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### 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
###
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* 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          484.050  0.259 530.377
tune.splsda        140.211  0.211 145.603
tune.pls            83.418  0.549  89.217
tune.plsda          66.790  0.120  73.527
tune.block.plsda    48.282  0.059  52.690
perf.assess         47.394  0.076  50.339
tune.block.splsda   18.244  0.090  68.997
biplot              17.833  0.087  18.653
background.predict  12.744  0.159  13.906
image.tune.rcc      12.618  0.039  13.731
tune.rcc            12.649  0.003  13.983
circosPlot           9.988  0.074  10.929
block.splsda         9.329  0.052  10.210
tune                 8.174  0.004   8.830
block.spls           7.789  0.048   8.338
tune.mint.splsda     6.613  0.168   7.117
pca                  5.772  0.040   6.121
perf                 5.312  0.016   5.454
plotArrow            5.225  0.020   6.036
* 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.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL mixOmics
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘mixOmics’ ...
** 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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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 6.31.4
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")
[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 6 | WARN 3 | SKIP 0 | PASS 565 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-diabolo.R:58:3'): block.splsda works ─────────────────────────
rowMeans(nutrimouse.sgccda$weights) not equal to c(gene = 0.694506104274723, lipid = 0.915845972615744).
2/2 mismatches (average diff: 0.0105)
[1] 0.684 - 0.695 == -0.0106
[2] 0.905 - 0.916 == -0.0104
── Failure ('test-diabolo.R:68:3'): block.splsda works ─────────────────────────
nutrimouse.sgccda$AVE$AVE_outer[1] not equal to 0.217938372815004.
1/1 mismatches
[1] 0.198 - 0.218 == -0.0202
── Failure ('test-diabolo.R:69:3'): block.splsda works ─────────────────────────
nutrimouse.sgccda$AVE$AVE_inner[1] not equal to 0.663209598406049.
1/1 mismatches
[1] 0.691 - 0.663 == 0.028
── Failure ('test-diabolo.R:78:3'): block.splsda works ─────────────────────────
nutrimouse.sgccda$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