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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 830/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomAutomorphism 1.10.0  (landing page)
Robersy Sanchez
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/GenomAutomorphism
git_branch: RELEASE_3_21
git_last_commit: bf02d1b
git_last_commit_date: 2025-04-15 12:54:12 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GenomAutomorphism on kunpeng2

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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2025-10-14 09:27:17 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 09:31:31 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 254.2 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomAutomorphism.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.10.0’
* 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 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
automorphisms  6.044  1.085   6.439
aminoacid_dist 6.081  0.859   6.388
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘GenomAutomorphism’ ...
** this is package ‘GenomAutomorphism’ version ‘1.10.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.179   0.045   0.212 

GenomAutomorphism.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 
 28.773   2.786  31.324 

Example timings

GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings

nameusersystemelapsed
AutomorphismByCoef0.5630.0040.569
AutomorphismList3.0270.0233.062
CodonMatrix0.2440.0010.245
CodonSeq0.5010.0000.502
GRangesMatrixSeq0.2350.0110.248
ListCodonMatrix0.3470.0000.348
MatrixSeq0.1160.0030.121
aa_phychem_index0.0920.0000.092
aaindex10.0330.0000.034
aaindex20.0150.0000.015
aaindex30.010.000.01
aln0.0720.0000.071
aminoacid_dist6.0810.8596.388
as.AutomorphismList0.8230.1480.722
aut3D1.7210.3511.826
autZ1253.1900.8423.102
autZ51.1790.3301.301
autZ642.2180.3532.342
autby_coef0.3840.0120.397
autm0.0670.0080.075
autm_3d0.1010.0040.106
autm_z1250.0940.0000.095
automorphismByRanges0.1530.0280.182
automorphism_bycoef0.1300.0270.159
automorphism_prob1.3810.0281.412
automorphisms6.0441.0856.439
base2codon0.0680.0000.068
base2int0.0070.0040.010
base_methods0.5270.0840.613
brca1_aln0.0640.0160.081
brca1_aln20.0750.0040.079
brca1_autm0.5060.0120.520
cdm_z640.1440.0680.212
codon_coord1.1060.1191.229
codon_dist0.4210.0000.423
codon_dist_matrix2.8210.4553.295
codon_matrix0.8370.1000.939
conserved_regions0.5520.0120.566
covid_aln0.0980.0080.106
covid_autm0.0910.0040.095
cyc_aln0.1520.0000.153
cyc_autm0.1780.0040.182
dna_phyche0.0080.0000.008
dna_phychem0.0030.0000.003
extract-methods0.6100.0190.630
getAutomorphisms0.2600.0240.285
get_coord0.6730.1310.806
get_mutscore0.1920.0080.200
matrices0.6720.0000.673
mod0.0020.0000.002
modeq0.0010.0000.001
modlineq0.0030.0000.003
mut_type0.0030.0000.003
peptide_phychem_index0.1100.0080.118
reexports0.1200.0000.121
seqranges0.7090.0040.715
slapply0.0020.0000.002
sortByChromAndStart0.0880.0000.088
str2chr000
str2dig0.0010.0000.000
translation1.0130.0041.020