition for ‘feat_sample’**
```r
  model <- model + feat_sample(sample_size, ploidy)
                   ^~~~~~~~~~~
```
[R/model.R:76:22:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L76) *warning:* **no visible global function definition for ‘locus_averaged’**
```r
    model <- model + locus_averaged(loci_number, loci_length)
                     ^~~~~~~~~~~~~~
```
[R/model.R:92:11:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L92) *warning:* **no visible global function definition for ‘read_cache’**
```r
  name <- read_cache(model, "simprog")
          ^~~~~~~~~~
```
[R/model.R:98:18:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L98) *warning:* **no visible global function definition for ‘get_simulator’**
```r
      simprog <- get_simulator(simprog_name)
                 ^~~~~~~~~~~~~
```
[R/model.R:109:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L109) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "simprog", name)
    ^~~~~
```
[R/model.R:126:7:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L126) *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:126:39:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L126) *style:* **Commas should never have a space before.**
```r
  sum(get_locus_length_matrix(model)[ , c(1:2, 4:5)]) > 0
                                     ~^
```
[R/model.R:132:12:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L132) *warning:* **no visible global function definition for ‘get_positions’**
```r
    pos <- get_positions(seg_sites[[locus]])
           ^~~~~~~~~~~~~
```
[R/model.R:133:21:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L133) *warning:* **no visible global function definition for ‘get_locus_length’**
```r
    locus_length <- get_locus_length(model, locus, total = FALSE)
                    ^~~~~~~~~~~~~~~~
```
[R/model.R:142:19:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/model.R#L142) *warning:* **no visible global function definition for ‘get_trio_locus’**
```r
    trio_locus <- get_trio_locus(seg_sites[[locus]])
                  ^~~~~~~~~~~~~~
```
[R/onLoad.R:3:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/onLoad.R#L3) *warning:* **no visible global function definition for ‘activate_scrm’**
```r
  activate_scrm()
  ^~~~~~~~~~~~~
```
[R/parameter_prior.R:30:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter_prior.R#L30) *warning:* **no visible binding for global variable ‘prior_par_class’**
```r
  prior_par_class$new(name, as.expression(substitute(prior)))
  ^~~~~~~~~~~~~~~
```
[R/parameter_prior.R:38:10:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter_prior.R#L38) *warning:* **no visible global function definition for ‘get_parameter’**
```r
  par <- get_parameter(model)
         ^~~~~~~~~~~~~
```
[R/parameter_prior.R:39:32:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter_prior.R#L39) *warning:* **no visible binding for global variable ‘is.prior_par’**
```r
  prior_par <- par[vapply(par, is.prior_par, logical(1))]
                               ^~~~~~~~~~~~
```
[R/parameter_variation.R:59:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter_variation.R#L59) *warning:* **no visible binding for global variable ‘variation_par_class’**
```r
  variation_par_class$new(par, variance)
  ^~~~~~~~~~~~~~~~~~~
```
[R/parameter.R:123:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L123) *warning:* **no visible binding for global variable ‘parameter_class’**
```r
  parameter_class$new(as.expression(substitute(expr)))
  ^~~~~~~~~~~~~~~
```
[R/parameter.R:135:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L135) *warning:* **no visible binding for global variable ‘parameter_class’**
```r
  parameter_class$new(as.expression(constant))
  ^~~~~~~~~~~~~~~
```
[R/parameter.R:144:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L144) *warning:* **no visible binding for global variable ‘named_par_class’**
```r
  named_par_class$new(name)
  ^~~~~~~~~~~~~~~
```
[R/parameter.R:166:11:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L166) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if ((!is.numeric(value)) || length(value) != 1) {
          ^
```
[R/parameter.R:192:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L192) *warning:* **no visible binding for global variable ‘range_par_class’**
```r
  range_par_class$new(lower, upper, name)
  ^~~~~~~~~~~~~~~
```
[R/parameter.R:203:25:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L203) *warning:* **no visible binding for global variable ‘par_eval_func’**
```r
    par_env[["par"]] <- par_eval_func
                        ^~~~~~~~~~~~~
```
[R/parameter.R:209:25:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L209) *warning:* **no visible binding for global variable ‘par_print_func’**
```r
    par_env[["par"]] <- par_print_func
                        ^~~~~~~~~~~~~~
```
[R/parameter.R:225:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L225) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.numeric(pars))
  ^~~~~~~~~~~
```
[R/parameter.R:229:18:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L229) *warning:* **no visible global function definition for ‘get_par_names’**
```r
    par_names <- get_par_names(model, without_priors = TRUE)
                 ^~~~~~~~~~~~~
```
[R/parameter.R:237:11:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/parameter.R#L237) *warning:* **no visible global function definition for ‘sample_par_priors’**
```r
  c(pars, sample_par_priors(model))
          ^~~~~~~~~~~~~~~~~
```
[R/segsites.R:47:11:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L47) *warning:* **no visible global function definition for ‘get_snps’**
```r
  snps <- get_snps(x)
          ^~~~~~~~
```
[R/segsites.R:48:28:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L48) *warning:* **no visible global function definition for ‘get_positions’**
```r
  colnames(snps) <- format(get_positions(x), scientific = FALSE)
                           ^~~~~~~~~~~~~
```
[R/segsites.R:62:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L62) *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:75:19:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L75) *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:83:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L83) *warning:* **no visible global function definition for ‘create_segsites’**
```r
  create_segsites(matrix(0, n_ind, 0), numeric(0))
  ^~~~~~~~~~~~~~~
```
[R/segsites.R:103:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L103) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.list(left) && is.list(middle) && is.list(right))
  ^~~~~~~~~~~
```
[R/segsites.R:104:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L104) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(length(left) == length(middle))
  ^~~~~~~~~~~
```
[R/segsites.R:105:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L105) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(length(left) == length(right))
  ^~~~~~~~~~~
```
[R/segsites.R:142:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L142) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
as.segsites.default <- function(data, ...) {
^~~~~~~~~~~~~~~~~~~
```
[R/segsites.R:147:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L147) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
as.segsites.list <- function(data, ...) {
