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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mixOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mixOmics’ version ‘6.32.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols-reordered-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols-with-set-pch-circle-for-all-samples.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-custom-cols-with-set-pch-triangle-for-all-samples.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups-reordered.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-coloured-by-primary-groups-with-set-pch-for-each-group.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-sample-names-coloured-by-primary-groups-custom-cols.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-with-centroids-coloured-by-primary-groups-custom-cols.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols-ellipse-level-0-5.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols-sample-names.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pca/pca-plot-with-ellipse-coloured-by-primary-groups-custom-cols.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/pca-plot-sample-names-coloured-by-primary-groups-custom-cols.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-coloured-by-primary-groups-custom-cols-reordered-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-coloured-by-primary-groups-custom-cols-with-set-pch-circle-for-all-samples.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-coloured-by-primary-groups-with-pch-for-secondary-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-coloured-by-primary-groups-with-set-pch-for-each-group.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-with-ellipse-coloured-by-primary-groups-ellipse-level-0-5.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/rcca-plot-with-pch-for-primary-groups-col-consistent.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/spls-plot-with-centroids-and-stars-coloured-by-primary-groups.svg
  mixOmics/tests/testthat/_snaps/plotIndiv.pls/splsda-plot-with-centroids-and-stars-custom-cols-pch-on-second-grouping.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-cols-and-borders-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-cols-and-borders-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-gene-names-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-gene-names-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-labels-and-label-sizes-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-labels-and-label-sizes-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-layout-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-change-layout-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-specific-study-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.pls/loadings-plot-mint-pls-specific-study-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.mint.plsda/mint-plsda-loadings-ggplot2-specific-study.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pca/loadings-plot-change-gene-names-and-plot-top-3-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pca/loadings-plot-change-gene-names-and-plot-top-3-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pca/loadings-plot-change-labels-and-label-sizes-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pca/loadings-plot-change-labels-and-label-sizes-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-cols-and-borders-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-cols-and-borders-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-gene-names-and-plot-top-3-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-gene-names-and-plot-top-3-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-labels-and-label-sizes-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.pls/loadings-plot-spls-change-labels-and-label-sizes-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-legend-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-legend-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-names-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-title-and-labels-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.plsda/loadings-plot-splsda-with-custom-title-and-labels-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.sgccda/loadings-plot-diablo-block-specific-with-contrib-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.sgccda/loadings-plot-diablo-block-specific-with-contrib-graphics.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.sgccda/loadings-plot-diablo-change-labels-and-label-sizes-ggplot2.svg
  mixOmics/tests/testthat/_snaps/plotLoadings.sgccda/loadings-plot-diablo-change-labels-and-label-sizes-graphics.svg

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
tune.spls          466.351 11.340 491.029
tune.splsda        189.627  5.742 205.695
tune.plsda          95.343  2.697 100.011
tune.pls            79.847  2.120  82.786
tune.block.plsda    76.061  0.407  78.683
perf.assess         51.515  0.931  56.105
plotIndiv           37.423  1.273  40.218
tune.block.splsda   28.732  0.241 101.752
biplot              25.180  0.129  27.217
background.predict  17.085  1.178  18.988
circosPlot          16.293  0.137  19.338
block.splsda        15.388  0.119  17.309
block.spls          12.169  0.102  13.814
tune                11.218  0.454  11.833
pca                  9.400  0.082  10.540
tune.mint.splsda     8.112  0.156   8.330
spca                 6.312  0.134   6.503
perf                 5.278  0.148   5.775
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘mixOmics’ ...
** this is package ‘mixOmics’ version ‘6.32.0’
** 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)

R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(mixOmics)
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2

Loaded mixOmics 6.32.0
Thank you for using mixOmics!
Tutorials: http://mixomics.org
Bookdown vignette: https://mixomicsteam.github.io/Bookdown
Questions, issues: Follow the prompts at http://mixomics.org/contact-us
Cite us:  citation('mixOmics')

> 
> test_check("mixOmics")
2025-08-01 06:51:25.637 R[46850:291409485] XType: com.apple.fonts is not accessible.
2025-08-01 06:51:25.638 R[46850:291409485] XType: XTFontStaticRegistry is enabled.
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..."