Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-09 12:06 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1323/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.33.0  (landing page)
Eva Hamrud
Snapshot Date: 2025-10-08 14:17 -0400 (Wed, 08 Oct 2025)
git_url: https://git.bioconductor.org/packages/mixOmics
git_branch: devel
git_last_commit: bf2cf80
git_last_commit_date: 2025-04-15 11:39:07 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for mixOmics on kjohnson3

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.

raw results


Summary

Package: mixOmics
Version: 6.33.0
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_6.33.0.tar.gz
StartedAt: 2025-10-08 20:35:37 -0400 (Wed, 08 Oct 2025)
EndedAt: 2025-10-08 20:43:19 -0400 (Wed, 08 Oct 2025)
EllapsedTime: 462.2 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_6.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mixOmics.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mixOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mixOmics’ version ‘6.33.0’
* 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 ... NOTE
Found the following non-portable file paths:
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols-reordered-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols-with-set-pch-circle-for-all-samples.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols-with-set-pch-triangle-for-all-samples.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups-reordered.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-set-pch-for-each-group.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-sample-names-coloured-by-primary-groups-custom-cols.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-with-centroids-coloured-by-primary-groups-custom-cols.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols-ellipse-level-0-5.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols-sample-names.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/pca-plot-sample-names-coloured-by-primary-groups-custom-cols.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-coloured-by-primary-groups-custom-cols-reordered-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-coloured-by-primary-groups-custom-cols-with-set-pch-circle-for-all-samples.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-coloured-by-primary-groups-with-set-pch-for-each-group.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-with-ellipse-coloured-by-primary-groups-ellipse-level-0-5.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-with-pch-for-primary-groups-col-consistent.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/spls-plot-with-centroids-and-stars-coloured-by-primary-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/splsda-plot-with-centroids-and-stars-custom-cols-pch-on-second-grouping.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-cols-and-borders-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-cols-and-borders-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-gene-names-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-gene-names-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-labels-and-label-sizes-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-labels-and-label-sizes-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-layout-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-layout-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-specific-study-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-specific-study-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-specific-study.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pca/loadings-plot-change-gene-names-and-plot-top-3-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pca/loadings-plot-change-gene-names-and-plot-top-3-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pca/loadings-plot-change-labels-and-label-sizes-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pca/loadings-plot-change-labels-and-label-sizes-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-cols-and-borders-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-cols-and-borders-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-gene-names-and-plot-top-3-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-gene-names-and-plot-top-3-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-labels-and-label-sizes-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-labels-and-label-sizes-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-legend-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-legend-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-names-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-title-and-labels-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-title-and-labels-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.sgccda/loadings-plot-diablo-block-specific-with-contrib-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.sgccda/loadings-plot-diablo-block-specific-with-contrib-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.sgccda/loadings-plot-diablo-change-labels-and-label-sizes-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.sgccda/loadings-plot-diablo-change-labels-and-label-sizes-graphics.svg