^~~~~~~~~~~~~~~~
```
[R/segsites.R:148:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L148) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(all(vapply(data, is_segsites, logical(1))))
  ^~~~~~~~~~~
```
[R/segsites.R:148:32:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/segsites.R#L148) *warning:* **no visible binding for global variable ‘is_segsites’**
```r
  assert_that(all(vapply(data, is_segsites, logical(1))))
                               ^~~~~~~~~~~
```
[R/simulator_class.R:28:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L28) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is_simulator(simulator))
  ^~~~~~~~~~~
```
[R/simulator_class.R:28:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L28) *warning:* **no visible global function definition for ‘is_simulator’**
```r
  assert_that(is_simulator(simulator))
              ^~~~~~~~~~~~
```
[R/simulator_class.R:33:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L33) *warning:* **no visible binding for global variable ‘simulators’**
```r
  simulators[[name]]
  ^~~~~~~~~~
```
[R/simulator_class.R:40:19:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L40) *warning:* **no visible global function definition for ‘get_locus_length’**
```r
  locus_length <- get_locus_length(model, group = locus_group)
                  ^~~~~~~~~~~~~~~~
```
[R/simulator_class.R:41:25:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L41) *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:64:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L64) *warning:* **no visible global function definition for ‘reduce_sim_commands’**
```r
  reduce_sim_commands(sim_cmds)
  ^~~~~~~~~~~~~~~~~~~
```
[R/simulator_class.R:70:44:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L70) *style:* **Commas should never have a space before.**
```r
  grouped_commands <- unique(sim_commands[ , 2])
                                          ~^
```
[R/simulator_class.R:73:36:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L73) *style:* **Commas should never have a space before.**
```r
    sum(sim_commands[sim_commands[ , 2] == cmd, 1])
                                  ~^
```
[R/simulator_class.R:90:13:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_class.R#L90) *warning:* **no visible global function definition for ‘get_simulator’**
```r
    info <- get_simulator(simulator)$get_info()
            ^~~~~~~~~~~~~
```
[R/simulator_ms.R:67:37:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_ms.R#L67) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        paste("ms", sample_size, cmd[ , 1], cmd[ , 2])
                                    ^
```
[R/simulator_ms.R:87:39:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_ms.R#L87) *style:* **Commas should never have a space before.**
```r
        paste("ms", sample_size, cmd[ , 1], cmd[ , 2])
                                     ~^
```
[R/simulator_ms.R:87:50:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_ms.R#L87) *style:* **Commas should never have a space before.**
```r
        paste("ms", sample_size, cmd[ , 1], cmd[ , 2])
                                                ~^
```
[R/simulator_ms.R:136:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_ms.R#L136) *warning:* **no visible global function definition for ‘register_simulator’**
```r
  register_simulator(ms_class$new(priority))
  ^~~~~~~~~~~~~~~~~~
```
[R/simulator_ms.R:136:22:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_ms.R#L136) *warning:* **no visible binding for global variable ‘ms_class’**
```r
  register_simulator(ms_class$new(priority))
                     ^~~~~~~~
```
[R/simulator_ms.R:137:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_ms.R#L137) *warning:* **no visible global function definition for ‘reset_cache’**
```r
  reset_cache()
  ^~~~~~~~~~~
```
[R/simulator_msms.R:109:41:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_msms.R#L109) *style:* **Commas should never have a space before.**
```r
        paste("msms", sample_size, cmd[ , 1], cmd[ , 2])
                                       ~^
```
[R/simulator_msms.R:109:52:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_msms.R#L109) *style:* **Commas should never have a space before.**
```r
        paste("msms", sample_size, cmd[ , 1], cmd[ , 2])
                                                  ~^
```
[R/simulator_msms.R:158:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_msms.R#L158) *warning:* **no visible global function definition for ‘reset_cache’**
```r
  reset_cache()
  ^~~~~~~~~~~
```
[R/simulator_scrm.R:11:10:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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:83:41:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_scrm.R#L83) *style:* **Commas should never have a space before.**
```r
        paste("scrm", sample_size, cmd[ , 1], cmd[ , 2])
                                       ~^
```
[R/simulator_scrm.R:83:52:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_scrm.R#L83) *style:* **Commas should never have a space before.**
```r
        paste("scrm", sample_size, cmd[ , 1], cmd[ , 2])
                                                  ~^
```
[R/simulator_scrm.R:129:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_scrm.R#L129) *warning:* **no visible global function definition for ‘register_simulator’**
```r
  register_simulator(scrm_class$new(priority))
  ^~~~~~~~~~~~~~~~~~
```
[R/simulator_scrm.R:129:22:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_scrm.R#L129) *warning:* **no visible binding for global variable ‘scrm_class’**
```r
  register_simulator(scrm_class$new(priority))
                     ^~~~~~~~~~
```
[R/simulator_scrm.R:130:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_scrm.R#L130) *warning:* **no visible global function definition for ‘reset_cache’**
```r
  reset_cache()
  ^~~~~~~~~~~
```
[R/simulator_seqgen.R:5:17:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L5) *warning:* **no visible global function definition for ‘read_cache’**
```r
  tree_model <- read_cache(model, "tree_model")
                ^~~~~~~~~~
```
[R/simulator_seqgen.R:20:29:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L20) *warning:* **no visible global function definition for ‘create_sumstat_container’**
```r
    tree_model$sum_stats <- create_sumstat_container()
                            ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulator_seqgen.R:21:32:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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:41:20:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L41) *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:47:10:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L47) *warning:* **no visible global function definition for ‘sg_generate_opt_cmd’**
```r
  cmd <- sg_generate_opt_cmd(model)
         ^~~~~~~~~~~~~~~~~~~
```
[R/simulator_seqgen.R:61:10:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L61) *warning:* **no visible global function definition for ‘read_cache’**
```r
  cmd <- read_cache(model, "seqgen_cmd")
         ^~~~~~~~~~
```
[R/simulator_seqgen.R:74:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L74) *warning:* **no visible global function definition for ‘cache’, Did you mean 'cycle'?**
```r
    cache(model, "seqgen_cmd", cmd)
