Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:41 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 805/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomAutomorphism 1.7.0 (landing page) Robersy Sanchez
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.7.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.7.0.tar.gz |
StartedAt: 2024-08-16 01:04:03 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 01:09:56 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 353.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomAutomorphism.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GenomAutomorphism.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GenomAutomorphism/DESCRIPTION' ... OK * this is package 'GenomAutomorphism' version '1.7.0' * 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 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 aminoacid_dist 3.71 0.19 69.93 codon_dist_matrix 0.04 0.03 7.28 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/GenomAutomorphism.Rcheck/00check.log' for details.
GenomAutomorphism.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GenomAutomorphism ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 0.15 0.10 0.29
GenomAutomorphism.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 33 ] > > proc.time() user system elapsed 20.51 5.59 47.31
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
name | user | system | elapsed | |
AutomorphismByCoef | 0.41 | 0.00 | 0.41 | |
AutomorphismList | 3.09 | 0.38 | 3.47 | |
CodonMatrix | 0.17 | 0.00 | 0.17 | |
CodonSeq | 0.55 | 0.55 | 1.09 | |
GRangesMatrixSeq | 0.22 | 0.06 | 0.28 | |
ListCodonMatrix | 0.37 | 0.00 | 0.38 | |
MatrixSeq | 0.14 | 0.01 | 0.15 | |
aa_phychem_index | 0.06 | 0.10 | 0.16 | |
aaindex1 | 0.04 | 0.01 | 0.05 | |
aaindex2 | 0.01 | 0.02 | 0.03 | |
aaindex3 | 0.02 | 0.00 | 0.01 | |
aln | 0.15 | 0.37 | 0.54 | |
aminoacid_dist | 3.71 | 0.19 | 69.93 | |
as.AutomorphismList | 0.64 | 0.02 | 0.66 | |
aut3D | 1.52 | 0.33 | 1.84 | |
autZ125 | 2.50 | 0.35 | 2.86 | |
autZ5 | 0.73 | 0.21 | 0.94 | |
autZ64 | 1.69 | 0.22 | 1.90 | |
autby_coef | 0.38 | 0.00 | 0.38 | |
autm | 0.17 | 0.37 | 0.55 | |
autm_3d | 0.16 | 0.14 | 0.30 | |
autm_z125 | 0.17 | 0.66 | 0.82 | |
automorphismByRanges | 0.27 | 0.28 | 0.55 | |
automorphism_bycoef | 0.29 | 0.39 | 0.69 | |
automorphisms | 4.53 | 0.33 | 4.86 | |
base2codon | 0.30 | 0.30 | 0.59 | |
base2int | 0 | 0 | 0 | |
base_methods | 0.50 | 0.36 | 0.86 | |
brca1_aln | 0.06 | 0.02 | 0.08 | |
brca1_aln2 | 0.05 | 0.01 | 0.06 | |
brca1_autm | 0.47 | 0.00 | 0.47 | |
cdm_z64 | 0.39 | 0.27 | 0.65 | |
codon_coord | 1.09 | 0.31 | 1.41 | |
codon_dist | 0.68 | 0.53 | 1.20 | |
codon_dist_matrix | 0.04 | 0.03 | 7.28 | |
codon_matrix | 0.67 | 0.00 | 0.68 | |
conserved_regions | 0.72 | 0.89 | 1.60 | |
covid_aln | 0.18 | 0.35 | 0.52 | |
covid_autm | 0.31 | 0.36 | 0.67 | |
cyc_aln | 0.20 | 0.40 | 0.61 | |
cyc_autm | 0.32 | 0.60 | 0.92 | |
dna_phyche | 0.02 | 0.00 | 0.01 | |
dna_phychem | 0 | 0 | 0 | |
extract-methods | 0.73 | 0.01 | 0.75 | |
getAutomorphisms | 0.41 | 0.35 | 0.75 | |
get_coord | 0.78 | 0.29 | 1.10 | |
get_mutscore | 0.21 | 0.06 | 0.26 | |
matrices | 0.65 | 0.30 | 0.96 | |
mod | 0 | 0 | 0 | |
modeq | 0 | 0 | 0 | |
modlineq | 0.02 | 0.00 | 0.01 | |
mut_type | 0 | 0 | 0 | |
peptide_phychem_index | 0.11 | 0.03 | 0.16 | |
reexports | 0.39 | 0.66 | 1.05 | |
seqranges | 0.65 | 0.39 | 1.04 | |
slapply | 0.02 | 0.00 | 0.02 | |
sortByChromAndStart | 0.08 | 0.00 | 0.08 | |
str2chr | 0 | 0 | 0 | |
str2dig | 0.01 | 0.00 | 0.01 | |
translation | 1.08 | 0.52 | 1.60 | |