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mixOmics’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   3.3Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘gsignal’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotLoadings_barplot: no visible binding for global variable
  ‘size.axis’
perf.assess.sgccda: no visible binding for global variable
  ‘signif.threshold’
plotLoadings.mint.pls: no visible binding for global variable
  ‘importance’
plotLoadings.mint.pls: no visible binding for global variable ‘color’
plotLoadings.mint.plsda: no visible binding for global variable
  ‘importance’
plotLoadings.mint.plsda: no visible binding for global variable ‘color’
plotLoadings.mint.spls: no visible binding for global variable
  ‘importance’
plotLoadings.mint.spls: no visible binding for global variable ‘color’
plotLoadings.mint.splsda: no visible binding for global variable
  ‘importance’
plotLoadings.mint.splsda: no visible binding for global variable
  ‘color’
plotLoadings.mixo_pls: no visible binding for global variable
  ‘importance’
plotLoadings.mixo_plsda: no visible binding for global variable
  ‘importance’
plotLoadings.mixo_plsda: no visible binding for global variable ‘color’
plotLoadings.mixo_plsda: no visible binding for global variable ‘group’
plotLoadings.mixo_spls: no visible binding for global variable
  ‘importance’
plotLoadings.mixo_splsda: no visible binding for global variable
  ‘importance’
plotLoadings.mixo_splsda: no visible binding for global variable
  ‘color’
plotLoadings.mixo_splsda: no visible binding for global variable
  ‘group’
plotLoadings.pca: no visible binding for global variable ‘importance’
plotLoadings.rcc: no visible binding for global variable ‘importance’
plotLoadings.rgcca: no visible binding for global variable ‘importance’
plotLoadings.sgcca: no visible binding for global variable ‘importance’
plotLoadings.sgccda: no visible binding for global variable
  ‘importance’
plotLoadings.sgccda: no visible binding for global variable ‘color’
plotLoadings.sgccda: no visible binding for global variable ‘group’
Undefined global functions or variables:
  color group importance signif.threshold size.axis
* checking Rd files ... NOTE
checkRd: (-1) plotLoadings.Rd:479: Lost braces
   479 | For code{mint.pls}, \code{mint.spls}: when \code{study="all.partial"}, 
       |         ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  perf.Rd: BiocParallelParam-class
  perf.assess.Rd: BiocParallelParam-class
  rcc.Rd: estimate.lambda
  tune.Rd: BiocParallelParam-class
  tune.block.plsda.Rd: BiocParallelParam-class
  tune.block.splsda.Rd: BiocParallelParam-class
  tune.pls.Rd: BiocParallelParam-class
  tune.plsda.Rd: BiocParallelParam-class
  tune.spca.Rd: BiocParallelParam-class
  tune.spls.Rd: BiocParallelParam-class
  tune.splsda.Rd: BiocParallelParam-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in Rd file 'perf.assess.Rd':
  ‘perf.assess’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
tune.spls         80.696  5.158  86.090
tune.splsda       31.801  2.663  34.534
tune.plsda        14.350  0.817  15.176
tune.pls          11.907  0.769  12.686
perf.assess        8.495  0.529   9.068
tune.block.plsda   8.748  0.101   8.862
plotIndiv          7.450  1.027   8.496
biplot             5.812  0.039   5.895
tune.block.splsda  4.029  0.057  14.153
* 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/mixOmics.Rcheck/00check.log’
for details.


Installation output

mixOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘mixOmics’ ...
** this is package ‘mixOmics’ version ‘6.33.0’
** 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)

Tests output

mixOmics.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 6.33.0
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")
2025-10-08 20:40:14.498 R[29984:419628230] XType: Using static font registry.
character(0)
character(0)
[1] "test.keepX is set to NULL, tuning only for number of components..."
[1] "test.keepX is set to NULL, tuning only for number of components..."
[1] "test.keepX set to NULL, tuning only for number of components..."
[1] "test.keepX and test.keepY are set to NULL, tuning only for number of components..."
[1] "test.keepX and test.keepY are set to NULL, tuning only for number of components..."
[1] "test.keepX and test.keepY are set to NULL, tuning only for number of components..."
[1] "test.keepX set to NULL, tuning only for number of components..."
[ FAIL 0 | WARN 3 | SKIP 51 | PASS 663 ]