    ^~~~~
```
[R/simulator_seqgen.R:222:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L222) *warning:* **no visible global function definition for ‘register_simulator’**
```r
  register_simulator(seqgen_class$new(binary, priority))
  ^~~~~~~~~~~~~~~~~~
```
[R/simulator_seqgen.R:222:22:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L222) *warning:* **no visible binding for global variable ‘seqgen_class’**
```r
  register_simulator(seqgen_class$new(binary, priority))
                     ^~~~~~~~~~~~
```
[R/simulator_seqgen.R:223:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/simulator_seqgen.R#L223) *warning:* **no visible global function definition for ‘reset_cache’**
```r
  reset_cache()
  ^~~~~~~~~~~
```
[R/sumstat_dna.R:40:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_dna.R#L40) *warning:* **no visible binding for global variable ‘stat_dna_class’**
```r
  stat_dna_class$new(name, transformation)
  ^~~~~~~~~~~~~~
```
[R/sumstat_file.R:46:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_file.R#L46) *warning:* **no visible binding for global variable ‘stat_file_class’**
```r
  stat_file_class$new(folder)
  ^~~~~~~~~~~~~~~
```
[R/sumstat_four_gamete.R:73:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_four_gamete.R#L73) *warning:* **no visible binding for global variable ‘stat_four_gamete_class’**
```r
  stat_four_gamete_class$new(name, population, transformation)
  ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat_ihh.R:53:45:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_ihh.R#L53) *style:* **Commas should never have a space before.**
```r
                      iHS = data.frame(ihh[ , 1:2], iHS = rep(NA, n_snps))))
                                           ~^
```
[R/sumstat_ihh.R:61:55:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_ihh.R#L61) *style:* **Commas should never have a space before.**
```r
            data.frame(ihh2ihs(ihh, freqbin)$res.ihs[ , -4])
                                                     ~^
```
[R/sumstat_ihh.R:148:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_ihh.R#L148) *warning:* **no visible binding for global variable ‘stat_ihh_class’**
```r
  stat_ihh_class$new(name, population, max_snps, calc_ihs, transformation)
  ^~~~~~~~~~~~~~
```
[R/sumstat_jsfs.R:60:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_jsfs.R#L60) *warning:* **no visible binding for global variable ‘stat_jsfs_class’**
```r
  stat_jsfs_class$new(name, populations, per_locus, transformation)
  ^~~~~~~~~~~~~~~
```
[R/sumstat_mcmf.R:44:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_mcmf.R#L44) *warning:* **no visible binding for global variable ‘stat_mcmf_class’**
```r
  stat_mcmf_class$new(name, population, transformation)
  ^~~~~~~~~~~~~~~
```
[R/sumstat_nucleotide_div.R:46:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_nucleotide_div.R#L46) *warning:* **no visible binding for global variable ‘stat_pi_class’**
```r
  stat_pi_class$new(name, population, transformation)
  ^~~~~~~~~~~~~
```
[R/sumstat_omega.R:156:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_omega.R#L156) *warning:* **no visible binding for global variable ‘stat_omega_class’**
```r
  stat_omega_class$new(name, min_win, max_win, grid, binary, transformation)
  ^~~~~~~~~~~~~~~~
```
[R/sumstat_omega.R:160:12:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_omega.R#L160) *warning:* **no visible global function definition for ‘search_executable’**
```r
  !is.null(search_executable("OmegaPlus", envir_var = "OMEGAPLUS"))
           ^~~~~~~~~~~~~~~~~
```
[R/sumstat_seg_sites.R:30:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_seg_sites.R#L30) *warning:* **no visible binding for global variable ‘stat_segsites_class’**
```r
  stat_segsites_class$new(name, transformation)
  ^~~~~~~~~~~~~~~~~~~
```
[R/sumstat_seg_sites.R:36:21:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_seg_sites.R#L36) *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:42:12:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_seg_sites.R#L42) *warning:* **no visible global function definition for ‘get_positions’**
```r
    pos <- get_positions(seg_sites[[i]])
           ^~~~~~~~~~~~~
```
[R/sumstat_seg_sites.R:51:38:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_seg_sites.R#L51) *style:* **Commas should never have a space before.**
```r
    trio_segsites <- seg_sites[[i]][ , left | middle | right]
                                    ~^
```
[R/sumstat_seg_sites.R:60:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_seg_sites.R#L60) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(nrow(seg_sites[[i]]) > 0)
    ^~~~~~~~~~~
```
[R/sumstat_sfs.R:38:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_sfs.R#L38) *warning:* **no visible binding for global variable ‘stat_sfs_class’**
```r
  stat_sfs_class$new(name, population, transformation)
  ^~~~~~~~~~~~~~
```
[R/sumstat_tajimas_d.R:62:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_tajimas_d.R#L62) *warning:* **no visible binding for global variable ‘stat_tajimas_d_class’**
```r
  stat_tajimas_d_class$new(name, population, transformation)
  ^~~~~~~~~~~~~~~~~~~~
```
[R/sumstat_trees.R:28:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_trees.R#L28) *warning:* **no visible binding for global variable ‘stat_trees_class’**
```r
  stat_trees_class$new(name, identity)
  ^~~~~~~~~~~~~~~~
```
[R/sumstat_trees.R:57:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat_trees.R#L57) *warning:* **no visible binding for global variable ‘stat_sg_trees_class’**
```r
  stat_sg_trees_class$new("trees", identity)
  ^~~~~~~~~~~~~~~~~~~
```
[R/sumstat.R:71:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L71) *warning:* **no visible global function definition for ‘get_id’, Did you mean 'getwd'?**
```r
  model$id <- get_id()
              ^~~~~~
```
[R/sumstat.R:87:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L87) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.model(model))
  ^~~~~~~~~~~
```
[R/sumstat.R:87:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L87) *warning:* **no visible global function definition for ‘is.model’**
```r
  assert_that(is.model(model))
              ^~~~~~~~
```
[R/sumstat.R:89:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L89) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(!is.null(segsites_list))
    ^~~~~~~~~~~
```
[R/sumstat.R:90:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L90) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(all(vapply(segsites_list, is_segsites, logical(1))))
    ^~~~~~~~~~~
```
[R/sumstat.R:90:43:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L90) *warning:* **no visible binding for global variable ‘is_segsites’**
```r
    assert_that(all(vapply(segsites_list, is_segsites, logical(1))))
                                          ^~~~~~~~~~~
```
[R/sumstat.R:93:24:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L93) *warning:* **no visible global function definition for ‘remove_singletons’**
```r
      segsites_list <- remove_singletons(segsites_list)
                       ^~~~~~~~~~~~~~~~~
```
[R/sumstat.R:96:7:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L96) *warning:* **no visible global function definition for ‘requires_trees’**
```r
  if (requires_trees(model)) assert_that(!is.null(trees))
