Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-11 12:06 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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 1324/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.33.0  (landing page)
Eva Hamrud
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: mixOmics
Version: 6.33.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mixOmics_6.33.0.tar.gz
StartedAt: 2025-10-10 10:53:17 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 11:27:16 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 2039.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: mixOmics.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mixOmics_6.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/mixOmics.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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          431.564  0.211 432.750
tune.splsda        130.854  0.096 131.251
tune.pls            79.448  0.595  80.226
tune.plsda          62.914  0.095  63.188
tune.block.plsda    49.009  0.048  49.170
perf.assess         40.037  0.020  40.156
plotIndiv           32.038  0.064  32.181
biplot              22.795  0.200  23.061
tune.block.splsda   19.617  0.129  64.582
image.tune.rcc      12.754  0.036  12.822
tune.rcc            12.635  0.024  12.685
block.splsda        12.481  0.112  12.630
background.predict  11.646  0.119  11.802
block.spls          10.479  0.083  10.595
circosPlot          10.381  0.092  10.502
tune                 7.985  0.008   8.014
pca                  7.824  0.028   7.875
tune.mint.splsda     7.115  0.287   7.424
perf                 5.138  0.016   5.167
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • 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
  Error: Test failures
  Execution halted
* 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 ERROR, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/mixOmics.Rcheck/00check.log’
for details.


Installation output

mixOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 6.33.0
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")
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 6 | WARN 3 | SKIP 51 | PASS 657 ]

══ 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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-diabolo.R:58:3'): block.splsda works ─────────────────────────
rowMeans(nutrimouse.sgccda$weights) not equal to c(gene = 0.694506104274723, lipid = 0.915845972615744).
2/2 mismatches (average diff: 0.0105)
[1] 0.684 - 0.695 == -0.0106
[2] 0.905 - 0.916 == -0.0104
── Failure ('test-diabolo.R:68:3'): block.splsda works ─────────────────────────
nutrimouse.sgccda$AVE$AVE_outer[1] not equal to 0.217938372815004.
1/1 mismatches
[1] 0.198 - 0.218 == -0.0202
── Failure ('test-diabolo.R:69:3'): block.splsda works ─────────────────────────
nutrimouse.sgccda$AVE$AVE_inner[1] not equal to 0.663209598406049.
1/1 mismatches
[1] 0.691 - 0.663 == 0.028
── Failure ('test-diabolo.R:78:3'): block.splsda works ─────────────────────────
nutrimouse.sgccda$variates$gene[1, 1] not equal to 2.9424296984024.
1/1 mismatches
[1] 2.25 - 2.94 == -0.689
── Failure ('test-diabolo.R:79:3'): block.splsda works ─────────────────────────
nutrimouse.sgccda$variates$lipid[1, 1] not equal to 2.73351593820324.
1/1 mismatches
[1] 0.0769 - 2.73 == -2.66
── Failure ('test-diabolo.R:80:3'): block.splsda works ─────────────────────────
nutrimouse.sgccda$variates$Y[1, 1] not equal to 0.639567998302767.
1/1 mismatches
[1] 0.0493 - 0.64 == -0.59

[ FAIL 6 | WARN 3 | SKIP 51 | PASS 657 ]
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
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• 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
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• plotLoadings.mint.plsda/mint-plsda-loadings-custom-names.svg
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• plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-custom-labels.svg
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• plotLoadings.pca/loadings-plot-change-labels-and-label-sizes-graphics.svg
• plotLoadings.pls/loadings-plot-spls-change-block-ggplot2.svg
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• 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
Error: Test failures
Execution halted

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0650.0000.065
auroc1.6430.0401.688
background.predict11.646 0.11911.802
biplot22.795 0.20023.061
block.pls1.1020.0121.117
block.plsda1.7280.0041.736
block.spls10.479 0.08310.595
block.splsda12.481 0.11212.630
cim0.050.000.05
cimDiablo0.3840.0040.388
circosPlot10.381 0.09210.502
colors0.0340.0000.035
explained_variance0.1810.0000.182
get.confusion_matrix0.2670.0000.268
image.tune.rcc12.754 0.03612.822
imgCor0.1620.0040.166
impute.nipals0.0250.0000.026
ipca1.9090.0161.931
logratio-transformations0.0730.0000.073
map0.0040.0000.004
mat.rank0.0020.0000.003
mint.block.pls0.2070.0000.207
mint.block.plsda0.1560.0000.156
mint.block.spls0.2320.0000.234
mint.block.splsda0.1900.0000.191
mint.pca0.9200.0000.923
mint.pls1.5600.0001.564
mint.plsda1.6260.0041.635
mint.spls1.5880.0201.613
mint.splsda1.8940.0081.908
mixOmics0.6090.0080.619
nearZeroVar0.8100.0110.825
network0.060.000.06
pca7.8240.0287.875
perf5.1380.0165.167
perf.assess40.037 0.02040.156
plot.rcc0.0610.0000.061
plot.tune0.0010.0000.000
plotArrow3.2170.0123.238
plotDiablo0.2510.0000.252
plotIndiv32.038 0.06432.181
plotLoadings0.8820.0160.900
plotMarkers000
plotVar1.4040.0001.407
pls0.0050.0040.008
plsda0.8140.0000.816
predict0.2700.0000.271
rcc0.0030.0000.004
selectVar0.5330.0000.534
sipca1.0360.0001.038
spca4.7740.0084.793
spls0.4020.0000.403
splsda0.7820.0040.787
study_split0.0010.0040.005
summary0.0760.0000.077
tune7.9850.0088.014
tune.block.plsda49.009 0.04849.170
tune.block.splsda19.617 0.12964.582
tune.mint.plsda1.6620.1151.782
tune.mint.splsda7.1150.2877.424
tune.pca1.3330.0241.360
tune.pls79.448 0.59580.226
tune.plsda62.914 0.09563.188
tune.rcc12.635 0.02412.685
tune.spca1.1290.0081.140
tune.spls431.564 0.211432.750
tune.splsda130.854 0.096131.251
unmap0.0000.0040.004
vip0.0130.0000.013
withinVariation1.9980.0042.007
wrapper.rgcca0.0930.0000.093
wrapper.sgcca0.2040.0000.205