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This page was generated on 2025-09-26 12:04 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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

Package 829/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomAutomorphism 1.11.2  (landing page)
Robersy Sanchez
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/GenomAutomorphism
git_branch: devel
git_last_commit: 85d32ad
git_last_commit_date: 2025-07-28 14:45:12 -0400 (Mon, 28 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GenomAutomorphism on lconway

To the developers/maintainers of the GenomAutomorphism package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomAutomorphism.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GenomAutomorphism
Version: 1.11.2
Command: /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_1.11.2.tar.gz
StartedAt: 2025-09-25 21:22:00 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 21:29:05 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 425.0 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomAutomorphism.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GenomAutomorphism.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.11.2’
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
  ‘[S4Vectors:S4Vectors-internals]{setValidity2}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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     6.502  0.151  63.329
aminoacid_dist    3.401  0.989  10.878
autZ64            2.360  0.057  21.305
aut3D             1.971  0.109  21.349
autZ125           1.917  0.051  16.861
autZ5             1.404  0.048  19.788
codon_dist_matrix 0.038  0.010   7.296
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/GenomAutomorphism.Rcheck/00check.log’
for details.


Installation output

GenomAutomorphism.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomAutomorphism
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘GenomAutomorphism’ ...
** this is package ‘GenomAutomorphism’ version ‘1.11.2’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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

GenomAutomorphism.Rcheck/tests/spelling.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE, error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
All Done!
> 
> proc.time()
   user  system elapsed 
  0.191   0.077   0.261 

GenomAutomorphism.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.

> library(testthat)
> library(GenomAutomorphism)
> 
> test_check("GenomAutomorphism")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 24.772   1.174  76.279 

Example timings

GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings

nameusersystemelapsed
AutomorphismByCoef0.5260.0130.542
AutomorphismList2.8130.0502.887
CodonMatrix0.2140.0030.218
CodonSeq0.4950.0250.525
GRangesMatrixSeq0.2150.0190.235
ListCodonMatrix0.2480.0060.259
MatrixSeq0.1010.0050.106
aa_phychem_index0.0970.0120.109
aaindex10.0340.0030.037
aaindex20.0150.0020.017
aaindex30.0090.0020.011
aln0.1080.0060.115
aminoacid_dist 3.401 0.98910.878
as.AutomorphismList0.6430.0390.688
aut3D 1.971 0.10921.349
autZ125 1.917 0.05116.861
autZ5 1.404 0.04819.788
autZ64 2.360 0.05721.305
autby_coef0.3340.0050.343
autm0.0450.0040.050
autm_3d0.0650.0040.069
autm_z1250.0540.0040.057
automorphismByRanges0.1110.0070.119
automorphism_bycoef0.0930.0070.100
automorphism_prob1.1000.0401.146
automorphisms 6.502 0.15163.329
base2codon0.1180.0240.153
base2int0.0090.0010.010
base_methods0.5460.0320.582
brca1_aln0.0730.0040.077
brca1_aln20.0770.0040.082
brca1_autm0.5260.0070.541
cdm_z640.2230.4750.705
codon_coord0.9850.0111.006
codon_dist0.3370.0070.346
codon_dist_matrix0.0380.0107.296
codon_matrix0.6680.0150.685
conserved_regions0.4030.0050.410
covid_aln0.1150.0060.122
covid_autm0.0530.0030.055
cyc_aln0.1550.0060.159
cyc_autm0.0740.0030.077
dna_phyche0.0060.0020.007
dna_phychem0.0030.0000.003
extract-methods0.5490.0060.558
getAutomorphisms0.1950.0060.201
get_coord0.6570.0100.669
get_mutscore0.1750.0090.185
matrices0.5890.0110.602
mod0.0020.0000.003
modeq0.0010.0000.001
modlineq0.0040.0010.004
mut_type0.0020.0000.002
peptide_phychem_index0.1140.0080.122
reexports0.0680.0030.071
seqranges0.6210.0070.631
slapply0.0020.0010.002
sortByChromAndStart0.0730.0010.074
str2chr0.0000.0000.001
str2dig0.0000.0000.001
translation0.8710.0140.889