══ Skipped tests (51) ══════════════════════════════════════════════════════════
• On CRAN (51): 'test-biplot.R:17:3', 'test-biplot.R:39:3',
  'test-biplot.R:63:3', 'test-plotArrow.R:50:3', 'test-plotArrow.R:81:3',
  'test-plotIndiv.mint.R:76:3', 'test-plotIndiv.mint.R:99:3',
  'test-plotIndiv.mint.R:131:3', 'test-plotIndiv.mint.R:145:3',
  'test-plotIndiv.mint.R:168:3', 'test-plotIndiv.pca.R:152:3',
  'test-plotIndiv.pca.R:176:3', 'test-plotIndiv.pca.R:210:3',
  'test-plotIndiv.pca.R:244:3', 'test-plotIndiv.pca.R:263:3',
  'test-plotIndiv.pls.R:419:3', 'test-plotIndiv.pls.R:442:3',
  'test-plotIndiv.pls.R:468:3', 'test-plotIndiv.pls.R:486:3',
  'test-plotIndiv.pls.R:498:3', 'test-plotIndiv.pls.R:531:3',
  'test-plotIndiv.pls.R:564:3', 'test-plotIndiv.pls.R:581:3',
  'test-plotIndiv.pls.R:599:3', 'test-plotIndiv.pls.R:610:3',
  'test-plotIndiv.pls.R:622:3', 'test-plotIndiv.pls.R:655:3',
  'test-plotIndiv.pls.R:666:3', 'test-plotIndiv.pls.R:683:3',
  'test-plotIndiv.pls.R:694:3', 'test-plotIndiv.pls.R:712:3',
  'test-plotIndiv.pls.R:741:3', 'test-plotLoadings.mint.pls.R:11:3',
  'test-plotLoadings.mint.pls.R:62:3', 'test-plotLoadings.mint.pls.R:121:3',
  'test-plotLoadings.mint.plsda.R:14:5', 'test-plotLoadings.mint.plsda.R:61:5',
  'test-plotLoadings.mint.plsda.R:91:5',
  'test-plotLoadings.mint.plsda.R:143:5', 'test-plotLoadings.pca.R:11:3',
  'test-plotLoadings.pca.R:50:3', 'test-plotLoadings.pca.R:84:3',
  'test-plotLoadings.pls.R:43:3', 'test-plotLoadings.pls.R:91:3',
  'test-plotLoadings.plsda.R:109:3', 'test-plotLoadings.plsda.R:148:3',
  'test-plotLoadings.sgccda.R:16:3', 'test-plotLoadings.sgccda.R:32:3',
  'test-plotLoadings.sgccda.R:47:3', 'test-plotLoadings.sgccda.R:95:3',
  'test-plotLoadings.sgccda.R:133:3'