      ^~~~~~~~~~~~~~
```
[R/sumstat.R:96:30:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L96) *warning:* **no visible global function definition for ‘assert_that’**
```r
  if (requires_trees(model)) assert_that(!is.null(trees))
                             ^~~~~~~~~~~
```
[R/sumstat.R:97:7:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L97) *warning:* **no visible global function definition for ‘requires_files’**
```r
  if (requires_files(model)) assert_that(!is.null(files))
      ^~~~~~~~~~~~~~
```
[R/sumstat.R:97:30:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L97) *warning:* **no visible global function definition for ‘assert_that’**
```r
  if (requires_files(model)) assert_that(!is.null(files))
                             ^~~~~~~~~~~
```
[R/sumstat.R:111:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L111) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.model(model))
  ^~~~~~~~~~~
```
[R/sumstat.R:111:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L111) *warning:* **no visible global function definition for ‘is.model’**
```r
  assert_that(is.model(model))
              ^~~~~~~~
```
[R/sumstat.R:120:20:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L120) *warning:* **no visible global function definition for ‘conv_for_trios’**
```r
      seg_sites <- conv_for_trios(seg_sites, model)
                   ^~~~~~~~~~~~~~
```
[R/sumstat.R:176:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L176) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.model(model))
  ^~~~~~~~~~~
```
[R/sumstat.R:176:15:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L176) *warning:* **no visible global function definition for ‘is.model’**
```r
  assert_that(is.model(model))
              ^~~~~~~~
```
[R/sumstat.R:179:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L179) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is.list(trios))
    ^~~~~~~~~~~
```
[R/sumstat.R:180:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L180) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(!is.null(segsites_list))
    ^~~~~~~~~~~
```
[R/sumstat.R:186:7:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L186) *warning:* **no visible global function definition for ‘assert_that’**
```r
      assert_that(is.numeric(trio))
      ^~~~~~~~~~~
```
[R/sumstat.R:188:7:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L188) *warning:* **no visible global function definition for ‘assert_that’**
```r
      assert_that(length(trio) == 3)
      ^~~~~~~~~~~
```
[R/sumstat.R:196:22:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L196) *warning:* **no visible global function definition for ‘as.segsites’**
```r
    segsites_list <- as.segsites(segsites_list, ...)
                     ^~~~~~~~~~~
```
[R/sumstat.R:200:5:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L200) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(length(segsites_list) == get_locus_number(model))
    ^~~~~~~~~~~
```
[R/sumstat.R:200:42:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L200) *warning:* **no visible global function definition for ‘get_locus_number’**
```r
    assert_that(length(segsites_list) == get_locus_number(model))
                                         ^~~~~~~~~~~~~~~~
```
[R/sumstat.R:209:3:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L209) *warning:* **no visible global function definition for ‘calc_sumstats’**
```r
  calc_sumstats(model, segsites_list, tree_list)
  ^~~~~~~~~~~~~
```
[R/sumstat.R:214:14:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L214) *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:219:14:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L219) *warning:* **no visible global function definition for ‘get_summary_statistics’**
```r
  any(sapply(get_summary_statistics(model), function(x) x$requires_trees()))
             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat.R:224:14:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/R/sumstat.R#L224) *warning:* **no visible global function definition for ‘get_summary_statistics’**
```r
  any(sapply(get_summary_statistics(model), function(x) x$requires_files()))
             ^~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-feature-ign-singletons.R:13:45:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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-cache.R:47:1:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/tests/testthat/test-model-cache.R#L47) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-model-class.R:241:44:](https://github.com/statgenlmu/coala/blob/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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/3fa518b1ef77351afe5be34be90175f6446c8e98/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))
                               ~^
```


Given I just ported it away from my config, it isn't really documented yet.
Until a few hours ago, it was called "findabettername". With the screenshot
it become clear.
On Mar 10, 2016 4:18 AM, "Uli Schlachter" <notifications@github.com> wrote:

> No idea what this one does, but I guess that's the WIP-part here. :-)
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/Elv13/awesome-1/commit/1ff14dea5d2003c27b2a36c50ba7cbe9989f2d3f#commitcomment-16611337>
> .
>


Same comment here


alles idioten... außer ich :D :P


The line 968 and 973 was removed. The system.out at line 260 was added at the commit: 02fdf3f. In the current head verison of the branch it is removed.


you were right, reopened.


validated with atlas team?


Nice


Great, thanks! I'll let you know if I run into any problems. :)


I'll just cut that section.  However, I'm currently at Kubecon and have a talk today ... @bproffitt, if there's any way you can make the edits @jlebron is asking for, that would be great.


beware when merging to not forget the migration 1114


Fixed. Will be in next PR.


If you are still not happy with it, then we could simply add a title-background class to the old stylesheets that is the same as title. Note the bootstrap does differentiate between title and title-background.


499 is no good because it's not RFC and it gets confused with antivirus nonsense.

I kinda wonder if 403 is correct. We know what you're talking but we can't go any further till you change your headers. What do you think?


Not efficient


Is there a dependency relationship between zimbra-clamav and zimbra-clamav-db?


You cannot request  a token from production and user in `Sandbox`


Imported module unused


Interesting.  Why is `r` determined by `m`?  Given that I can't see it, would it make sense to comment on it?


Full translation version 5.2.1 + FIX


Wow thanks, I hadn't noticed that had expired.


Probably not the best place to ask this question, but -

You can't do what you want using prepared statements. You should either do

`db.query("select ' + 'column1' + ' as a, ' + 'column2' + ' as b from tablename", [], function (error, result, info)`

or use dynamic SQL.

In both cases, if the column names come from an untrusted source you *must* ensure that they are properly quoted to avoid SQL injection.


The new iframe code also knows to look for "title" as a class when trying to determine a title for a tab.

Bootstrap should be modified to fit OpenEMR's existing style sheets, not the other way around.


