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 12:07 -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 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: 2025-10-07 09:46:36 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 10:20:20 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 2024.0 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          421.552  0.311 422.800
tune.splsda        127.810  0.168 128.286
tune.pls            76.180  0.539  76.900
tune.plsda          59.768  0.048  59.968
tune.block.plsda    48.143  0.052  48.327
perf.assess         38.762  0.044  38.907
plotIndiv           31.473  0.060  31.625
biplot              22.156  0.155  22.359
tune.block.splsda   18.522  0.141  64.723
image.tune.rcc      12.537  0.036  12.593
tune.rcc            12.518  0.036  12.575
block.splsda        11.997  0.056  12.079
background.predict  11.031  0.140  11.198
block.spls           9.957  0.084  10.064
circosPlot           9.474  0.040   9.537
pca                  7.789  0.096   7.902
tune                 7.573  0.016   7.611
tune.mint.splsda     6.721  0.215   6.957
* 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
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• 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
auroc1.5970.0361.638
background.predict11.031 0.14011.198
biplot22.156 0.15522.359
block.pls1.0310.0121.045
block.plsda1.6670.0081.680
block.spls 9.957 0.08410.064
block.splsda11.997 0.05612.079
cim0.050.000.05
cimDiablo0.3510.0000.351
circosPlot9.4740.0409.537
colors0.0330.0000.033
explained_variance0.1580.0120.170
get.confusion_matrix0.2710.0000.272
image.tune.rcc12.537 0.03612.593
imgCor0.1590.0040.163
impute.nipals0.0190.0040.023
ipca1.6860.0241.715
logratio-transformations0.0730.0040.077
map0.0040.0000.004
mat.rank0.0020.0000.003
mint.block.pls0.1880.0000.189
mint.block.plsda0.1880.0360.225
mint.block.spls0.2040.0040.208
mint.block.splsda0.180.000.18
mint.pca0.7890.0070.799
mint.pls1.4100.0001.413
mint.plsda1.4870.0011.491
mint.spls1.4170.0001.421
mint.splsda1.5240.0111.539
mixOmics0.6300.0040.635
nearZeroVar0.8850.0000.888
network0.060.000.06
pca7.7890.0967.902
perf4.9460.0044.960
perf.assess38.762 0.04438.907
plot.rcc0.0610.0000.061
plot.tune000
plotArrow3.1250.0083.141
plotDiablo0.2370.0080.246
plotIndiv31.473 0.06031.625
plotLoadings0.8830.0040.890
plotMarkers000
plotVar1.3640.0001.368
pls0.0080.0000.007
plsda0.8060.0040.813
predict0.2640.0000.266
rcc0.0030.0000.003
selectVar0.4510.0120.463
sipca1.0020.0041.009
spca4.4670.0084.489
spls0.4120.0000.413
splsda1.0100.0081.019
study_split0.0020.0040.006
summary0.0770.0000.077
tune7.5730.0167.611
tune.block.plsda48.143 0.05248.327
tune.block.splsda18.522 0.14164.723
tune.mint.plsda1.6460.0681.719
tune.mint.splsda6.7210.2156.957
tune.pca1.2840.0201.307
tune.pls76.180 0.53976.900
tune.plsda59.768 0.04859.968
tune.rcc12.518 0.03612.575
tune.spca1.0620.0161.081
tune.spls421.552 0.311422.800
tune.splsda127.810 0.168128.286
unmap0.0040.0000.004
vip0.0110.0000.011
withinVariation1.9680.0001.973
wrapper.rgcca0.0890.0000.089
wrapper.sgcca0.1760.0000.176