No, I meant :

CreationMessage testMessage = CreationMessage.builder()
                .mailboxIds(ImmutableList.of("dead-bada55"))
                .subject("subject")
                .from(DraftEmailer.builder().name("sender").build())
                .textBody("")
                .build();

In one test and :

CreationMessage testMessage = CreationMessage.builder()
                .mailboxIds(ImmutableList.of("dead-bada55"))
                .subject("subject")
                .from(DraftEmailer.builder().name("sender").build())
                .htmlBody("")
                .build();

In an othet test...


Почему бы кстати не сделать замену средствами питона?


update the file


이것도 import 끼리 모아주시면 더 보기 좋지 않을까요


I like this, but isn't it a *de*generalization, making types more specific?


the lines with the System.out were removed not added.


Usually _shutdown_ are performed in the @After method.


> This spec file is picked from trunk/xen-dist-ocaml.hg/SPECS/stunnel_xs.spec

I think I'm right in saying that this is not the spec file used any more in the build and that's why the version you found is not the latest. xen-dist-ocaml.hg has moved to xen-api-base-specs.git. @euanh can you confirm?

I think the base version you import should be this version and you will still need to change the release to be at least one greater or maybe even something more descriptive for the backport?


Because what you writed here in this test is covered by an other one (convertToMimeShouldFailWhenHtmlBodyAndTxtBodyProvided )


Great, I can revert nl again :angry:


Я думаю это не очень хорошая идея - делать греп вот так. Например, под виндой этот код не заработает. Насколько я понимаю файл `gut_bact_list_path` небольшой и поместится в память, можно его загрузить и в питоне проделать все операции

Получается что в коде есть зависимость от баша)


