############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mixOmics_6.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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 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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 6.3Mb sub-directories of 1Mb or more: R 1.3Mb data 3.4Mb * 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 219.556 0.507 222.580 tune.splsda 92.830 0.133 92.965 tune.plsda 45.266 0.313 46.140 tune.pls 33.227 0.506 33.735 tune.block.plsda 31.074 0.066 31.141 perf.assess 22.262 0.098 22.360 plotIndiv 21.255 0.078 21.352 biplot 17.043 0.127 17.171 tune.block.splsda 12.448 0.061 43.921 block.splsda 8.239 0.089 8.339 background.predict 7.407 0.120 7.533 block.spls 6.552 0.044 6.598 circosPlot 6.269 0.048 6.317 pca 5.324 0.051 5.375 tune 5.299 0.007 5.306 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck/00check.log’ for details.