Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-01-23 12:10 -0500 (Thu, 23 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
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 815/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomAutomorphism 1.8.1 (landing page) Robersy Sanchez
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.8.1 |
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_1.8.1.tar.gz |
StartedAt: 2025-01-21 20:24:12 -0500 (Tue, 21 Jan 2025) |
EndedAt: 2025-01-21 20:30:59 -0500 (Tue, 21 Jan 2025) |
EllapsedTime: 407.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomAutomorphism.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomAutomorphism.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK * this is package ‘GenomAutomorphism’ version ‘1.8.1’ * 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 ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'AutomorphismList,ANY' generic '[' and siglist 'ListCodonMatrix,ANY' generic '[' and siglist 'MatrixSeq,ANY' generic '[[' and siglist 'AutomorphismList' generic '[[' and siglist 'ListCodonMatrix' generic 'names<-' and siglist 'AutomorphismList' generic 'names<-' and siglist 'MatrixSeq' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 6.942 0.147 58.304 aminoacid_dist 3.549 0.977 10.203 autZ64 2.531 0.050 20.498 aut3D 2.093 0.175 21.437 autZ125 2.151 0.053 16.751 autZ5 1.624 0.053 19.807 codon_dist_matrix 0.041 0.010 6.305 * 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 WARNING See ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/library’ * installing *source* package ‘GenomAutomorphism’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 + ) + } NULL > > proc.time() user system elapsed 0.213 0.054 0.253
GenomAutomorphism.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 27.012 1.027 76.365
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
name | user | system | elapsed | |
AutomorphismByCoef | 0.478 | 0.012 | 0.489 | |
AutomorphismList | 2.724 | 0.033 | 2.758 | |
CodonMatrix | 0.188 | 0.004 | 0.192 | |
CodonSeq | 0.407 | 0.019 | 0.426 | |
GRangesMatrixSeq | 0.223 | 0.016 | 0.239 | |
ListCodonMatrix | 0.248 | 0.004 | 0.252 | |
MatrixSeq | 0.136 | 0.005 | 0.141 | |
aa_phychem_index | 0.133 | 0.010 | 0.143 | |
aaindex1 | 0.049 | 0.002 | 0.051 | |
aaindex2 | 0.020 | 0.001 | 0.022 | |
aaindex3 | 0.013 | 0.002 | 0.015 | |
aln | 0.085 | 0.003 | 0.088 | |
aminoacid_dist | 3.549 | 0.977 | 10.203 | |
as.AutomorphismList | 0.576 | 0.061 | 0.636 | |
aut3D | 2.093 | 0.175 | 21.437 | |
autZ125 | 2.151 | 0.053 | 16.751 | |
autZ5 | 1.624 | 0.053 | 19.807 | |
autZ64 | 2.531 | 0.050 | 20.498 | |
autby_coef | 0.322 | 0.005 | 0.331 | |
autm | 0.073 | 0.005 | 0.078 | |
autm_3d | 0.125 | 0.004 | 0.130 | |
autm_z125 | 0.099 | 0.004 | 0.103 | |
automorphismByRanges | 0.135 | 0.008 | 0.143 | |
automorphism_bycoef | 0.127 | 0.008 | 0.134 | |
automorphism_prob | 1.116 | 0.029 | 1.145 | |
automorphisms | 6.942 | 0.147 | 58.304 | |
base2codon | 0.089 | 0.006 | 0.109 | |
base2int | 0.006 | 0.001 | 0.007 | |
base_methods | 0.442 | 0.026 | 0.469 | |
brca1_aln | 0.064 | 0.004 | 0.068 | |
brca1_aln2 | 0.073 | 0.004 | 0.077 | |
brca1_autm | 0.278 | 0.005 | 0.288 | |
cdm_z64 | 0.103 | 0.207 | 0.316 | |
codon_coord | 0.983 | 0.012 | 0.998 | |
codon_dist | 0.341 | 0.009 | 0.350 | |
codon_dist_matrix | 0.041 | 0.010 | 6.305 | |
codon_matrix | 0.559 | 0.015 | 0.575 | |
conserved_regions | 0.416 | 0.009 | 0.425 | |
covid_aln | 0.083 | 0.003 | 0.088 | |
covid_autm | 0.116 | 0.005 | 0.121 | |
cyc_aln | 0.111 | 0.004 | 0.115 | |
cyc_autm | 0.208 | 0.006 | 0.214 | |
dna_phyche | 0.006 | 0.002 | 0.008 | |
dna_phychem | 0.002 | 0.001 | 0.003 | |
extract-methods | 0.522 | 0.007 | 0.529 | |
getAutomorphisms | 0.196 | 0.009 | 0.205 | |
get_coord | 0.608 | 0.008 | 0.616 | |
get_mutscore | 0.204 | 0.007 | 0.211 | |
matrices | 0.631 | 0.020 | 0.651 | |
mod | 0.002 | 0.001 | 0.003 | |
modeq | 0.001 | 0.000 | 0.002 | |
modlineq | 0.002 | 0.002 | 0.004 | |
mut_type | 0.002 | 0.001 | 0.002 | |
peptide_phychem_index | 0.150 | 0.007 | 0.156 | |
reexports | 0.151 | 0.006 | 0.157 | |
seqranges | 0.671 | 0.006 | 0.677 | |
slapply | 0.002 | 0.001 | 0.003 | |
sortByChromAndStart | 0.035 | 0.001 | 0.038 | |
str2chr | 0.000 | 0.001 | 0.001 | |
str2dig | 0.000 | 0.001 | 0.001 | |
translation | 0.841 | 0.013 | 0.860 | |