Multiple platform build/check report for BioC 3.16 - CHECK results for GenomAutomorphism on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4502
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4282
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4310
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_1.0.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/GenomAutomorphism.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.0.3’
* 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 ... WARNING
Undocumented S4 methods:
  generic 'names<-' and siglist 'AutomorphismList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
aminoacid_dist    4.757  3.999  10.321
automorphisms     4.398  0.757 144.663
autZ64            1.724  0.289  58.415
autZ125           1.506  0.377  56.049
aut3D             1.527  0.330  58.737
autZ5             1.211  0.302  80.356
codon_dist_matrix 0.037  0.010   6.544
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/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/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.161   0.058   0.211


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 17.258   2.502 201.201

Example timings

name	user	system	elapsed
AutomorphismByCoef	0.762	0.011	0.777
AutomorphismList	2.215	0.063	2.281
CodonSeq	0.463	0.015	0.479
aa_mutmat	0.023	0.005	0.029
aaindex2	0.008	0.001	0.009
aaindex3	0.005	0.001	0.006
aminoacid_dist	4.757	3.999	10.321
as.AutomorphismList	2.387	1.969	0.561
aut3D	1.527	0.330	58.737
autZ125	1.506	0.377	56.049
autZ5	1.211	0.302	80.356
autZ64	1.724	0.289	58.415
autm	0.094	0.224	0.455
automorphismByRanges	0.107	0.007	0.114
automorphism_bycoef	0.101	0.005	0.106
automorphisms	4.398	0.757	144.663
base2codon	0.098	0.022	0.123
base2int	0.002	0.001	0.002
base_coord	0.199	0.010	0.210
cdm_z64	0.021	0.001	0.023
codon_coord	0.857	0.014	0.871
codon_dist	0.323	0.008	0.332
codon_dist_matrix	0.037	0.010	6.544
conserved_regions	0.353	0.022	0.376
extract-methods	0.738	0.014	0.755
getAutomorphisms	0.154	0.009	0.162
get_coord	0.488	0.021	0.510
get_mutscore	0.113	0.002	0.115
matrices	0.480	0.008	0.490
mod	0.002	0.001	0.003
modeq	0.000	0.001	0.002
modlineq	0.002	0.002	0.004
mut_type	0.002	0.000	0.003
reexports	0.116	0.006	0.122
seqranges	0.504	0.004	0.511
slapply	0.002	0.000	0.002
sortByChromAndStart	0.049	0.000	0.049
str2chr	0.001	0.001	0.001
str2dig	0.000	0.001	0.001
translation	0.829	0.007	0.839

CHECK results for GenomAutomorphism on lconway

Summary

Command output

Installation output

Tests output

Example timings