**SUCCESS** - TeamCity HotRod C# Client :: Pull requests monitor - WIN_S2012 [Build 101](http://ci.infinispan.org/viewLog.html?buildId=37269&buildTypeId=HotRodCSharp_PullRequestsMonitorWinS2012&guest=1) for 6396809633bf909a9a6f7540994af9804d44f89f
Tests: 0, 0 failed (0 new), 0 ignored. Build time: 00:12:45


yes i know there's this problem if the modman file is like that :

`app/etc/modules/*   app/etc/modules/`

the script need to be improved


Merging from pidconsortium


iteration (axelstudios) - x86_64-Linux-Ubuntu-14.04-clang-3.5: OK (2327 of 2398 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-97.04%25-yellow.svg)


There was an incorrect assignment. Internal was assigned to external and vice versa. External heartbeat defaulted to 700 ms


Why are you creating a token request and then adding an authUrl?  authUrl is used to obtain a token or token request, but then you are providing a token?  Also, RequestToken signature is `requestToken(TokenParams, AuthOptions)` so not sure how you can pass in a TokenRequest?


it'd be nice to check that `avocado.app` message was not outputted.


sign in the service -> sign into the service
or an other identity you have gotten from en external -> or another identity belonging to an external


https://github.com/copperspice/copperspice/pull/32 should work with both MSVC and new versions of MinGW by adding a new defines for the cases that are different between the compilers. Given that both compilers are shipping, working around the fact that they require different things is probably best even if they eventually achieve consistency in a future release.


Yeah quite possibly. I don't think there is a code that perfectly suits our needs. 403 is probably generic enough.
I think we have a good case for claiming to be a teapot though.

On 10 March 2016 09:26:10 GMT+00:00, Ben Marvell <notifications@github.com> wrote:
>499 is no good because it's not RFC and it gets confused with antivirus
>nonsense.
>
>I kinda wonder if 403 is correct. We know what you're talking but we
>can't go any further till you change your headers. What do you think?
>
>---
>Reply to this email directly or view it on GitHub:
>https://github.com/UKHomeOffice/brp_app/commit/3678134d1ffa1e3c3aa926d2d2c7df9be7a36e73#commitcomment-16611548

--
Sent from my Android device with K-9 Mail. Please excuse my brevity.


@vilchik-elena Isn't it a bit overkill?


Ah ok!


I would drop the exclamation mark


Helst to blanke linjer mellom hver metode-definisjon


You need to add some retry logic here. If the publish fails we need to retry a few times before giving up. Also place the os.Rename call after the consume is successful


also drop exclamation mark


Mangler doxy for argumentet silence (vil gi warning ved make doc).


I'd be more strict and use `result.stderr.strip()`, just to be sure...


Nop it's not. Would it lead to problems ?


Dette virker unødig komplisert bare for å finne max p1 of p2 over alle basiser. Hva med flg. istedet som jeg finner mye mer lesbart (gitt at det blir det samme da):

size_t p1 = 0, p2 = 0
for (auto it = m_basis.begin(); it != m_basis.end(); ++it) {
  if ((*it)->order_u() > p1) p1 = (*it)->order_u();
  if ((*it)->order_v() > p2) p2 = (*it)->order_v();
}


Samme her som for tilsvarende 2D-metode: Bruk helt enkel løkke over m_basis for å finne max order, f.eks.

size_t p[3] = { 0, 0, 0 };
for (auto it = m_basis.begin(); it != m_basis.end(); ++it)
  for (int d = 0; d < 3; d++)
    if ((*it)->order(d) > p[d]) p[d] = (*it)->order(d);


The large scale of the changes here is what troubles me...

The goal of a much better looking interface can be achieved without needing to hit so many files.

The new classes like "load_compendium" are good, in that they are OpenEMR context though.


Could you take the comment from the commit message and move it to a haddock comment in some (arbitrary) appropriate place in the test suite and make it a FUTUREWORK?


Faudrait trouver un moyen de cacher cette ligne !


Totally agreed. If it were the 1950's I'd be straight in there with teapot.


This (and the file you renamed) is intentional, the bug happens when there is a space in the file name, with this change the test does nothing.


remove print


drop the exclamation mark


:elephant:


also leave the `!` out here


it's not working for me on Android


ok, then the issue is your new iframe code, which I agree is important. Would placing both title and title-background for these classes then be acceptable?(Note I had Tony not do this since you had an issue with adding a new class like that)


In `website_slides` it's "Published"


If you look at the IDL definition for connect, you'll see that it does not wait on IO i.e. it's `connect()` not `connect() => io`.  As such, there is no need to have an async task for this method.  The reasoning is simply because a `connect` request can lead to a `disconnected` and `suspended` state if the connection is not available, yet that is not a failure necessarily.  So we can provide as a convenience, but it could lead to developers thinking that they should use this method whereas we recommend they use the `on(state)` handlers instead so that they don't have any surprises.


Yes, will just remove.


Fails to build: http://hydra.nixos.org/build/33068140/nixlog/6/raw


kfree(str)


Displays message body


Nice, my idea was to write probably even less functional tests than you did here and instead create a script which imports logging, does some outputs before init, after init ... and invoke it from unit test.


return 0; // success


It hits a lot of files in a very minimal way. Look through it first to get an idea of what it does.


As above, the problem is suspended is not a permanent failure at all, it just means the connection state cannot be resumed, but we'll keep trying to reestablish a connection.


Please leave this empty line there.


drop the `!`


kfree(str);


iteration (axelstudios) - x86_64-Linux-Ubuntu-14.04-cppcheck-1.61: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.svg)


drop `!`


Why did you change the visibility of these methods?  They are not part of our API?


This return type does not match.


accepts only -> only accepts


Should be ok, besides that.


pat_mega_branch_rc (macumber) - x86_64-Linux-Ubuntu-14.04-clang-3.5: Build Failed

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-NA-red.svg)


What forces us to use `Persist` here instead of `r`?


