Robersy Sanchez
| Snapshot Date: 2025-12-03 13:40 -0500 (Wed, 03 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/GenomAutomorphism |
| git_branch: devel |
| git_last_commit: 7283b3b |
| git_last_commit_date: 2025-10-29 11:17:59 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-04 11:35 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 831/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.13.0 (landing page) Robersy Sanchez
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.13.0 |
| 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_1.13.0.tar.gz |
| StartedAt: 2025-12-03 22:34:44 -0500 (Wed, 03 Dec 2025) |
| EndedAt: 2025-12-03 22:40:47 -0500 (Wed, 03 Dec 2025) |
| EllapsedTime: 362.6 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_1.13.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/GenomAutomorphism.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 2.339 0.061 20.744
autZ64 0.877 0.021 7.069
aut3D 0.737 0.046 6.861
autZ125 0.750 0.016 5.552
autZ5 0.558 0.020 6.596
* 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-3.23-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/4.6-arm64/Resources/library’ * installing *source* package ‘GenomAutomorphism’ ... ** this is package ‘GenomAutomorphism’ version ‘1.13.0’ ** 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)
GenomAutomorphism.Rcheck/tests/spelling.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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
0.073 0.026 0.097
GenomAutomorphism.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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
9.732 0.401 26.824
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.148 | 0.003 | 0.151 | |
| AutomorphismList | 0.937 | 0.014 | 0.951 | |
| CodonMatrix | 0.050 | 0.001 | 0.051 | |
| CodonSeq | 0.128 | 0.004 | 0.130 | |
| GRangesMatrixSeq | 0.063 | 0.001 | 0.065 | |
| ListCodonMatrix | 0.057 | 0.000 | 0.058 | |
| MatrixSeq | 0.039 | 0.001 | 0.041 | |
| aa_phychem_index | 0.036 | 0.003 | 0.040 | |
| aaindex1 | 0.013 | 0.000 | 0.013 | |
| aaindex2 | 0.006 | 0.000 | 0.006 | |
| aaindex3 | 0.004 | 0.000 | 0.003 | |
| aln | 0.020 | 0.001 | 0.021 | |
| aminoacid_dist | 1.155 | 0.316 | 3.461 | |
| as.AutomorphismList | 0.197 | 0.019 | 0.215 | |
| aut3D | 0.737 | 0.046 | 6.861 | |
| autZ125 | 0.750 | 0.016 | 5.552 | |
| autZ5 | 0.558 | 0.020 | 6.596 | |
| autZ64 | 0.877 | 0.021 | 7.069 | |
| autby_coef | 0.102 | 0.003 | 0.105 | |
| autm | 0.012 | 0.001 | 0.013 | |
| autm_3d | 0.017 | 0.001 | 0.018 | |
| autm_z125 | 0.016 | 0.002 | 0.018 | |
| automorphismByRanges | 0.029 | 0.002 | 0.031 | |
| automorphism_bycoef | 0.026 | 0.000 | 0.027 | |
| automorphism_prob | 0.292 | 0.008 | 0.299 | |
| automorphisms | 2.339 | 0.061 | 20.744 | |
| base2codon | 0.021 | 0.006 | 0.028 | |
| base2int | 0.002 | 0.000 | 0.003 | |
| base_methods | 0.140 | 0.010 | 0.151 | |
| brca1_aln | 0.022 | 0.001 | 0.024 | |
| brca1_aln2 | 0.019 | 0.001 | 0.020 | |
| brca1_autm | 0.162 | 0.001 | 0.164 | |
| cdm_z64 | 0.070 | 0.191 | 0.264 | |
| codon_coord | 0.396 | 0.003 | 0.399 | |
| codon_dist | 0.093 | 0.002 | 0.095 | |
| codon_dist_matrix | 0.015 | 0.005 | 2.332 | |
| codon_matrix | 0.170 | 0.002 | 0.174 | |
| conserved_regions | 0.103 | 0.001 | 0.104 | |
| covid_aln | 0.023 | 0.001 | 0.024 | |
| covid_autm | 0.015 | 0.001 | 0.016 | |
| cyc_aln | 0.030 | 0.001 | 0.032 | |
| 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 | 0.184 | 0.003 | 0.187 | |
| getAutomorphisms | 0.057 | 0.003 | 0.060 | |
| get_coord | 0.225 | 0.003 | 0.228 | |
| get_mutscore | 0.065 | 0.002 | 0.067 | |
| matrices | 0.217 | 0.001 | 0.219 | |
| mod | 0.000 | 0.000 | 0.001 | |
| modeq | 0.001 | 0.000 | 0.000 | |
| modlineq | 0.001 | 0.001 | 0.001 | |
| mut_type | 0 | 0 | 0 | |
| peptide_phychem_index | 0.047 | 0.003 | 0.049 | |
| reexports | 0.026 | 0.001 | 0.028 | |
| seqranges | 0.229 | 0.002 | 0.231 | |
| slapply | 0 | 0 | 0 | |
| sortByChromAndStart | 0.019 | 0.000 | 0.018 | |
| str2chr | 0.000 | 0.000 | 0.001 | |
| str2dig | 0 | 0 | 0 | |
| translation | 0.372 | 0.004 | 0.376 | |