Mac ARM64 build report for BioC 3.17 - CHECK results for GenomAutomorphism on kjohnson2

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson2	macOS 12.6.1 Monterey	arm64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4347
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomAutomorphism_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenomAutomorphism.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.2.0’
* 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 ‘GenomAutomorphism’ 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘mod’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
automorphisms     4.880  0.194  99.313
aminoacid_dist    2.738  0.594  20.189
AutomorphismList  2.700  0.060   6.388
autZ64            1.794  0.063  32.713
aut3D             1.486  0.104  32.715
autZ125           1.456  0.063  33.568
autZ5             1.019  0.056  32.686
codon_dist_matrix 0.040  0.013   9.988
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(GenomAutomorphism)
  > 
  > test_check("GenomAutomorphism")
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 30 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-aa_mutmat.R:7:6'): multiplication works ──────────────────────
  mat && aa is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 30 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenomAutomorphism.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomAutomorphism
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘GenomAutomorphism’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘mod’ in package ‘GenomAutomorphism’
** help
*** installing help indices
*** copying figures
** 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 (GenomAutomorphism)

Tests output


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE, error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.213   0.065   0.353


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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.

> library(testthat)
> library(GenomAutomorphism)
> 
> test_check("GenomAutomorphism")
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 30 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-aa_mutmat.R:7:6'): multiplication works ──────────────────────
mat && aa is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 7 | SKIP 0 | PASS 30 ]
Error: Test failures
Execution halted

Example timings

name	user	system	elapsed
AutomorphismByCoef	0.529	0.016	1.264
AutomorphismList	2.700	0.060	6.388
CodonSeq	0.539	0.009	1.264
aa_mutmat	0.025	0.007	0.068
aaindex2	0.009	0.003	0.026
aaindex3	0.005	0.003	0.009
aminoacid_dist	2.738	0.594	20.189
as.AutomorphismList	0.646	0.053	1.091
aut3D	1.486	0.104	32.715
autZ125	1.456	0.063	33.568
autZ5	1.019	0.056	32.686
autZ64	1.794	0.063	32.713
autm	0.099	0.003	0.152
automorphismByRanges	0.188	0.004	0.289
automorphism_bycoef	0.162	0.004	0.256
automorphisms	4.880	0.194	99.313
base2codon	0.116	0.005	0.165
base2int	0.002	0.001	0.007
base_coord	0.247	0.008	0.324
cdm_z64	0.029	0.004	0.041
codon_coord	0.886	0.013	1.172
codon_dist	0.404	0.010	0.522
codon_dist_matrix	0.040	0.013	9.988
conserved_regions	0.564	0.035	0.762
extract-methods	0.560	0.020	0.746
getAutomorphisms	0.247	0.012	0.326
get_coord	0.593	0.016	0.767
get_mutscore	0.140	0.007	0.184
matrices	0.572	0.010	0.744
mod	0.002	0.000	0.003
modeq	0.001	0.000	0.001
modlineq	0.002	0.001	0.005
mut_type	0.002	0.000	0.002
reexports	0.174	0.006	0.233
seqranges	0.611	0.008	0.801
slapply	0.003	0.001	0.004
sortByChromAndStart	0.074	0.001	0.093
str2chr	0.000	0.000	0.001
str2dig	0.001	0.000	0.002
translation	0.877	0.012	1.151

CHECK results for GenomAutomorphism on kjohnson2

Summary

Command output

Installation output

Tests output

Example timings