Merge conflict here needs to be fixed


Great approach! Looking good.


how about using `tty.tcgetattr(1)`?


please ignore.  nothing does, you fixed it further down.


Done


Uploaded!


>At first: The whole android-n branch (where this commit lives in) is as experimental as the build-tool-chain used in it and as experimental as Android N itself.

Wouldn't it be better to fix any of URGENT issues? AIMISICD as a security projects should not be treated as experiment for unreleased experimental features. I understand you do it for your experience and it's fine, but this branch and experiment on the project is pointless.

No worries, I know what java8 is ;) This experiment can introduce nothing more but regressions, even things like unreproducible builds, which already lacks trust because of travis-based releases.


TeamCity libpalaso :: palaso-precise64-lfmerge Continuous [Build 2.6.17.3563b6494c9bc84047e03e545b43f25af6067f85](http://build.palaso.org/viewLog.html?buildId=70151&buildTypeId=PalasoPrecise64lfmergeContinuous) outcome was **FAILURE**
Summary: Exit code 1 (new) Build time: 00:01:23


权限问题怎么解决呢？


If we are going to introduce an interface for this, can we please try and be consistent with Java naming, see https://github.com/ably/ably-java/blob/master/lib/src/main/java/io/ably/lib/realtime/Channel.java#L237-L239.  So `IMessageListener` instead of `IMessageHandler` and the method to receive events should be `onMessage`


Thanks! Replied [here](http://forum.starling-framework.org/topic/heads-up-starling-2-performance-issues#post-90822).


Why do we have an Async and non Async version?


Collaborator:
A review for this commit was created. [Link to review](http://localhost:8080/ui#review:id=30)


As above, listener as opposed to handler please


I guess `catchAulaExcept` does. For sure something does.


En fait le systeme de classe ici ne veux plus rien dire ...
mettre a vide c'est bien il me semble


Hi @logrusorgru

Thank you for your report, just fixed it.


pat_mega_branch_rc (macumber) - x86_64-Linux-Ubuntu-14.04-cppcheck-1.61: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.svg)


TeamCity libpalaso :: palaso-win32-master Continuous [Build 3.0.701.3517469600a60e2949c903d54916d7a177b813e8](http://build.palaso.org/viewLog.html?buildId=70155&buildTypeId=bt223) outcome was **SUCCESS**
Summary: Tests passed: 3337, ignored: 130 Build time: 00:10:45


Renaming an existing css class is NOT minimal...

The reason why the existing styles still look ok is that there is an explicit <b> tag (bold) tag added to all of the titles.    That's poor css implementation.  The font-weight should be kept as part of the .css style.

Would like to make sure that Tony and Rod weigh in on this before you bring this commit in to the official code base.


Seems to be the best compromise in order to make sure that the UoM is correct before calling `_onchange_product_id_check_availability`. On the other hand, we will probably go through `_onchange_product_id_check_availability` an extra time, and therefore display the warning twice.


+1 for having some kind of defaults. elements should work and lood good out
of the box

On Tue, Mar 8, 2016 at 11:22 AM, Dami <notifications@github.com> wrote:

> fine for me. I've just brought them back
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/zalando/dress-code/commit/5b04e675751b9e2dfc2505e76a31624d1aaebba4#commitcomment-16557875>
> .
>

--

Gabriel Lovato
Visual Designer / Brand Solutions
Zalando SE

POSTAL ADDRESS
Zalando SE
11501 Berlin

OFFICE
Zalando SE
Mollstraße 1
10178 Berlin
Germany

Fax: +493027594693
Email: gabriel.lovato@zalando.de
Web: corporate.zalando.de
Jobs: jobs.zalando.de

Zalando SE, Tamara-Danz-Straße 1, 10243 Berlin
Company registration: Amtsgericht Charlottenburg, HRB 158855 B
Tax ID: 29/560/00596 * VAT registration number: DE 260543043
Management Board: Robert Gentz, David Schneider, Rubin Ritter
Chairperson of the Supervisory Board: Cristina Stenbeck
Registered office: Berlin


During implementation I needed to import user in Organization (which will happen here as well). So I try to maintain some separation of concerns, where User API is only concerned with User resource, and keep other API concerned with their own resources (e.g. organization will handle any Organization related requests, etc ...)


ready_aim_fire (macumber) - x86_64-Linux-Ubuntu-14.04-clang-3.5: Build Failed

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-NA-red.svg)


Use conventions for tests methods. For example : add_route_should_add_tag with test annotation


Everything is in the jira issue. As can be seen on https://github.com/apache/mesos/blob/master/src/docker/executor.cpp#L226 - before mesos issues something like `docker stop -H /var/run/docker.sock -t 10 mesos-1234-5678-98767` it calls `run->discard()` - which closes the stderr/our streams and then, you can see in the /var/log/upstart/docker.log something like
`ERRO[0366] attach: stdout: write unix @: broken pipe`

If you want to try it, just run that docker image i provided (bydga/marathon-test-api):

`curl -XPOST -d '{"args": ["./script.py"], "container": {"type": "DOCKER", "docker": {"image": "bydga/marathon-test-api"}}, "id": "python-docker", "instances": 1, "cpus": 0.2}' -H "Content-Type: application/json" http://localhost:8080/v2/apps`

And do the restart in marathon. You should see in the stdout messages like
```
...
Iteration #96
15:40:45.377367
Iteration #97
Killing docker task
Shutting down
got 15
15:40:45.603347
15:40:47.605719
ending
Goodbye
```
But without this change, you will see only
```
...
Iteration #96
15:40:45.377367
Iteration #97
Killing docker task
Shutting down
```


And `catchAulaExcept` needs this variable fixed, because it appears in the result types as well. Can't have `r` either.


Don't commit composer.lock


That is a sort of valid question. Theoretically you could set the node owner just on the initial revision and the node create time on the initial revision as well. On the other hand though, this could be really annoying when it comes down to developer experience, because you first have to always load first revision, for the really common usecase of getting the author of an entity.


Code formatting issue (missing space)


On Wed, Mar 09, 2016 at 07:27:03PM -0800, Felipe Dau wrote:
> Hi @crooks, I tried to explain the reason for that `is True` when I
> made #2.

