############################################################################## ############################################################################## ### ### 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_6.31.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * 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 ‘6.31.4’ * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘mixOmics’ can be installed ... OK * checking installed package size ... INFO installed size is 6.4Mb sub-directories of 1Mb or more: R 1.5Mb 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 ...Warning: program compiled against libxml 212 using older 211 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 ... OK * checking Rd files ... OK * 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 484.008 0.449 508.746 tune.splsda 144.164 0.242 157.995 tune.pls 85.348 0.506 87.597 tune.plsda 66.681 0.092 69.169 tune.block.plsda 48.495 0.052 48.983 perf.assess 46.159 0.104 47.335 tune.block.splsda 19.302 0.157 65.808 biplot 17.986 0.112 18.209 tune.rcc 12.840 0.020 12.966 image.tune.rcc 12.776 0.022 13.752 background.predict 12.504 0.116 12.761 block.splsda 9.687 0.076 9.790 circosPlot 9.506 0.048 9.944 tune 8.524 0.032 8.763 block.spls 7.645 0.036 7.752 tune.mint.splsda 6.828 0.180 7.109 pca 6.219 0.056 6.288 perf 5.285 0.000 5.297 plotArrow 5.142 0.004 5.193 * 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: 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 0 | PASS 565 ] 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck/00check.log’ for details.