Fix CRAN issues - Githubissues

Dear maintainer,

Please see the problems shown on
[<https://cran.r-project.org/web/checks/check_results_pirouette.html>](https://cran.r-project.org/web/checks/check_results_pirouette.html).

Please correct before 2022-10-21 to safely retain your package on CRAN.

There is a check service for M1mac issues: see
https://www.stats.ox.ac.uk/pub/bdr/M1mac/README.txt .

The CRAN Team

From https://www.stats.ox.ac.uk/pub/bdr/M1mac/pirouette.out:

* using log directory ‘/Users/ripley/R/packages/tests-devel/pirouette.Rcheck’
* using R Under development (unstable) (2022-10-10 r83059)
* using platform: aarch64-apple-darwin21.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘pirouette/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pirouette’ version ‘1.6.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pirouette’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘pirouette-Ex.R’ failed
The error most likely occurred in:

> ### Name: sim_true_alignment
> ### Title: Simulate the true alignment from the true phylogeny
> ### Aliases: sim_true_alignment
> 
> ### ** Examples
> 
> 
> # Create the phylogeny to simulate the alignment on
> n_taxa <- 5
> true_phylogeny <- ape::rcoal(n_taxa)
> 
> root_sequence <- "aaaacgt"
> 
> # Use default settings to create the alignment
> alignment_params <- create_alignment_params(
+   sim_tral_fun =
+     get_sim_tral_with_std_nsm_fun(
+       mutation_rate = 1.0
+   ),
+   root_sequence = root_sequence
+ )
> 
> # Simulate the alignment
> alignment <- sim_true_alignment(
+   true_phylogeny = true_phylogeny,
+   alignment_params = alignment_params,
+ )
Error: sum(freqs) == 1 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [20s/20s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/ripley/R/packages/tests-devel/pirouette.Rcheck/00check.log’
for details.

       52.40 real        44.91 user         6.06 sys

richelbilderbeek / pirouette

Fix CRAN issues #432