Robersy Sanchez
| Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-22 12:05 -0400 (Mon, 22 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| 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 829/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.11.2 (landing page) Robersy Sanchez
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| 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: 2025-09-21 19:38:48 -0400 (Sun, 21 Sep 2025) |
| EndedAt: 2025-09-21 19:41:08 -0400 (Sun, 21 Sep 2025) |
| EllapsedTime: 139.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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 2.491 0.067 21.083
aut3D 0.926 0.066 7.084
autZ64 0.895 0.022 7.075
autZ125 0.767 0.020 5.711
autZ5 0.579 0.024 6.913
* 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.
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-arm64/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)
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: aarch64-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
0.072 0.019 0.086
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: aarch64-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
9.470 0.387 26.050
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.142 | 0.004 | 0.149 | |
| AutomorphismList | 0.863 | 0.010 | 0.876 | |
| CodonMatrix | 0.050 | 0.001 | 0.051 | |
| CodonSeq | 0.123 | 0.006 | 0.128 | |
| GRangesMatrixSeq | 0.066 | 0.004 | 0.069 | |
| ListCodonMatrix | 0.064 | 0.001 | 0.065 | |
| MatrixSeq | 0.040 | 0.002 | 0.042 | |
| aa_phychem_index | 0.039 | 0.003 | 0.041 | |
| aaindex1 | 0.014 | 0.000 | 0.014 | |
| aaindex2 | 0.007 | 0.000 | 0.007 | |
| aaindex3 | 0.004 | 0.001 | 0.004 | |
| aln | 0.022 | 0.001 | 0.024 | |
| aminoacid_dist | 1.219 | 0.384 | 3.530 | |
| as.AutomorphismList | 0.194 | 0.024 | 0.218 | |
| aut3D | 0.926 | 0.066 | 7.084 | |
| autZ125 | 0.767 | 0.020 | 5.711 | |
| autZ5 | 0.579 | 0.024 | 6.913 | |
| autZ64 | 0.895 | 0.022 | 7.075 | |
| autby_coef | 0.104 | 0.002 | 0.107 | |
| autm | 0.014 | 0.000 | 0.014 | |
| autm_3d | 0.017 | 0.000 | 0.019 | |
| autm_z125 | 0.016 | 0.001 | 0.016 | |
| automorphismByRanges | 0.032 | 0.003 | 0.034 | |
| automorphism_bycoef | 0.028 | 0.003 | 0.031 | |
| automorphism_prob | 0.32 | 0.01 | 0.33 | |
| automorphisms | 2.491 | 0.067 | 21.083 | |
| base2codon | 0.022 | 0.003 | 0.028 | |
| base2int | 0.002 | 0.002 | 0.004 | |
| base_methods | 0.132 | 0.021 | 0.160 | |
| brca1_aln | 0.021 | 0.003 | 0.037 | |
| brca1_aln2 | 0.023 | 0.003 | 0.027 | |
| brca1_autm | 0.151 | 0.004 | 0.169 | |
| cdm_z64 | 0.073 | 0.314 | 0.401 | |
| codon_coord | 0.368 | 0.008 | 0.388 | |
| codon_dist | 0.079 | 0.002 | 0.081 | |
| codon_dist_matrix | 0.015 | 0.005 | 2.241 | |
| codon_matrix | 0.171 | 0.011 | 0.186 | |
| conserved_regions | 0.105 | 0.001 | 0.115 | |
| covid_aln | 0.024 | 0.001 | 0.026 | |
| covid_autm | 0.016 | 0.001 | 0.017 | |
| cyc_aln | 0.031 | 0.002 | 0.035 | |
| cyc_autm | 0.024 | 0.001 | 0.025 | |
| dna_phyche | 0.002 | 0.001 | 0.003 | |
| dna_phychem | 0.001 | 0.000 | 0.001 | |
| extract-methods | 0.173 | 0.003 | 0.179 | |
| getAutomorphisms | 0.057 | 0.002 | 0.059 | |
| get_coord | 0.252 | 0.002 | 0.269 | |
| get_mutscore | 0.061 | 0.002 | 0.063 | |
| matrices | 0.221 | 0.004 | 0.226 | |
| mod | 0.000 | 0.000 | 0.001 | |
| modeq | 0.001 | 0.000 | 0.000 | |
| modlineq | 0.000 | 0.000 | 0.001 | |
| mut_type | 0 | 0 | 0 | |
| peptide_phychem_index | 0.045 | 0.003 | 0.047 | |
| reexports | 0.023 | 0.001 | 0.023 | |
| seqranges | 0.220 | 0.002 | 0.221 | |
| slapply | 0.001 | 0.000 | 0.000 | |
| sortByChromAndStart | 0.021 | 0.000 | 0.021 | |
| str2chr | 0 | 0 | 0 | |
| str2dig | 0 | 0 | 0 | |
| translation | 0.379 | 0.003 | 0.382 | |