Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:05 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 1299/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mixOmics 6.28.0 (landing page) Max Bladen
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the mixOmics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mixOmics.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: mixOmics |
Version: 6.28.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings mixOmics_6.28.0.tar.gz |
StartedAt: 2024-05-31 05:40:42 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 05:53:42 -0400 (Fri, 31 May 2024) |
EllapsedTime: 779.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mixOmics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings mixOmics_6.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/mixOmics.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘mixOmics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mixOmics’ version ‘6.28.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘mixOmics’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: R 1.2Mb data 3.4Mb doc 1.7Mb * checking package 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biplot 14.259 0.084 14.343 background.predict 7.186 0.136 7.323 block.splsda 6.537 0.080 6.616 circosPlot 5.619 0.032 5.653 block.spls 5.458 0.044 5.502 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/mixOmics.Rcheck/00check.log’ for details.
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘mixOmics’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (mixOmics)
mixOmics.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(mixOmics) Loading required package: MASS Loading required package: lattice Loading required package: ggplot2 Loaded mixOmics 6.28.0 Thank you for using mixOmics! Tutorials: http://mixomics.org Bookdown vignette: https://mixomicsteam.github.io/Bookdown Questions, issues: Follow the prompts at http://mixomics.org/contact-us Cite us: citation('mixOmics') > > test_check("mixOmics") [ FAIL 0 | WARN 4 | SKIP 0 | PASS 236 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 236 ] Warning messages: 1: In for (m in seq_len(M)) { : closing unused connection 6 (<-localhost:11015) 2: In for (m in seq_len(M)) { : closing unused connection 5 (<-localhost:11015) > > proc.time() user system elapsed 99.738 3.688 117.802
mixOmics.Rcheck/mixOmics-Ex.timings
name | user | system | elapsed | |
S3methods-print | 0.019 | 0.000 | 0.019 | |
auroc | 1.058 | 0.036 | 1.094 | |
background.predict | 7.186 | 0.136 | 7.323 | |
biplot | 14.259 | 0.084 | 14.343 | |
block.pls | 0.464 | 0.016 | 0.479 | |
block.plsda | 0.638 | 0.004 | 0.643 | |
block.spls | 5.458 | 0.044 | 5.502 | |
block.splsda | 6.537 | 0.080 | 6.616 | |
cim | 0.036 | 0.004 | 0.040 | |
cimDiablo | 0.257 | 0.000 | 0.258 | |
circosPlot | 5.619 | 0.032 | 5.653 | |
colors | 0.024 | 0.004 | 0.027 | |
explained_variance | 0.119 | 0.012 | 0.131 | |
get.confusion_matrix | 0.140 | 0.009 | 0.149 | |
image.tune.rcc | 2.093 | 0.006 | 2.100 | |
imgCor | 0.077 | 0.000 | 0.077 | |
impute.nipals | 0.011 | 0.000 | 0.011 | |
ipca | 0.728 | 0.000 | 0.728 | |
logratio-transformations | 0.067 | 0.000 | 0.068 | |
map | 0.005 | 0.000 | 0.005 | |
mat.rank | 0.002 | 0.000 | 0.003 | |
mint.block.pls | 0.161 | 0.000 | 0.161 | |
mint.block.plsda | 0.114 | 0.004 | 0.119 | |
mint.block.spls | 0.157 | 0.000 | 0.158 | |
mint.block.splsda | 0.139 | 0.024 | 0.164 | |
mint.pca | 0.354 | 0.016 | 0.369 | |
mint.pls | 0.499 | 0.000 | 0.498 | |
mint.plsda | 0.588 | 0.000 | 0.587 | |
mint.spls | 0.503 | 0.000 | 0.503 | |
mint.splsda | 0.577 | 0.004 | 0.580 | |
mixOmics | 0.321 | 0.012 | 0.333 | |
nearZeroVar | 0.998 | 0.016 | 1.014 | |
network | 0.013 | 0.000 | 0.014 | |
pca | 4.168 | 0.060 | 4.227 | |
perf | 2.760 | 0.012 | 2.772 | |
plot.rcc | 0.015 | 0.000 | 0.015 | |
plot.tune | 0.000 | 0.002 | 0.001 | |
plotArrow | 3.428 | 0.010 | 3.438 | |
plotDiablo | 0.179 | 0.000 | 0.179 | |
plotIndiv | 0.303 | 0.000 | 0.303 | |
plotLoadings | 0.106 | 0.007 | 0.114 | |
plotMarkers | 0.000 | 0.000 | 0.001 | |
plotVar | 0.560 | 0.004 | 0.564 | |
pls | 0.006 | 0.000 | 0.006 | |
plsda | 0.303 | 0.004 | 0.308 | |
predict | 0.156 | 0.004 | 0.160 | |
rcc | 0.003 | 0.000 | 0.003 | |
selectVar | 0.647 | 0.004 | 0.652 | |
sipca | 0.446 | 0.004 | 0.450 | |
spca | 2.912 | 0.016 | 2.928 | |
spls | 0.509 | 0.032 | 0.541 | |
splsda | 0.352 | 0.000 | 0.352 | |
study_split | 0.006 | 0.001 | 0.007 | |
summary | 0.014 | 0.002 | 0.016 | |
tune | 4.126 | 0.014 | 4.161 | |
tune.block.splsda | 0.001 | 0.000 | 0.000 | |
tune.mint.splsda | 2.292 | 0.016 | 2.308 | |
tune.pca | 0.166 | 0.004 | 0.169 | |
tune.rcc | 1.988 | 0.004 | 1.992 | |
tune.spca | 0.619 | 0.004 | 0.623 | |
tune.spls | 0.000 | 0.000 | 0.001 | |
tune.splsda | 4.006 | 0.024 | 4.051 | |
tune.splslevel | 0.757 | 0.004 | 0.761 | |
unmap | 0.003 | 0.002 | 0.006 | |
vip | 0.008 | 0.001 | 0.009 | |
withinVariation | 0.781 | 0.008 | 0.789 | |
wrapper.rgcca | 0.072 | 0.000 | 0.072 | |
wrapper.sgcca | 0.105 | 0.000 | 0.105 | |