Let's change to `Compatible with Cs-Cart version 4.3.x`


many comments... but new faster code


[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))
                               ~^
```


This was added to verify request data during developer testing. Removed with later commits.


Not sure about the value of these changes. I don't think most people working on this code will have an `.idea` file, and it looks like you just fixed up the quotes because your IDE flagged it somehow. However, this broke the automated tests and doesn't actually improve anything materially. So I would prefer to just leave out the changes in this commit.


This actually happens during the `pretty-expanded` tests. `rustc --pretty=expanded` outputs the injected prelude import declarations explicitly, so when we compile this output, the explicit prelude overwrites the injected prelude.

I don't think this is that big of a deal since `#[prelude_import]` isn't meant for end users.


Acknowledged, Can't fix as this code is obsolete and no longer exists.


:+1: for not suppressing the warning :laughing:


I think we shouldn't return assemblies here if the Extensions directory doesn't exist, because in this case we will have an empty assemblies set. We only need to skip "using" block in the case if directory doesn't exist and still execute the rest of the method to get available assemblies.


fixedup again


Recommender with Cosine Similarity


If you call it TODO, you have to fix it before merging.  (-:

- https://github.com/liqd/aula/blob/90c7fb649483302c7998c22882bbe3f7928a81e2/docs/styleguide.md
- https://github.com/liqd/thentos/blob/ca9e16a342b885ebb0f209efe60415990adeca05/docs/styleguide.md#source-comment-keywords


(Wait, you actually did that.  Please ignore.)


or even the plugin allready built, it would be wonderful :p


There is a bug in line 28:
```cpp
else(tt[i][i] == 99)
 {
 	return 0;
 }
```
should be
```cpp
else if(tt[i][i] == 99)
 {
 	return 0;
 }
```


опечатку исправил, попадёт в следующий пул реквест. Тайтлы убрал, сам не знаю для чего их туда впихнул. Видимо перезанимался =)


agree, it will be necessary to fix


I'd forgotten that deleting a blank line could require a gofmt...


Nice.


It is absolutely NOT acceptable to change existing css classes to something new...
(title to title-background) as it will break existing style sheets.


Do we have to memoize this or is it cheap enough to calculate twice?

I'm not a fan of using `defined?` so I'm worried this increases complexity with disproportionate gain.


yep


why I think it doesn't work?

First it runs for long time and then at the end it lists all tests which were ran and surprisingly there are almost all *.windup.test.xml files listed that passed. I haven't gone deeply into discovery why it happened and ignored filter for the given ID but now as you see it as it should work, I probably need to debug the processing.
Anyway thanks for confirmation I also thought it should work at least while looking at the code.


这个用法不好，可能会导致生成一堆线程，应该把文件里的文件分成多份，起几个线程，每个线程去跑其中的一份，否则像现在这样写如果有1000个文件就起了1000个线程，这是不对的。


I kinda understand your point of view, but then - Mesos treats inconsistently dockerized vs. non-dockerized tasks. As I exhaustively described in the Jira task: for my tests I use simple python script which I use as a

1. standalone script
2. same script wrapped in a simple docker container

And when I restart (from marathon) the "standalone" script, mesos sends SIGTERM as well - the script traps the signal (like the dockerized version), ends peacefully and mesos shows TASK_FINISHED - unlike the dockerized version, which  shows TASK_KILLED..

When you consider the usecase of using Marathon - you use it for long running APIs, websites, databases, etc.. And none of them usually quits "themselves". You only want to restart them during upgrade/change configuration/redeploy... And you want them to restart gracefully, so you ask them to end with SIGTERM - and when they end - they are FINISHED.

But again - when you think I'm not right - you should consider changing the standard executor as well - as http://prntscr.com/adelm6 - because mesos then inconsistently handles docker/non-docker tasks.


Wow!
It seems now you have much more time for coding.
And i have lots of tasks at my primary work.
Some later i will learn every new line!


Why was this comment added


Just found this on stackoverflow when looking for something else

// Make alert snipped

UIWindow *alertWindow = [[UIWindow alloc] initWithFrame:[UIScreen
mainScreen].bounds];alertWindow.rootViewController = [[UIViewController
alloc] init];
alertWindow.windowLevel = UIWindowLevelAlert + 1;
[alertWindow makeKeyAndVisible];
[alertWindow.rootViewController presentViewController:alert animated:YES
completion:nil];

You mean something similar to this?

Not played with any other window than the default.

Wondering at what stage in the lifecycle things like loading the coredata
stuff happen (since we alert if that fails) - are we still showing splash
screen and can we overlay a window over it? And at what point does the
window get disposed of (ARC) ?

On 16 February 2016 at 23:00, ronnienessa <notifications@github.com> wrote:

> In cases were we don´t have a view controller to present the alert on we
> could create a separate UIWindow with a transparent root view controller to
> present the alert on.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/javaBin/ems-ios/commit/a16f1402935efffa382e12725a79d68a9d27352d#commitcomment-16131664>
> .
>


这是 pycharm 的配置文件，不需要提交上来了。


hmm, even more human readable than silence stdout...


No idea what this one does, but I guess that's the WIP-part here. :-)


@yutongche - sent you the info in another channel.  Users always seem to find a way :)


Is it surprising that two invalid URNs would not be equal?

```ruby
URN.new('foo') == URN.new('foo')
#=> false
```


:+1: looks good!


Hi emufreak, thank you for taking the some time and doing this. ;-)


@jmwatsonuk that's how you avoid needing an empty constructor (there may be some magic annotation that solves the "problem" some other way) :wink:


Isn't this test already out there?


@spras the copy/remove function is great ! i only had a problem with an extension just puttin the standard app/etc/modules folder in modman file - after removing all module xml files were removed. but thats a problem of writing a good modman file. or perhaps logic can be improved like in the https://github.com/mhauri/generate-modman script - never delete standard magento folders


All right. I made this comment as an optional improvement suggestion since I spotted a potential opportunity to help make a Go project slightly better, that's all.

I understand you're not actively working on/supporting this project, so it's fair if you choose not to implement it. I agree that it's quite unlikely to make a difference in real world situations. People usually don't write their import paths [this way](https://play.golang.org/p/Ed9BLgJiel) hehe. ;)


Yep. A very sensible set of rules, BTW.


Sorry for the lame question, but are you 100% sure that the `libpcre3-dev` package is not needed?

I started to get `invalid regular expression '[^\p{L}]+'` errors after this commit, eg at https://travis-ci.org/Rapporter/pander/builds/109239605 and for any build since then.

The most recent builds includes some more debugging info in this, eg in https://travis-ci.org/Rapporter/pander/builds/114996544

