Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:43 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the mixOmics package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1161/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mixOmics 6.16.3 (landing page) Al J Abadi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: mixOmics |
Version: 6.16.3 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mixOmics_6.16.3.tar.gz |
StartedAt: 2021-10-14 21:16:16 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:22:00 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 343.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mixOmics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mixOmics_6.16.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/mixOmics.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mixOmics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mixOmics’ version ‘6.16.3’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 6.0Mb sub-directories of 1Mb or more: R 2.0Mb data 3.3Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’. 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biplot 14.072 0.071 14.162 background.predict 9.646 1.250 10.910 tune 5.695 0.269 5.968 pca 5.643 0.035 5.683 tune.splsda 5.332 0.196 5.538 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/mixOmics.Rcheck/00check.log’ for details.
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘mixOmics’ ... ** using staged installation It is recommended to use ‘given’ instead of ‘middle’. It is recommended to use ‘given’ instead of ‘middle’. ** 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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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 6.16.3 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") $Comp1 AUC p-value AF vs BE 0.863 2.473e-05 $Comp2 AUC p-value AF vs BE 0.9981 7.124e-09 Performing repeated cross-validation with nrepeat = 3... | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Performing repeated cross-validation with nrepeat = 3... | | | 0%[ FAIL 0 | WARN 2 | SKIP 0 | PASS 136 ] > > proc.time() user system elapsed 72.964 4.518 71.505
mixOmics.Rcheck/mixOmics-Ex.timings
name | user | system | elapsed | |
S3methods-print | 0.027 | 0.005 | 0.032 | |
auroc | 0.672 | 0.020 | 0.692 | |
background.predict | 9.646 | 1.250 | 10.910 | |
biplot | 14.072 | 0.071 | 14.162 | |
block.pls | 0.656 | 0.010 | 0.667 | |
block.plsda | 0.875 | 0.006 | 0.883 | |
block.spls | 0.594 | 0.008 | 0.604 | |
block.splsda | 0.767 | 0.015 | 0.784 | |
cim | 0.036 | 0.008 | 0.044 | |
cimDiablo | 0.197 | 0.008 | 0.205 | |
circosPlot | 1.426 | 0.017 | 1.446 | |
colors | 0.029 | 0.003 | 0.031 | |
explained_variance | 0.214 | 0.016 | 0.230 | |
get.confusion_matrix | 0.217 | 0.003 | 0.221 | |
image.tune.rcc | 2.859 | 0.054 | 2.922 | |
imgCor | 0.093 | 0.012 | 0.105 | |
impute.nipals | 0.022 | 0.005 | 0.026 | |
ipca | 1.033 | 0.019 | 1.054 | |
logratio-transformations | 0.085 | 0.004 | 0.089 | |
map | 0.006 | 0.004 | 0.010 | |
mat.rank | 0.002 | 0.000 | 0.002 | |
mint.block.pls | 0.180 | 0.006 | 0.186 | |
mint.block.plsda | 0.127 | 0.004 | 0.131 | |
mint.block.spls | 0.198 | 0.006 | 0.204 | |
mint.block.splsda | 0.127 | 0.004 | 0.131 | |
mint.pca | 0.568 | 0.005 | 0.574 | |
mint.pls | 0.701 | 0.008 | 0.710 | |
mint.plsda | 0.763 | 0.004 | 0.768 | |
mint.spls | 0.658 | 0.005 | 0.666 | |
mint.splsda | 0.848 | 0.005 | 0.854 | |
mixOmics | 0.706 | 0.018 | 0.724 | |
nearZeroVar | 1.142 | 0.029 | 1.171 | |
network | 0.017 | 0.006 | 0.022 | |
pca | 5.643 | 0.035 | 5.683 | |
perf | 4.512 | 0.088 | 4.604 | |
plot.rcc | 0.014 | 0.006 | 0.019 | |
plot.tune | 0.000 | 0.001 | 0.002 | |
plotArrow | 4.276 | 0.053 | 4.345 | |
plotDiablo | 0.234 | 0.007 | 0.241 | |
plotIndiv | 0.300 | 0.006 | 0.306 | |
plotLoadings | 0.153 | 0.016 | 0.170 | |
plotVar | 0.623 | 0.009 | 0.633 | |
pls | 0.007 | 0.001 | 0.009 | |
plsda | 0.472 | 0.007 | 0.479 | |
predict | 0.219 | 0.008 | 0.227 | |
rcc | 0.003 | 0.002 | 0.004 | |
selectVar | 0.915 | 0.051 | 0.967 | |
sipca | 0.595 | 0.010 | 0.604 | |
spca | 4.180 | 0.084 | 4.267 | |
spls | 0.480 | 0.017 | 0.498 | |
splsda | 0.551 | 0.013 | 0.565 | |
study_split | 0.008 | 0.003 | 0.011 | |
summary | 0.021 | 0.003 | 0.024 | |
tune | 5.695 | 0.269 | 5.968 | |
tune.block.splsda | 0.000 | 0.001 | 0.001 | |
tune.mint.splsda | 3.789 | 0.063 | 3.856 | |
tune.pca | 0.291 | 0.011 | 0.302 | |
tune.rcc | 2.506 | 0.031 | 2.543 | |
tune.spca | 0.988 | 0.026 | 1.015 | |
tune.spls | 0 | 0 | 0 | |
tune.splsda | 5.332 | 0.196 | 5.538 | |
tune.splslevel | 1.255 | 0.029 | 1.310 | |
unmap | 0.006 | 0.008 | 0.014 | |
vip | 0.010 | 0.004 | 0.014 | |
withinVariation | 1.174 | 0.010 | 1.185 | |
wrapper.rgcca | 0.094 | 0.005 | 0.099 | |
wrapper.sgcca | 0.252 | 0.008 | 0.259 | |