Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:39:33 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.28.0.tar.gz |
StartedAt: 2024-05-03 23:17:39 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 23:24:41 -0400 (Fri, 03 May 2024) |
EllapsedTime: 422.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mixOmics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mixOmics.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 8.8Mb sub-directories of 1Mb or more: R 2.0Mb data 3.3Mb doc 1.9Mb * 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 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 11.970 0.127 12.179 background.predict 7.728 1.468 9.303 circosPlot 7.710 0.152 7.943 block.splsda 7.595 0.143 7.830 block.spls 6.560 0.118 6.752 tune 4.580 0.465 5.108 * 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 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-3.19-bioc/meat/mixOmics.Rcheck/00check.log’ for details.
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 beta (2024-04-14 r86421) -- "Puppy Cup" Copyright (C) 2024 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(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") 2024-05-03 23:21:55.830 R[55965:1726162845] XType: com.apple.fonts is not accessible. 2024-05-03 23:21:55.830 R[55965:1726162845] XType: XTFontStaticRegistry is enabled. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 236 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 236 ] Warning messages: 1: In for (h in 1:ncomp) { : closing unused connection 6 (<-localhost:11135) 2: In for (h in 1:ncomp) { : closing unused connection 5 (<-localhost:11135) > > proc.time() user system elapsed 120.476 5.720 162.003
mixOmics.Rcheck/mixOmics-Ex.timings
name | user | system | elapsed | |
S3methods-print | 0.020 | 0.004 | 0.024 | |
auroc | 1.187 | 0.057 | 1.255 | |
background.predict | 7.728 | 1.468 | 9.303 | |
biplot | 11.970 | 0.127 | 12.179 | |
block.pls | 0.575 | 0.015 | 0.596 | |
block.plsda | 0.835 | 0.016 | 0.860 | |
block.spls | 6.560 | 0.118 | 6.752 | |
block.splsda | 7.595 | 0.143 | 7.830 | |
cim | 0.039 | 0.007 | 0.047 | |
cimDiablo | 0.323 | 0.015 | 0.345 | |
circosPlot | 7.710 | 0.152 | 7.943 | |
colors | 0.031 | 0.002 | 0.033 | |
explained_variance | 0.110 | 0.007 | 0.120 | |
get.confusion_matrix | 0.219 | 0.017 | 0.239 | |
image.tune.rcc | 2.518 | 0.081 | 2.622 | |
imgCor | 0.096 | 0.020 | 0.118 | |
impute.nipals | 0.015 | 0.004 | 0.018 | |
ipca | 1.237 | 0.038 | 1.287 | |
logratio-transformations | 0.066 | 0.005 | 0.073 | |
map | 0.005 | 0.003 | 0.008 | |
mat.rank | 0.002 | 0.000 | 0.002 | |
mint.block.pls | 0.157 | 0.009 | 0.169 | |
mint.block.plsda | 0.119 | 0.005 | 0.126 | |
mint.block.spls | 0.178 | 0.012 | 0.190 | |
mint.block.splsda | 0.132 | 0.006 | 0.139 | |
mint.pca | 0.411 | 0.007 | 0.421 | |
mint.pls | 0.594 | 0.011 | 0.611 | |
mint.plsda | 0.678 | 0.011 | 0.696 | |
mint.spls | 0.619 | 0.013 | 0.639 | |
mint.splsda | 0.713 | 0.014 | 0.735 | |
mixOmics | 0.370 | 0.034 | 0.408 | |
nearZeroVar | 0.730 | 0.016 | 0.754 | |
network | 0.016 | 0.004 | 0.020 | |
pca | 4.650 | 0.067 | 4.750 | |
perf | 2.899 | 0.161 | 3.092 | |
plot.rcc | 0.015 | 0.005 | 0.020 | |
plot.tune | 0.000 | 0.002 | 0.002 | |
plotArrow | 4.165 | 0.099 | 4.301 | |
plotDiablo | 0.175 | 0.008 | 0.186 | |
plotIndiv | 0.357 | 0.014 | 0.373 | |
plotLoadings | 0.120 | 0.009 | 0.131 | |
plotMarkers | 0 | 0 | 0 | |
plotVar | 0.729 | 0.018 | 0.757 | |
pls | 0.008 | 0.001 | 0.010 | |
plsda | 0.408 | 0.014 | 0.426 | |
predict | 0.183 | 0.012 | 0.196 | |
rcc | 0.002 | 0.002 | 0.003 | |
selectVar | 0.444 | 0.061 | 0.510 | |
sipca | 0.506 | 0.019 | 0.529 | |
spca | 3.534 | 0.143 | 3.706 | |
spls | 0.205 | 0.015 | 0.221 | |
splsda | 0.351 | 0.013 | 0.364 | |
study_split | 0.004 | 0.002 | 0.005 | |
summary | 0.020 | 0.004 | 0.023 | |
tune | 4.580 | 0.465 | 5.108 | |
tune.block.splsda | 0.000 | 0.001 | 0.001 | |
tune.mint.splsda | 2.589 | 0.138 | 2.751 | |
tune.pca | 0.198 | 0.016 | 0.214 | |
tune.rcc | 2.297 | 0.076 | 2.392 | |
tune.spca | 0.783 | 0.017 | 0.807 | |
tune.spls | 0.001 | 0.000 | 0.000 | |
tune.splsda | 4.227 | 0.376 | 4.658 | |
tune.splslevel | 1.243 | 0.072 | 1.326 | |
unmap | 0.005 | 0.005 | 0.009 | |
vip | 0.010 | 0.003 | 0.013 | |
withinVariation | 0.944 | 0.016 | 0.966 | |
wrapper.rgcca | 0.082 | 0.003 | 0.086 | |
wrapper.sgcca | 0.133 | 0.009 | 0.143 | |