> It is possible that a user thinks that when configuring their nym,
> they have to provide the `delete` option in their message and if by
> mistake they fail to type `0`, `no`, `none` or `false` their nym will
> be deleted, as any string in `moddict['delete']` evaluates to `True`.
> That might apply to other cases in the nymserv that expect `True` but
> end up accepting any string. When deleting a nym, is think that making
> sure that the value was correctly parsed to `True` is important.

Hi Felipe,

I see your point now.  I hadn't appreciated that "is True" was evaluated
differently to just testing for truth.  It's now fixed.

Many thanks,
Steve


Thanks, makes sense now :-)


mortalboy became bartek94ka


This doesn't look good!


The title-background in the NEW css should be modified to be title.  The NEW css should be made consistent with the existing css, not the other way around.


astropy (1.0.5)
Cython (0.21)
decorator (4.0.9)
h5py (2.5.0)
Jinja2 (2.8)
MarkupSafe (0.23)
matplotlib (1.4.3)
networkx (1.10)
numexpr (2.4.4)
numpy (1.10.0.post2)
pandas (0.16.2)
pip (8.1.0)
py (1.4.31)
pyparsing (2.0.3)
pytest (2.6.3)
python-dateutil (2.4.2)
pytz (2015.7)
PyYAML (3.11)
scipy (0.17.0)
setuptools (20.2.2)
six (1.10.0)
tables (3.2.2)
tardis-sn (1.0.1)
wheel (0.29.0)
these are the versions


I have started to test that doesn't break ceilometer, otherwise, I will bump the major version and update requirements and ceilometer when master have to switch to N release


No, unfortunately, in this case I couldn't easily fix this. But I agree, this can be parameterized further, just with some extra work that is hard to justify at this stage.


Collaborator:
A review for this commit was created. [Link to review](http://localhost:8080/ui#review:id=31)


ok for me
 Linux chrome Version 49.0.2623.75 (64-bit)
 and old iceweasel
 and firefox 42


add the several since 5.5


@vilchik-elena it seems that `visitMemberAccess` does something similar and that's probably more costly. Let's improve later both cases.


Hi @simonjbeaumont , Thanks.
I've rebased stunnel_xs to xen-api-base-specs.git.

I think the diff is simple and no related stunnel functions
```
diff --git a/stunnel_xs.spec b/stunnel_xs.spec
index c34e961..528ca8a 100644
--- a/stunnel_xs.spec
+++ b/stunnel_xs.spec
@@ -1,13 +1,13 @@
 Summary: An SSL-encrypting socket wrapper
 Name: stunnel_xs
 Version: 4.56
-Release: 4%{?dist}.xs1
+Release: 5%{?dist}.xs1
 License: GPLv2
 Group: Applications/Internet
 URL: http://www.stunnel.org/
-Source0: https://www.stunnel.org/downloads/stunnel-%{version}.tar.gz
-Source1: https://www.stunnel.org/downloads/stunnel-%{version}.tar.gz.asc
-Source7: https://www.stunnel.org/downloads/stunnel-%{version}.tar.gz.sha256
+Source0: https://www.stunnel.org/downloads/archive/4.x/stunnel-%{version}.tar.gz
+Source1: https://www.stunnel.org/downloads/archive/4.x/stunnel-%{version}.tar.gz.asc
+Source7: https://www.stunnel.org/downloads/archive/4.x/stunnel-%{version}.tar.gz.sha256
 Source2: Certificate-Creation
 Source3: sfinger.xinetd
 Source4: stunnel-sfinger.conf
@@ -86,6 +86,9 @@ rm -rf $RPM_BUILD_ROOT
 %exclude %{_sysconfdir}/stunnel/*

 %changelog
+* Tue Feb 02 2016 Euan Harris <euan.harris@citrix.com> - 4.56-5.xs1
+- Use correct source URLs
+
 * Fri Jun 05 2015 Thomas Sanders <thomas.sanders@citrix.com> - 4.56-4.xs1
 - Rename package to stunnel_xs
 - Add pollhup.patch from Ross Lagerwall
```


I like to have the little dot here :(


Right, thanks.


ready_aim_fire (macumber) - x86_64-Linux-Ubuntu-14.04-cppcheck-1.61: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.svg)


Hvorfor denne utkommenteringen? Ser ikke at det er noe ny output


Tomme constructors som denne ville jeg helst inlinet


@aelintra what do you think to this for license checking?

What scenarios should contribute to licensing limits?


I agree, thanks for this.


Leyendo los medios sobre este tema, todo son congratulaciones y festejos, como suele pasar. Toda crítica es omitida.

Dicen que al desvincular los cálculos económicos del gobierno al salario mínimo, el salario mínimo "podria" crecer sin afectar multas, impuestos, intereses, etcétera.

Sustituyen al salario mínimo por un nebuloso e indefinido concepto de **Unidad de Medida y Actualización**.

Mi lectura es que esta desvinculación es para invisibilizar, esconder, las operaciones financieras gubernamentales y que el ciudadano no pueda ver la relación de estos con sus ingresos. Ya no habrá una manera directa y clara de ver las grandes diferencias económicas entre la población de México y su gobierno.

Claro, prometen tonterías como la posibilidad del aumento del salario mínimo cuando en realidad están invisibilizando ante la ley, las injusticia social que produce las diferencias salariales y de ingresos. Además de avanzar en el proyecto de convertir al Gobierno Méxicano en un instrumento financiero más, y no un rector y promotor de la vida social del país.


indent problem


develop (evanweaver) - i386-Windows-7-VisualStudio-12: OK (2362 of 2398 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-98.5%25-yellow.svg)


最近两个一起看，笑出声了。


TeamCity libpalaso :: palaso-precise64-master Continuous [Build 3.0.710.3517469600a60e2949c903d54916d7a177b813e8](http://build.palaso.org/viewLog.html?buildId=70156&buildTypeId=bt322) outcome was **SUCCESS**
Summary: Tests passed: 3377, ignored: 124 Build time: 00:10:03


The issue here is that title and title-background are both used by the bootstrap class (in one the title doesn't have a highlighted background and in the other it does). So, what would be the best way to support this? I see two options here:
1. Add title-background class to the old stylesheets(which will cause issues with your iframe stuff, although your code could likely grab the title by looking for title and then title-background if title does not exist).
