Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1327/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.33.0  (landing page)
Eva Hamrud
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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 12.7.6 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: 2025-10-17 11:09:31 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 11:43:49 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 2058.0 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          436.717  0.204 438.166
tune.splsda        132.124  0.187 132.752
tune.pls            79.850  0.184  80.244
tune.plsda          63.132  0.075  63.400
tune.block.plsda    50.160  0.020  50.349
perf.assess         39.586  0.024  39.684
plotIndiv           32.800  0.004  32.866
biplot              22.799  0.155  23.004
tune.block.splsda   20.136  0.169  65.592
image.tune.rcc      12.687  0.032  12.736
block.splsda        12.647  0.012  12.690
tune.rcc            12.609  0.000  12.631
background.predict  11.841  0.531  12.406
block.spls          10.514  0.060  10.600
circosPlot          10.294  0.012  10.331
tune                 8.280  0.036   8.345
pca                  7.967  0.012   7.996
tune.mint.splsda     6.786  0.084   6.890
perf                 5.011  0.020   5.038
* 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
• 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
Error: Test failures
Execution halted

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0650.0000.066
auroc1.7550.0001.759
background.predict11.841 0.53112.406
biplot22.799 0.15523.004
block.pls1.0770.0001.079
block.plsda1.6650.0081.677
block.spls10.514 0.06010.600
block.splsda12.647 0.01212.690
cim0.0510.0000.052
cimDiablo0.3790.0000.380
circosPlot10.294 0.01210.331
colors0.0320.0000.033
explained_variance0.1900.0040.194
get.confusion_matrix0.2690.0200.289
image.tune.rcc12.687 0.03212.736
imgCor0.1790.0000.179
impute.nipals0.0090.0040.013
ipca1.7560.0081.767
logratio-transformations0.0790.0040.083
map0.0050.0000.004
mat.rank0.0030.0000.002
mint.block.pls0.4830.0040.488
mint.block.plsda0.1470.0000.147
mint.block.spls0.2290.0000.230
mint.block.splsda0.1610.0000.161
mint.pca0.8180.0320.852
mint.pls1.4020.0041.408
mint.plsda1.4910.0001.493
mint.spls1.4640.0001.467
mint.splsda1.5480.0001.552
mixOmics0.6400.0200.662
nearZeroVar0.8720.0000.874
network0.060.000.06
pca7.9670.0127.996
perf5.0110.0205.038
perf.assess39.586 0.02439.684
plot.rcc0.0720.0020.074
plot.tune0.0000.0010.000
plotArrow3.4960.0053.507
plotDiablo0.2510.0000.252
plotIndiv32.800 0.00432.866
plotLoadings0.9100.0040.916
plotMarkers000
plotVar1.4270.0001.429
pls0.0080.0000.008
plsda0.7930.0000.794
predict0.2840.0000.284
rcc0.0030.0000.004
selectVar0.4870.0040.492
sipca1.0750.0001.077
spca4.6980.0124.723
spls0.4440.0000.445
splsda0.8090.0070.822
study_split0.0050.0000.005
summary0.0780.0000.078
tune8.2800.0368.345
tune.block.plsda50.160 0.02050.349
tune.block.splsda20.136 0.16965.592
tune.mint.plsda1.6150.0631.684
tune.mint.splsda6.7860.0846.890
tune.pca1.2820.0081.294
tune.pls79.850 0.18480.244
tune.plsda63.132 0.07563.400
tune.rcc12.609 0.00012.631
tune.spca1.0740.0001.078
tune.spls436.717 0.204438.166
tune.splsda132.124 0.187132.752
unmap0.0040.0000.004
vip0.0120.0000.013
withinVariation2.0400.0042.050
wrapper.rgcca0.0910.0000.092
wrapper.sgcca0.1800.0010.182