Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:31 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1272/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mixOmics 6.27.0 (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 | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 6.27.0 |
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_6.27.0.tar.gz |
StartedAt: 2024-03-02 06:58:24 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 07:13:25 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 900.1 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_6.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mixOmics.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 ‘6.27.0’ * 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 8.1Mb sub-directories of 1Mb or more: R 1.4Mb 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 R 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 22.078 0.188 26.635 block.splsda 14.573 0.152 17.841 background.predict 13.583 0.824 17.679 circosPlot 14.022 0.228 17.895 block.spls 11.960 0.129 14.552 pca 9.071 0.126 11.348 plotArrow 8.329 0.150 10.422 tune 7.467 0.280 9.209 spca 6.791 0.169 8.485 tune.splsda 6.639 0.272 8.298 perf 5.405 0.164 6.926 tune.mint.splsda 5.161 0.131 6.522 image.tune.rcc 3.947 0.074 5.083 * 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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 6.27.0 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") 2024-03-02 07:07:35.225 R[81268:964242204] XType: com.apple.fonts is not accessible. 2024-03-02 07:07:35.225 R[81268:964242204] 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 (i in ic) value[[i]] <- as.vector(x[, i]) : closing unused connection 6 (<-localhost:11753) 2: In for (i in ic) value[[i]] <- as.vector(x[, i]) : closing unused connection 5 (<-localhost:11753) > > proc.time() user system elapsed 231.206 8.058 347.109
mixOmics.Rcheck/mixOmics-Ex.timings
name | user | system | elapsed | |
S3methods-print | 0.030 | 0.008 | 0.045 | |
auroc | 1.984 | 0.131 | 2.584 | |
background.predict | 13.583 | 0.824 | 17.679 | |
biplot | 22.078 | 0.188 | 26.635 | |
block.pls | 1.039 | 0.018 | 1.265 | |
block.plsda | 1.554 | 0.017 | 1.915 | |
block.spls | 11.960 | 0.129 | 14.552 | |
block.splsda | 14.573 | 0.152 | 17.841 | |
cim | 0.061 | 0.012 | 0.090 | |
cimDiablo | 0.695 | 0.016 | 0.863 | |
circosPlot | 14.022 | 0.228 | 17.895 | |
colors | 0.053 | 0.005 | 0.076 | |
explained_variance | 0.209 | 0.009 | 0.272 | |
get.confusion_matrix | 0.370 | 0.011 | 0.484 | |
image.tune.rcc | 3.947 | 0.074 | 5.083 | |
imgCor | 0.130 | 0.021 | 0.194 | |
impute.nipals | 0.021 | 0.005 | 0.037 | |
ipca | 1.689 | 0.039 | 2.202 | |
logratio-transformations | 0.410 | 0.018 | 0.522 | |
map | 0.006 | 0.005 | 0.014 | |
mat.rank | 0.004 | 0.001 | 0.004 | |
mint.block.pls | 0.207 | 0.012 | 0.277 | |
mint.block.plsda | 0.179 | 0.010 | 0.242 | |
mint.block.spls | 0.251 | 0.015 | 0.345 | |
mint.block.splsda | 0.194 | 0.008 | 0.246 | |
mint.pca | 0.826 | 0.018 | 1.031 | |
mint.pls | 1.149 | 0.021 | 1.414 | |
mint.plsda | 1.364 | 0.018 | 1.697 | |
mint.spls | 1.170 | 0.018 | 1.434 | |
mint.splsda | 1.422 | 0.023 | 1.795 | |
mixOmics | 0.508 | 0.023 | 0.660 | |
nearZeroVar | 1.556 | 0.037 | 1.986 | |
network | 0.024 | 0.006 | 0.037 | |
pca | 9.071 | 0.126 | 11.348 | |
perf | 5.405 | 0.164 | 6.926 | |
plot.rcc | 0.026 | 0.007 | 0.044 | |
plot.tune | 0.001 | 0.004 | 0.007 | |
plotArrow | 8.329 | 0.150 | 10.422 | |
plotDiablo | 0.292 | 0.014 | 0.378 | |
plotIndiv | 0.682 | 0.023 | 0.856 | |
plotLoadings | 0.181 | 0.018 | 0.469 | |
plotMarkers | 0.001 | 0.001 | 0.001 | |
plotVar | 1.291 | 0.025 | 1.597 | |
pls | 0.013 | 0.003 | 0.020 | |
plsda | 0.984 | 0.017 | 1.231 | |
predict | 0.389 | 0.018 | 0.551 | |
rcc | 0.005 | 0.004 | 0.014 | |
selectVar | 0.641 | 0.055 | 0.908 | |
sipca | 1.003 | 0.027 | 1.285 | |
spca | 6.791 | 0.169 | 8.485 | |
spls | 0.332 | 0.027 | 0.443 | |
splsda | 0.970 | 0.020 | 1.175 | |
study_split | 0.007 | 0.004 | 0.013 | |
summary | 0.029 | 0.006 | 0.039 | |
tune | 7.467 | 0.280 | 9.209 | |
tune.block.splsda | 0.000 | 0.001 | 0.002 | |
tune.mint.splsda | 5.161 | 0.131 | 6.522 | |
tune.pca | 0.383 | 0.019 | 0.521 | |
tune.rcc | 3.871 | 0.076 | 4.608 | |
tune.spca | 1.575 | 0.031 | 1.881 | |
tune.spls | 0.000 | 0.001 | 0.002 | |
tune.splsda | 6.639 | 0.272 | 8.298 | |
tune.splslevel | 2.054 | 0.057 | 2.457 | |
unmap | 0.007 | 0.010 | 0.022 | |
vip | 0.019 | 0.005 | 0.027 | |
withinVariation | 2.096 | 0.030 | 2.418 | |
wrapper.rgcca | 0.167 | 0.012 | 0.202 | |
wrapper.sgcca | 0.337 | 0.014 | 0.408 | |