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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rhinotypeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rhinotypeR_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/rhinotypeR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rhinotypeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhinotypeR’ version ‘1.3.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rhinotypeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assignTypes: no visible binding for global variable ‘prototypes’
Undefined global functions or variables:
  prototypes
* checking Rd files ... NOTE
checkRd: (-1) rhinotypeR.Rd:54: Escaped LaTeX specials: \~
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'alignToRefs.Rd':
  ‘deleteMissingDataSites’

Missing link(s) in Rd file 'getPrototypeSeqs.Rd':
  ‘alignToRefs()’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  alignToRefs.Rd: deleteMissingDataSites
  getPrototypeSeqs.Rd: alignToRefs()
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rhinotypeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SNPeek-internal
> ### Title: Internal helpers for SNPeek/plotAA
> ### Aliases: SNPeek-internal compareAndColorSequences compute_cache
> ###   SNPeekCache subset_cache plot_window
> ### Keywords: internal
> 
> ### ** Examples
> 
> seqs <- c(Ref="ATGC", S1="ATGT", S2="ATAC")
> cmap <- c(A="green", T="red", C="blue", G="gold")
> compareAndColorSequences(seqs, cmap)
Error in compareAndColorSequences(seqs, cmap) : 
  could not find function "compareAndColorSequences"
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `assignTypes(test_aln, model = "JC69")` produced output.
  ── Failure ('test-07_overallMeanDistance.R:50:3'): overallMeanDistance runs with common models ──
  `overallMeanDistance(simple_dna, model = "IUPAC")` produced output.
  ── Failure ('test-07_overallMeanDistance.R:51:3'): overallMeanDistance runs with common models ──
  `overallMeanDistance(simple_dna, model = "raw")` produced output.
  ── Failure ('test-07_overallMeanDistance.R:52:3'): overallMeanDistance runs with common models ──
  `overallMeanDistance(simple_dna, model = "JC69")` produced output.
  ── Error ('test-10_plotTree.R:3:1'): (code run outside of `test_that()`) ───────
  Error: 'local_null_device' is not an exported object from 'namespace:testthat'
  ── Error ('test-11_plotAA.R:2:1'): (code run outside of `test_that()`) ─────────
  Error: 'local_null_device' is not an exported object from 'namespace:testthat'
  
  [ FAIL 17 | WARN 0 | SKIP 0 | PASS 72 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ≈ (U+2248)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE

Status: 3 ERRORs, 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/rhinotypeR.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rhinotypeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘rhinotypeR’ ...
** this is package ‘rhinotypeR’ version ‘1.3.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rhinotypeR)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(rhinotypeR)
> 
> test_check("rhinotypeR")
use default substitution matrix
use default substitution matrix
use default substitution matrix
use default substitution matrix
use default substitution matrix

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[ FAIL 17 | WARN 0 | SKIP 0 | PASS 72 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-02_alignToRefs.R:44:3'): alignToRefs: invalid method is rejected ──
Error in `match.arg(method, c("ClustalW", "ClustalOmega", "Muscle"))`: 'arg' should be one of "ClustalW", "ClustalOmega", "Muscle"
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test-02_alignToRefs.R:44:3
 2. │ └─testthat:::expect_condition_matching(...)
 3. │   └─testthat:::quasi_capture(...)
 4. │     ├─testthat (local) .capture(...)
 5. │     │ └─base::withCallingHandlers(...)
 6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 7. └─rhinotypeR::alignToRefs(seqs, method = "BogusMethod")
 8.   └─base::match.arg(method, c("ClustalW", "ClustalOmega", "Muscle"))
── Error ('test-03_SNPeek.R:3:1'): (code run outside of `test_that()`) ─────────
Error: 'local_null_device' is not an exported object from 'namespace:testthat'
── Failure ('test-04_countSNPs.R:47:3'): countSNPs diagonal is zero ────────────
diag(result) (`actual`) not equal to rep(0L, 4) (`expected`).

`names(actual)` is a character vector ('Seq1', 'Seq2', 'Seq3', 'Seq4')
`names(expected)` is absent
── Failure ('test-04_countSNPs.R:116:3'): countSNPs handles ambiguous bases ────
`result <- countSNPs(ambiguous)` produced output.
── Failure ('test-05_pairwiseDistances.R:47:3'): pairwiseDistances diagonal is zero ──
diag(result) (`actual`) not equal to rep(0, 4) (`expected`).

`names(actual)` is a character vector ('Seq1', 'Seq2', 'Seq3', 'Seq4')
`names(expected)` is absent
── Failure ('test-05_pairwiseDistances.R:83:3'): pairwiseDistances model parameter works ──
`pairwiseDistances(simple_dna, model = "IUPAC")` produced output.
── Failure ('test-05_pairwiseDistances.R:84:3'): pairwiseDistances model parameter works ──
`pairwiseDistances(simple_dna, model = "raw")` produced output.
── Failure ('test-05_pairwiseDistances.R:85:3'): pairwiseDistances model parameter works ──
`pairwiseDistances(simple_dna, model = "JC69")` produced output.
── Failure ('test-05_pairwiseDistances.R:121:3'): pairwiseDistances handles ambiguous bases ──
`result <- pairwiseDistances(ambiguous, model = "IUPAC")` produced output.
── Failure ('test-06_assignTypes.R:83:3'): assignTypes model parameter works ───
`assignTypes(test_aln, model = "IUPAC")` produced output.
── Failure ('test-06_assignTypes.R:84:3'): assignTypes model parameter works ───
`assignTypes(test_aln, model = "raw")` produced output.
── Failure ('test-06_assignTypes.R:85:3'): assignTypes model parameter works ───
`assignTypes(test_aln, model = "JC69")` produced output.
── Failure ('test-07_overallMeanDistance.R:50:3'): overallMeanDistance runs with common models ──
`overallMeanDistance(simple_dna, model = "IUPAC")` produced output.
── Failure ('test-07_overallMeanDistance.R:51:3'): overallMeanDistance runs with common models ──
`overallMeanDistance(simple_dna, model = "raw")` produced output.
── Failure ('test-07_overallMeanDistance.R:52:3'): overallMeanDistance runs with common models ──
`overallMeanDistance(simple_dna, model = "JC69")` produced output.
── Error ('test-10_plotTree.R:3:1'): (code run outside of `test_that()`) ───────
Error: 'local_null_device' is not an exported object from 'namespace:testthat'
── Error ('test-11_plotAA.R:2:1'): (code run outside of `test_that()`) ─────────
Error: 'local_null_device' is not an exported object from 'namespace:testthat'

[ FAIL 17 | WARN 0 | SKIP 0 | PASS 72 ]
Error: Test failures
Execution halted