Eva Hamrud
| Snapshot Date: 2025-11-27 13:45 -0500 (Thu, 27 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/mixOmics |
| git_branch: RELEASE_3_22 |
| git_last_commit: 553e6cc |
| git_last_commit_date: 2025-10-29 10:48:48 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-01 12:01 -0500 (Mon, 01 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4610 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1333/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mixOmics 6.34.0 (landing page) Eva Hamrud
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: mixOmics |
| Version: 6.34.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.34.0.tar.gz |
| StartedAt: 2025-11-28 09:18:33 -0500 (Fri, 28 Nov 2025) |
| EndedAt: 2025-11-28 09:58:33 -0500 (Fri, 28 Nov 2025) |
| EllapsedTime: 2400.7 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: mixOmics.Rcheck |
| Warnings: NA |
##############################################################################
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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_6.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mixOmics.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘6.34.0’
* 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 487.506 8.942 566.052
tune.splsda 191.952 4.773 218.414
tune.plsda 94.714 1.949 113.746
tune.pls 83.681 1.964 102.565
tune.block.plsda 79.917 0.421 90.173
perf.assess 53.696 0.819 65.124
plotIndiv 52.968 1.088 62.194
biplot 31.270 0.173 42.829
tune.block.splsda 30.167 0.253 121.465
block.splsda 21.503 0.153 26.854
background.predict 16.928 0.891 24.638
block.spls 17.461 0.132 22.633
circosPlot 16.145 0.133 22.645
pca 12.788 0.117 17.393
tune 12.122 0.327 14.092
tune.mint.splsda 8.967 0.148 10.434
spca 8.529 0.137 9.588
perf 5.732 0.132 7.686
plotArrow 5.364 0.057 6.264
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘mixOmics’ ... ** this is package ‘mixOmics’ version ‘6.34.0’ ** 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)
mixOmics.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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 6.34.0
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")
2025-11-28 09:52:18.145 R[2384:64682500] XType: com.apple.fonts is not accessible.
2025-11-28 09:52:18.145 R[2384:64682500] XType: XTFontStaticRegistry is enabled.
mixOmics.Rcheck/mixOmics-Ex.timings
| name | user | system | elapsed | |
| S3methods-print | 0.026 | 0.008 | 0.051 | |
| auroc | 2.324 | 0.035 | 3.099 | |
| background.predict | 16.928 | 0.891 | 24.638 | |
| biplot | 31.270 | 0.173 | 42.829 | |
| block.pls | 1.680 | 0.025 | 2.244 | |
| block.plsda | 2.942 | 0.021 | 3.979 | |
| block.spls | 17.461 | 0.132 | 22.633 | |
| block.splsda | 21.503 | 0.153 | 26.854 | |
| cim | 0.072 | 0.012 | 0.108 | |
| cimDiablo | 0.662 | 0.016 | 0.852 | |
| circosPlot | 16.145 | 0.133 | 22.645 | |
| colors | 0.052 | 0.004 | 0.073 | |
| explained_variance | 0.183 | 0.009 | 0.258 | |
| get.confusion_matrix | 0.410 | 0.016 | 0.582 | |
| image.tune.rcc | 3.210 | 0.055 | 4.803 | |
| imgCor | 0.128 | 0.019 | 0.210 | |
| impute.nipals | 0.021 | 0.004 | 0.035 | |
| ipca | 2.799 | 0.041 | 3.947 | |
| logratio-transformations | 0.109 | 0.013 | 0.147 | |
| map | 0.007 | 0.004 | 0.013 | |
| mat.rank | 0.003 | 0.001 | 0.004 | |
| mint.block.pls | 0.521 | 0.022 | 0.686 | |
| mint.block.plsda | 0.144 | 0.009 | 0.186 | |
| mint.block.spls | 0.222 | 0.015 | 0.296 | |
| mint.block.splsda | 0.171 | 0.010 | 0.229 | |
| mint.pca | 1.449 | 0.021 | 1.855 | |
| mint.pls | 2.426 | 0.021 | 3.079 | |
| mint.plsda | 2.560 | 0.018 | 3.197 | |
| mint.spls | 2.424 | 0.019 | 3.014 | |
| mint.splsda | 2.584 | 0.018 | 3.052 | |
| mixOmics | 0.541 | 0.023 | 0.669 | |
| nearZeroVar | 1.594 | 0.046 | 1.965 | |
| network | 0.021 | 0.006 | 0.031 | |
| pca | 12.788 | 0.117 | 17.393 | |
| perf | 5.732 | 0.132 | 7.686 | |
| perf.assess | 53.696 | 0.819 | 65.124 | |
| plot.rcc | 0.022 | 0.006 | 0.034 | |
| plot.tune | 0.001 | 0.004 | 0.005 | |
| plotArrow | 5.364 | 0.057 | 6.264 | |
| plotDiablo | 0.301 | 0.014 | 0.377 | |
| plotIndiv | 52.968 | 1.088 | 62.194 | |
| plotLoadings | 1.075 | 0.047 | 1.313 | |
| plotMarkers | 0 | 0 | 0 | |
| plotVar | 2.300 | 0.021 | 2.635 | |
| pls | 0.013 | 0.004 | 0.019 | |
| plsda | 1.352 | 0.013 | 1.544 | |
| predict | 0.377 | 0.012 | 0.448 | |
| rcc | 0.005 | 0.004 | 0.010 | |
| selectVar | 0.658 | 0.053 | 0.839 | |
| sipca | 1.663 | 0.025 | 1.966 | |
| spca | 8.529 | 0.137 | 9.588 | |
| spls | 0.324 | 0.016 | 0.417 | |
| splsda | 1.355 | 0.024 | 1.545 | |
| study_split | 0.007 | 0.005 | 0.012 | |
| summary | 0.027 | 0.006 | 0.051 | |
| tune | 12.122 | 0.327 | 14.092 | |
| tune.block.plsda | 79.917 | 0.421 | 90.173 | |
| tune.block.splsda | 30.167 | 0.253 | 121.465 | |
| tune.mint.plsda | 2.061 | 0.043 | 2.323 | |
| tune.mint.splsda | 8.967 | 0.148 | 10.434 | |
| tune.pca | 2.282 | 0.039 | 2.600 | |
| tune.pls | 83.681 | 1.964 | 102.565 | |
| tune.plsda | 94.714 | 1.949 | 113.746 | |
| tune.rcc | 3.123 | 0.062 | 4.636 | |
| tune.spca | 1.863 | 0.029 | 2.853 | |
| tune.spls | 487.506 | 8.942 | 566.052 | |
| tune.splsda | 191.952 | 4.773 | 218.414 | |
| unmap | 0.007 | 0.011 | 0.027 | |
| vip | 0.020 | 0.006 | 0.036 | |
| withinVariation | 3.283 | 0.033 | 3.689 | |
| wrapper.rgcca | 0.146 | 0.009 | 0.183 | |
| wrapper.sgcca | 0.315 | 0.013 | 0.377 | |