Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1316/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mixOmics 6.32.0 (landing page) Eva Hamrud
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: mixOmics |
Version: 6.32.0 |
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_6.32.0.tar.gz |
StartedAt: 2025-10-14 11:20:51 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 11:58:50 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 2278.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mixOmics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_6.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * 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 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 518.437 0.670 521.077 tune.splsda 148.030 0.204 148.589 tune.pls 89.375 0.124 89.653 tune.plsda 69.216 0.143 69.572 perf.assess 50.972 0.084 51.174 tune.block.plsda 49.351 0.060 49.505 plotIndiv 35.866 0.111 36.078 biplot 23.562 0.140 23.753 tune.block.splsda 19.627 0.029 65.387 background.predict 13.517 0.176 13.738 tune.rcc 13.346 0.032 13.400 image.tune.rcc 13.337 0.032 13.395 block.splsda 13.141 0.128 13.298 block.spls 11.356 0.067 11.448 circosPlot 9.923 0.012 9.958 tune 9.093 0.024 9.135 pca 8.437 0.028 8.483 tune.mint.splsda 7.045 0.008 7.068 perf 5.954 0.008 5.975 spca 5.609 0.012 5.632 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck/00check.log’ for details.
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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)
mixOmics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 6.32.0 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") 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 0 | WARN 3 | SKIP 51 | PASS 663 ] ══ 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' [ FAIL 0 | WARN 3 | SKIP 51 | PASS 663 ] 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 > > proc.time() user system elapsed 654.387 10.339 889.302
mixOmics.Rcheck/mixOmics-Ex.timings
name | user | system | elapsed | |
S3methods-print | 0.067 | 0.000 | 0.069 | |
auroc | 1.841 | 0.019 | 1.876 | |
background.predict | 13.517 | 0.176 | 13.738 | |
biplot | 23.562 | 0.140 | 23.753 | |
block.pls | 1.200 | 0.016 | 1.219 | |
block.plsda | 1.783 | 0.004 | 1.791 | |
block.spls | 11.356 | 0.067 | 11.448 | |
block.splsda | 13.141 | 0.128 | 13.298 | |
cim | 0.045 | 0.004 | 0.050 | |
cimDiablo | 0.368 | 0.012 | 0.381 | |
circosPlot | 9.923 | 0.012 | 9.958 | |
colors | 0.033 | 0.000 | 0.033 | |
explained_variance | 0.227 | 0.004 | 0.231 | |
get.confusion_matrix | 0.294 | 0.008 | 0.302 | |
image.tune.rcc | 13.337 | 0.032 | 13.395 | |
imgCor | 0.159 | 0.004 | 0.163 | |
impute.nipals | 0.014 | 0.000 | 0.014 | |
ipca | 1.932 | 0.024 | 1.960 | |
logratio-transformations | 0.093 | 0.000 | 0.093 | |
map | 0.005 | 0.000 | 0.004 | |
mat.rank | 0.003 | 0.000 | 0.003 | |
mint.block.pls | 0.271 | 0.008 | 0.279 | |
mint.block.plsda | 0.162 | 0.008 | 0.170 | |
mint.block.spls | 0.271 | 0.000 | 0.272 | |
mint.block.splsda | 0.182 | 0.004 | 0.186 | |
mint.pca | 0.849 | 0.008 | 0.859 | |
mint.pls | 1.460 | 0.000 | 1.464 | |
mint.plsda | 1.555 | 0.000 | 1.558 | |
mint.spls | 1.512 | 0.008 | 1.524 | |
mint.splsda | 1.569 | 0.004 | 1.577 | |
mixOmics | 0.906 | 0.004 | 0.913 | |
nearZeroVar | 0.894 | 0.000 | 0.896 | |
network | 0.064 | 0.000 | 0.063 | |
pca | 8.437 | 0.028 | 8.483 | |
perf | 5.954 | 0.008 | 5.975 | |
perf.assess | 50.972 | 0.084 | 51.174 | |
plot.rcc | 0.065 | 0.000 | 0.065 | |
plot.tune | 0.001 | 0.000 | 0.000 | |
plotArrow | 3.488 | 0.008 | 3.506 | |
plotDiablo | 0.288 | 0.004 | 0.293 | |
plotIndiv | 35.866 | 0.111 | 36.078 | |
plotLoadings | 1.184 | 0.024 | 1.210 | |
plotMarkers | 0 | 0 | 0 | |
plotVar | 1.442 | 0.000 | 1.445 | |
pls | 0.009 | 0.000 | 0.009 | |
plsda | 0.837 | 0.004 | 0.842 | |
predict | 0.311 | 0.004 | 0.315 | |
rcc | 0.003 | 0.000 | 0.003 | |
selectVar | 1.055 | 0.004 | 1.062 | |
sipca | 1.089 | 0.000 | 1.092 | |
spca | 5.609 | 0.012 | 5.632 | |
spls | 0.540 | 0.000 | 0.541 | |
splsda | 0.839 | 0.000 | 0.841 | |
study_split | 0.006 | 0.000 | 0.005 | |
summary | 0.08 | 0.00 | 0.08 | |
tune | 9.093 | 0.024 | 9.135 | |
tune.block.plsda | 49.351 | 0.060 | 49.505 | |
tune.block.splsda | 19.627 | 0.029 | 65.387 | |
tune.mint.plsda | 1.667 | 0.020 | 1.698 | |
tune.mint.splsda | 7.045 | 0.008 | 7.068 | |
tune.pca | 1.475 | 0.008 | 1.491 | |
tune.pls | 89.375 | 0.124 | 89.653 | |
tune.plsda | 69.216 | 0.143 | 69.572 | |
tune.rcc | 13.346 | 0.032 | 13.400 | |
tune.spca | 1.152 | 0.004 | 1.159 | |
tune.spls | 518.437 | 0.670 | 521.077 | |
tune.splsda | 148.030 | 0.204 | 148.589 | |
unmap | 0.004 | 0.000 | 0.005 | |
vip | 0.012 | 0.000 | 0.013 | |
withinVariation | 2.009 | 0.000 | 2.014 | |
wrapper.rgcca | 0.082 | 0.000 | 0.083 | |
wrapper.sgcca | 0.185 | 0.000 | 0.185 | |