Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-03 12:05 -0400 (Wed, 03 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4826 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 824/2321 | 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: 2025-09-02 21:00:37 -0400 (Tue, 02 Sep 2025) |
EndedAt: 2025-09-02 21:07:37 -0400 (Tue, 02 Sep 2025) |
EllapsedTime: 420.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomAutomorphism.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 (2025-06-13) * 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 6.396 0.142 62.467 aminoacid_dist 3.357 0.983 11.248 autZ64 2.232 0.067 20.463 aut3D 2.082 0.114 21.218 autZ125 1.990 0.052 16.898 autZ5 1.477 0.055 20.545 codon_dist_matrix 0.044 0.010 7.522 * 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-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)
GenomAutomorphism.Rcheck/tests/spelling.Rout
R version 4.5.1 (2025-06-13) -- "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 0.200 0.077 0.270
GenomAutomorphism.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "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 25.069 1.127 74.834
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
name | user | system | elapsed | |
AutomorphismByCoef | 0.523 | 0.013 | 0.540 | |
AutomorphismList | 2.738 | 0.039 | 2.794 | |
CodonMatrix | 0.201 | 0.003 | 0.206 | |
CodonSeq | 0.516 | 0.021 | 0.540 | |
GRangesMatrixSeq | 0.200 | 0.019 | 0.222 | |
ListCodonMatrix | 0.256 | 0.007 | 0.263 | |
MatrixSeq | 0.123 | 0.006 | 0.130 | |
aa_phychem_index | 0.094 | 0.012 | 0.106 | |
aaindex1 | 0.037 | 0.003 | 0.040 | |
aaindex2 | 0.015 | 0.002 | 0.018 | |
aaindex3 | 0.009 | 0.002 | 0.011 | |
aln | 0.128 | 0.007 | 0.137 | |
aminoacid_dist | 3.357 | 0.983 | 11.248 | |
as.AutomorphismList | 0.682 | 0.044 | 0.734 | |
aut3D | 2.082 | 0.114 | 21.218 | |
autZ125 | 1.990 | 0.052 | 16.898 | |
autZ5 | 1.477 | 0.055 | 20.545 | |
autZ64 | 2.232 | 0.067 | 20.463 | |
autby_coef | 0.324 | 0.005 | 0.331 | |
autm | 0.045 | 0.004 | 0.050 | |
autm_3d | 0.054 | 0.003 | 0.058 | |
autm_z125 | 0.052 | 0.003 | 0.057 | |
automorphismByRanges | 0.107 | 0.006 | 0.114 | |
automorphism_bycoef | 0.102 | 0.007 | 0.109 | |
automorphism_prob | 1.076 | 0.035 | 1.116 | |
automorphisms | 6.396 | 0.142 | 62.467 | |
base2codon | 0.094 | 0.009 | 0.105 | |
base2int | 0.008 | 0.002 | 0.009 | |
base_methods | 0.486 | 0.027 | 0.516 | |
brca1_aln | 0.066 | 0.004 | 0.072 | |
brca1_aln2 | 0.074 | 0.003 | 0.077 | |
brca1_autm | 0.477 | 0.005 | 0.487 | |
cdm_z64 | 0.212 | 0.456 | 0.675 | |
codon_coord | 0.940 | 0.012 | 0.957 | |
codon_dist | 0.330 | 0.008 | 0.340 | |
codon_dist_matrix | 0.044 | 0.010 | 7.522 | |
codon_matrix | 0.665 | 0.014 | 0.685 | |
conserved_regions | 0.369 | 0.006 | 0.378 | |
covid_aln | 0.110 | 0.003 | 0.113 | |
covid_autm | 0.049 | 0.003 | 0.054 | |
cyc_aln | 0.142 | 0.006 | 0.150 | |
cyc_autm | 0.078 | 0.004 | 0.083 | |
dna_phyche | 0.005 | 0.001 | 0.007 | |
dna_phychem | 0.003 | 0.000 | 0.003 | |
extract-methods | 0.555 | 0.009 | 0.566 | |
getAutomorphisms | 0.191 | 0.010 | 0.203 | |
get_coord | 0.604 | 0.009 | 0.615 | |
get_mutscore | 0.172 | 0.008 | 0.182 | |
matrices | 0.570 | 0.013 | 0.585 | |
mod | 0.001 | 0.001 | 0.002 | |
modeq | 0.001 | 0.001 | 0.002 | |
modlineq | 0.003 | 0.002 | 0.005 | |
mut_type | 0.002 | 0.000 | 0.003 | |
peptide_phychem_index | 0.109 | 0.009 | 0.119 | |
reexports | 0.071 | 0.004 | 0.075 | |
seqranges | 0.602 | 0.009 | 0.612 | |
slapply | 0.002 | 0.000 | 0.003 | |
sortByChromAndStart | 0.073 | 0.001 | 0.074 | |
str2chr | 0.000 | 0.001 | 0.001 | |
str2dig | 0.000 | 0.001 | 0.001 | |
translation | 0.872 | 0.010 | 0.885 | |