```
2: In gsub("[^\\p{L}]+", "", word, perl = TRUE) :
  PCRE pattern compilation error
	'support for \P, \p, and \X has not been compiled'
	at 'p{L}]+'
```

Which made me think about this might be related. Sorry for the noise if not :)


Resolves https://github.com/Azure/azure-mobile-apps-node/issues/371.

@mamaso heads up on this minor change. You reckon this works well enough for single commit changes, i.e. no heavyweight PR required?


I am not clear what the benefit is to switching the order here?


What is `AblySimpleRestClient`?


Hi yehster,
I also had the same initial reaction, but then I tested it. Did you test it? Test it out and you will think differently...
-brady


yep, I'd also add equivalent of command `AVOCADO_LOG_EARLY=y avocado run passtest --silent`


perhaps you can change AAI to Authentication, Authorization and Identity


通过


Test


Crawled 1,000,000 apps and store them into MongoDB


this should maybe also cover a possible line break before ")"


And one more note: when I issue `docker stop` manually from the server - mesos shows the task as FINISHED too...


Please undo.


Yes, we can have this as some temporary solution, but we need to think how to make it more flexible in the future. I think we need some possibility to specify some rules for all types of the assemblies (controllers, view models, views, resources, data etc) to improve performance. Maybe we can use some assembly attributes for that...


Initial?


here is the demo(note the old theme titles still look good):
http://www.open-emr.org/wiki/index.php/Development_Demo#192.168.1.131


missing dot


Test test test


Remove instead of commenting out?  Alternatively, comment on why it's still there?


[add more stuff to your `.gitignore` next time](https://github.com/qianliok/spring-learning/blob/dxl_chapter01/chapter01/dxl/.gitignore) :wink:


Please move ahead


A belle-sip lefordul a 3.5.2-es antlr3-mal? Szerintem csak a 3.4-es jó neki.


Not necessarily
A) This means that you have to hit the FS
B) You might not have permissions to the path


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.

@agilob
>Most android devices on the market don't support java7. Android 6 is still on Java7. Pushing forward to java8, which is still not officially supported by android itself is asking for problems

The java8 compilation with jack bases its implementation of lambda expressions on anonymous classes. This approach allows them to be backwards compatible and executable on earlier versions of Android.
For more information read here: http://developer.android.com/preview/j8-jack.html


Shouldn't this have been stayed in the users.raml ?


Nice!


Bedankt voor de snelle reactie en de oplettendheid. Mathias fucked up again! Will work on it:)


Thinking of [WEWUT](https://leanpub.com/wewut)'s "no setup", would this be easier to read if the `foo` and `foo_eq` were defined here?

As it is, I have to scan up to work out what the actual equivalent values are and it feels more [DRY than DAMP](http://stackoverflow.com/questions/6453235/what-does-damp-not-dry-mean-when-talking-about-unit-tests).


According to https://msdn.microsoft.com/en-us/library/bb384267(v=vs.110).aspx#Anchor_1, `
These uses for DateTimeOffset values are much more common than those for DateTime values. As a result, DateTimeOffset should be considered the default date and time type for application development.`.  Are you sure this is the right move?


Typo, should be `script`, not `scrit` ...


better comment


Why is this pulled out of the users.raml?


Cool. I didn't split up my train set with Kfol. I might try this too. Cross validation seems to be a useful function, too.

There is no need to rename the file to titanic_LinReg.py. Just make a new branch and keep working on titanic.py. Git will make sure everything is kept separate until it is actually merged. You can also branch off from a branch as many times as you want.