[ FAIL 0 | WARN 3 | SKIP 51 | PASS 663 ]
Deleting unused snapshots:
• biplot/biplot-plot-pca-with-customised-colours.svg
• biplot/biplot-plot-plsda-model-with-customised-pch.svg
• plotArrow/arrow-plot-daiblo-with-customised-colours.svg
• plotArrow/arrow-plot-spls-with-customised-colours.svg
• plotIndiv.mint/mint-pls-plot-default-cols-custom-groups.svg
• plotIndiv.mint/mint-pls-plot-studies-facetted.svg
• plotIndiv.mint/mint-spls-plot-studies-facetted-different-layout.svg
• plotIndiv.mint/mint-splsda-plot-default-cols-custom-groups.svg
• plotIndiv.mint/mint-splsda-plot-studies-facetted-different-layout.svg
• plotIndiv.mint/mint-splsda-plot-studies-facetted.svg
• plotIndiv.mint/mint-splsda-plot-with-ellipse.svg
• plotIndiv.mint/mint-splsda-plot-with-star.svg
• plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols-reordered-groups.svg
• plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols-with-set-pch-triangle-for-all-samples.svg
• plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols.svg
• plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups-reordered.svg
• plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups.svg
• plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-set-pch-for-each-group.svg
• plotIndiv.pca/pca-plot-coloured-by-primary-groups.svg
• plotIndiv.pca/pca-plot-sample-names-coloured-by-primary-groups-custom-cols.svg
• plotIndiv.pca/pca-plot-sample-names-coloured-by-primary-groups.svg
• plotIndiv.pca/pca-plot-with-centroids-coloured-by-primary-groups-custom-cols.svg
• plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols-ellipse-level-0-5.svg
• plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols-sample-names.svg
• plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols.svg
• plotIndiv.pca/pca-plot-with-pch-for-primary-groups-col-consistent.svg
• plotIndiv.pls/pca-plot-sample-names-coloured-by-primary-groups-custom-cols.svg
• plotIndiv.pls/rcca-plot-coloured-by-primary-groups-custom-cols-reordered-groups.svg
• plotIndiv.pls/rcca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups.svg
• plotIndiv.pls/rcca-plot-coloured-by-primary-groups-with-set-pch-for-each-group.svg
• plotIndiv.pls/rcca-plot-coloured-by-primary-groups.svg
• plotIndiv.pls/rcca-plot-on-multi-variate-space.svg
• plotIndiv.pls/rcca-plot-on-x-variate-space.svg
• plotIndiv.pls/rcca-plot-on-y-variate-space.svg
• plotIndiv.pls/rcca-plot-sample-names-coloured-by-primary-groups.svg
• plotIndiv.pls/rcca-plot-with-ellipse-coloured-by-primary-groups-ellipse-level-0-5.svg
• plotIndiv.pls/rcca-plot-with-pch-for-primary-groups-col-consistent.svg
• plotIndiv.pls/spls-plot-coloured-by-primary-groups.svg
• plotIndiv.pls/spls-plot-on-multi-variate-space.svg
• plotIndiv.pls/spls-plot-on-x-variate-space.svg
• plotIndiv.pls/spls-plot-on-y-variate-space.svg
• plotIndiv.pls/spls-plot-sample-names-coloured-by-primary-groups.svg
• plotIndiv.pls/splsda-plot-on-multi-variate-space.svg
• plotIndiv.pls/splsda-plot-on-x-variate-space.svg
• plotIndiv.pls/splsda-plot-on-y-variate-space.svg
• plotIndiv.pls/splsda-plot-sample-names-coloured-by-custom-groups.svg
• plotIndiv.pls/splsda-plot-with-centroids-and-stars-custom-cols-pch-on-second-grouping.svg
• plotIndiv.pls/splsda-plot-with-centroids-and-stars-custom-cols.svg
• plotIndiv.pls/splsda-plot-with-ellipse-on-custom-groups.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-all-partial-ggplot2.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-all-partial-graphics.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-change-cols-and-borders-ggplot2.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-change-cols-and-borders-graphics.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-change-gene-names-ggplot2.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-change-gene-names-graphics.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-change-labels-and-label-sizes-ggplot2.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-change-labels-and-label-sizes-graphics.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-change-layout-ggplot2.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-change-layout-graphics.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-specific-study-ggplot2.svg
