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This page was generated on 2025-09-27 12:07 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
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: 2025-09-26 13:45 -0400 (Fri, 26 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GenomAutomorphism
Version: 1.11.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomAutomorphism_1.11.2.tar.gz
StartedAt: 2025-09-26 08:00:26 -0000 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 08:04:20 -0000 (Fri, 26 Sep 2025)
EllapsedTime: 233.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomAutomorphism.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomAutomorphism_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomAutomorphism.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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
aminoacid_dist 5.548  1.203   6.143
automorphisms  4.877  1.161   5.298
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomAutomorphism.Rcheck/00check.log’
for details.


Installation output

GenomAutomorphism.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GenomAutomorphism
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  0.202   0.023   0.211 

GenomAutomorphism.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
 26.089   3.527  29.336 

Example timings

GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings

nameusersystemelapsed
AutomorphismByCoef0.5610.0040.566
AutomorphismList2.8070.0202.836
CodonMatrix0.2460.0000.247
CodonSeq0.4710.0120.484
GRangesMatrixSeq0.2220.0280.250
ListCodonMatrix0.3140.0040.319
MatrixSeq0.1230.0000.124
aa_phychem_index0.0910.0040.094
aaindex10.0330.0000.034
aaindex20.0140.0000.015
aaindex30.0090.0000.010
aln0.0650.0000.065
aminoacid_dist5.5481.2036.143
as.AutomorphismList0.7550.1470.740
aut3D1.5050.3421.593
autZ1252.5700.8432.605
autZ51.0420.3581.179
autZ641.8800.4222.059
autby_coef0.3890.0160.405
autm0.0530.0000.053
autm_3d0.0510.0160.067
autm_z1250.0540.0040.058
automorphismByRanges0.1180.0310.150
automorphism_bycoef0.1100.0120.123
automorphism_prob1.4020.0751.482
automorphisms4.8771.1615.298
base2codon0.0580.0160.074
base2int0.0110.0000.012
base_methods0.6020.0800.684
brca1_aln0.0990.0000.099
brca1_aln20.0920.0000.093
brca1_autm0.4900.0080.499
cdm_z640.1410.0910.233
codon_coord0.8410.1520.995
codon_dist0.3370.0200.358
codon_dist_matrix2.8750.2713.153
codon_matrix0.8110.1230.937
conserved_regions0.4690.0080.478
covid_aln0.0640.0040.068
covid_autm0.0500.0030.054
cyc_aln0.1030.0120.116
cyc_autm0.0820.0040.086
dna_phyche0.0080.0000.009
dna_phychem0.0030.0000.004
extract-methods0.5900.0240.616
getAutomorphisms0.2320.0160.248
get_coord0.5550.0960.652
get_mutscore0.1880.0000.189
matrices0.5130.0240.538
mod0.0030.0000.002
modeq0.0020.0000.002
modlineq0.0040.0000.003
mut_type0.0030.0000.003
peptide_phychem_index0.1120.0080.121
reexports0.0750.0000.075
seqranges0.6200.0040.625
slapply0.0020.0000.002
sortByChromAndStart0.0850.0000.086
str2chr000
str2dig000
translation0.7440.0000.746