2. Use both the title and title-background class at same time, rather than just title-background alone.

Is one of the above options acceptable for you? Or do you know of a 3rd option?

I definitely agree that folks should weigh in before this goes to the codebase, which is why I posted it on the forum :)

-brady


I like it. Now I understand why the object type was changing, ... It could have been either so you were forcing it to be an object.
This is now super clear!


@earthgecko I did not change the default PICKLE_PORT in settings.py. But it failed.
Trying 127.0.0.1...
telnet: connect to address 127.0.0.1: Connection refused
telnet: Unable to connect to remote host


This also adds the `async


I don't believe this implementation is right, it should be when initialized, attaching, disconnected or suspended that we queue messages


Neither is acceptable: The new desired CSS formatting should rely on the existing title class.

All of the cases where new b and p tags are added should not be done that way.  Change display to "block" in the css and change the font-weight.  Things will ultimately be more consistent that way.

I will only consider this acceptable when the absolute minimum of changes to the existing files is done.


Bare ta vekk hele #ifdef blokke før endelig commit, hvis dette ikke lengre trengs.


Is this now a public method, I'm worried we're now exposing a lot of internal methods to developers that are not part of our API. Less is definitely more and we want to expose as little of the API as possible to meet the requirements of [our IDL](http://docs.ably.io/client-lib-development-guide/features/#idl)


А разве то, что у меня в position, это не фиксит?


Removing b and p tags can be done. Note this code has undergone several reviews; would of been nice to get this specific feedback previously...


thanks for the heads up man!


@vhuber it's fine for stokes_kovasnay.cpp


are you sure ?


`m` is supposed to be the action monad, so `r` is just the persistent implementation used by that particular action monad.


This also adds the `async` variable which is recommended from the mathjax docs.


Again,
If some titles will have a background and some titles will not have a background on the bootstrap theme via CSS, how can we then support this? Do you have a solution?


develop (evanweaver) - Win64-Windows-7-VisualStudio-12: OK (2363 of 2398 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-98.54%25-yellow.svg)


![screen-shot-2016-03-10-at-5 00 26-pm](https://cloud.githubusercontent.com/assets/1426799/13665768/fb6df440-e6e8-11e5-87db-e27527a7e4b4.jpg)


TeamCity libpalaso :: palaso-precise64-libpalaso-2.6 Continuous [Build 2.6.1059.3517469600a60e2949c903d54916d7a177b813e8](http://build.palaso.org/viewLog.html?buildId=70157&buildTypeId=PalasoPrecise64v26Cont) outcome was **SUCCESS**
Summary: Tests passed: 3377, ignored: 124 Build time: 00:05:04


This should generally be ignored and not included in source control.


Feel free to ignore xHN35RQ@9a5510d - I did a little cleanup while I had the files open.


**SUCCESS** - TeamCity HotRod C# Client :: Release Windows 2 [Build 9](http://ci.infinispan.org/viewLog.html?buildId=37272&buildTypeId=HotRodCSharp_ReleaseWindows2&guest=1) for 6396809633bf909a9a6f7540994af9804d44f89f
Tests: 0, 0 failed (0 new), 0 ignored. Build time: 00:11:42


**SUCCESS** - TeamCity HotRod C# Client :: Release Windows 2 [Build 9](http://ci.infinispan.org/viewLog.html?buildId=37272&buildTypeId=HotRodCSharp_ReleaseWindows2&guest=1) for 6ee9b91732e2f108349ff583e30b5c3bbfbad717
Tests: 0, 0 failed (0 new), 0 ignored. Build time: 00:11:42


This isn't the best way to handle this... just an interim. It would be better to move all marginnote and sidenote content into footnotes for feed.xml. This way if someone is reading the site via a feed reader, they could still see the content at the bottom of each article. ref #34


@monkstone are you saying this 'detect_offline_links' will translate to camelcase but the one below with `manifestFile' does not ? if yes, than I think this can be fixed.


yes


indeed


Why would you zip this?  Also, in ALL of our other libraries, we have added `ably-common` as a submodule so that we don't have to hard code these resources in here and can easily keep them in sync, see https://github.com/ably/ably-java/blob/master/.gitmodules.  Please add this as a submodule.


extra space


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 18766](https://teamcity.mesosphere.io/viewLog.html?buildId=159728&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 254 Build time: 00:10:45


The changes to admin/sources/maintenance.index.inc.php should not have been part of this commit. It's a security update for a separate issue.


ok


Why is this class in the Ably namespace?  It's designed ONLY for tests and should not pollute our namespace.


Unfortunately, it's not really possible to parametrize this, see http://stackoverflow.com/a/28570677.

But I changed the names and will remove the duplicate code.


private ?


no visibility ?


Why are you excluding name field here??
Name has to be shown in the form


Hvorfor må vi ha med integranden inn i denne metoden. Ser det er tilsvarende i de andre ASM-klassene også, men ikke at den brukes noen steder. Mystisk og forvirrende Bør ryddes opp i.


I personally like this, it makes things easier with less python magic exposed to bear writers


>this branch and experiment on the project is pointless.

Why? The App will run on android N devices sooner or later. I prefer testing this sooner than later

>even things like unreproducible builds

Why are the builds unreproducible?
And why should experimental builds be reproducible?

>already lacks trust because of travis-based releases

What leads you to this opinion?


you probably don't need a version here


Added to this, why are you duplicating code, this already exists, see https://github.com/ably/ably-dotnet/blob/715a0ec2ce5d4db608bad6110e8c17d87a552701/src/Ably.AcceptanceTests/TestsSetup.cs.  I am really not happy that we are recreating what we have instead of fixing and reusing.


addOp(ops, "head", path.getHead()); is the important part I think


noise ?