• plotLoadings.mint.pls/loadings-plot-mint-pls-specific-study-graphics.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-all-partial.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-custom-colors.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-custom-labels.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-custom-layout.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-custom-names.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-all-partial.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-custom-colors.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-custom-labels.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-custom-layout.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-custom-names.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-specific-study.svg
• plotLoadings.mint.plsda/mint-plsda-loadings-specific-study.svg
• plotLoadings.pca/loadings-plot-change-cols-and-borders-ggplot2.svg
• plotLoadings.pca/loadings-plot-change-cols-and-borders-graphics.svg
• plotLoadings.pca/loadings-plot-change-gene-names-and-plot-top-3-ggplot2.svg
• plotLoadings.pca/loadings-plot-change-gene-names-and-plot-top-3-graphics.svg
• plotLoadings.pca/loadings-plot-change-labels-and-label-sizes-ggplot2.svg
• plotLoadings.pca/loadings-plot-change-labels-and-label-sizes-graphics.svg
• plotLoadings.pls/loadings-plot-spls-change-block-ggplot2.svg
• plotLoadings.pls/loadings-plot-spls-change-block-graphics.svg
• plotLoadings.pls/loadings-plot-spls-change-cols-and-borders-ggplot2.svg
• plotLoadings.pls/loadings-plot-spls-change-cols-and-borders-graphics.svg
• plotLoadings.pls/loadings-plot-spls-change-gene-names-and-plot-top-3-ggplot2.svg
• plotLoadings.pls/loadings-plot-spls-change-gene-names-and-plot-top-3-graphics.svg
• plotLoadings.pls/loadings-plot-spls-change-labels-and-label-sizes-ggplot2.svg
• plotLoadings.pls/loadings-plot-spls-change-labels-and-label-sizes-graphics.svg
• plotLoadings.pls/loadings-plot-spls-change-layout-ggplot2.svg
• plotLoadings.pls/loadings-plot-spls-change-layout-graphics.svg
• plotLoadings.plsda/loadings-plot-splsda-with-custom-legend-ggplot2.svg
• plotLoadings.plsda/loadings-plot-splsda-with-custom-legend-graphics.svg
• plotLoadings.plsda/loadings-plot-splsda-with-custom-names-ggplot2.svg
• plotLoadings.plsda/loadings-plot-splsda-with-custom-names-graphics.svg
• plotLoadings.plsda/loadings-plot-splsda-with-custom-title-and-labels-ggplot2.svg
• plotLoadings.plsda/loadings-plot-splsda-with-custom-title-and-labels-graphics.svg
• plotLoadings.sgccda/loadings-plot-diablo-block-specific-with-contrib-ggplot2.svg
• plotLoadings.sgccda/loadings-plot-diablo-block-specific-with-contrib-graphics.svg
• plotLoadings.sgccda/loadings-plot-diablo-change-labels-and-label-sizes-ggplot2.svg
• plotLoadings.sgccda/loadings-plot-diablo-change-labels-and-label-sizes-graphics.svg
• plotLoadings.sgccda/loadings-plot-diablo-change-legend-ggplot2.svg
• plotLoadings.sgccda/loadings-plot-diablo-change-legend-graphics.svg
> 
> proc.time()
   user  system elapsed 
109.002  11.129 185.565 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0060.0010.007
auroc0.3550.0060.364
background.predict3.2841.0214.391
biplot5.8120.0395.895
block.pls0.3060.0050.315
block.plsda0.3410.0030.347
block.spls2.2990.0492.356
block.splsda2.6620.0702.773
cim0.0150.0020.018
cimDiablo0.0890.0040.102
circosPlot1.9200.0231.971
colors0.0120.0010.012
explained_variance0.0620.0070.068
get.confusion_matrix0.0600.0020.063
image.tune.rcc0.8250.0400.865
imgCor0.0230.0030.027
impute.nipals0.0040.0020.005
ipca0.3720.0150.387
logratio-transformations0.0360.0100.045
map0.0020.0010.003
mat.rank0.0010.0000.001
mint.block.pls0.0620.0030.065
mint.block.plsda0.0540.0020.056
mint.block.spls0.0640.0030.066
mint.block.splsda0.0550.0020.057
mint.pca0.1810.0070.188
mint.pls0.2940.0030.296
mint.plsda0.3350.0100.348
mint.spls0.3210.0040.326
mint.splsda0.3210.0040.327
mixOmics0.1340.0120.146
nearZeroVar0.3370.0120.357
network0.0040.0010.005
pca2.1090.0292.159
perf0.9340.0791.023
perf.assess8.4950.5299.068
plot.rcc0.0040.0010.006
plot.tune0.0010.0010.000
plotArrow0.6780.0130.696
plotDiablo0.0740.0050.079
plotIndiv7.4501.0278.496
plotLoadings0.1870.0210.208
plotMarkers000
plotVar0.2690.0030.271
pls0.0020.0010.002
plsda0.3090.0050.314
predict0.0560.0050.061
rcc0.0000.0000.001
selectVar0.1340.0210.157
sipca0.2120.0050.218
spca1.2060.0511.259
spls0.0760.0060.083
splsda0.1660.0030.169
study_split0.0030.0010.003
summary0.0050.0020.007
tune2.0260.1722.217
tune.block.plsda8.7480.1018.862
tune.block.splsda 4.029 0.05714.153
tune.mint.plsda0.2730.0220.297
tune.mint.splsda1.1720.0801.259
tune.pca0.3010.0190.320
tune.pls11.907 0.76912.686
tune.plsda14.350 0.81715.176
tune.rcc0.5260.0370.563
tune.spca0.2100.0070.217
tune.spls80.696 5.15886.090
tune.splsda31.801 2.66334.534
unmap0.0020.0020.004
vip0.0030.0010.004
withinVariation0.4110.0050.417
wrapper.rgcca0.0200.0020.023
wrapper.sgcca0.0330.0050.038