Mac ARM64 build report for BioC 3.18 - CHECK results for GenomAutomorphism on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4388
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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/GenomAutomorphism.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.4.0’
* 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     5.780  0.187  65.953
aminoacid_dist    3.557  0.933  11.473
autZ64            2.131  0.065  22.418
aut3D             1.814  0.143  23.135
autZ125           1.822  0.074  23.737
autZ5             1.311  0.066  21.822
codon_dist_matrix 0.043  0.009   6.702
* 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-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 
  0.234   0.058   0.281


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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	0.543	0.010	0.559
AutomorphismList	3.153	0.034	3.244
CodonSeq	0.437	0.011	0.448
aa_mutmat	0.028	0.005	0.033
aaindex2	0.012	0.001	0.012
aaindex3	0.008	0.001	0.009
aminoacid_dist	3.557	0.933	11.473
as.AutomorphismList	0.681	0.058	0.751
aut3D	1.814	0.143	23.135
autZ125	1.822	0.074	23.737
autZ5	1.311	0.066	21.822
autZ64	2.131	0.065	22.418
autm	0.084	0.006	0.099
automorphismByRanges	0.151	0.005	0.156
automorphism_bycoef	0.139	0.004	0.144
automorphisms	5.780	0.187	65.953
base2codon	0.078	0.005	0.110
base2int	0.002	0.000	0.003
base_coord	0.173	0.009	0.182
cdm_z64	0.032	0.002	0.034
codon_coord	1.088	0.012	1.102
codon_dist	0.315	0.007	0.322
codon_dist_matrix	0.043	0.009	6.702
conserved_regions	0.466	0.042	0.509
extract-methods	0.637	0.015	0.652
getAutomorphisms	0.202	0.012	0.215
get_coord	0.544	0.012	0.560
get_mutscore	0.113	0.003	0.115
matrices	0.551	0.027	0.583
mod	0.002	0.001	0.003
modeq	0.001	0.001	0.001
modlineq	0.002	0.002	0.004
mut_type	0.002	0.000	0.002
reexports	0.149	0.010	0.160
seqranges	0.654	0.007	0.662
slapply	0.003	0.001	0.003
sortByChromAndStart	0.057	0.000	0.058
str2chr	0.000	0.000	0.001
str2dig	0	0	0
translation	1.017	0.011	1.029

CHECK results for GenomAutomorphism on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings