##############################################################################
##############################################################################
###
### 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_6.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mixOmics.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (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 ‘6.30.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mixOmics’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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.rcc           28.760  0.171  14.488
image.tune.rcc     28.658  0.075  14.421
biplot             18.139  0.103  18.277
background.predict 11.547  0.128  11.695
block.splsda        9.559  0.128   9.710
circosPlot          8.880  0.168   9.081
perf                8.139  0.056   5.975
block.spls          7.839  0.056   7.912
tune                6.645  0.030   6.623
pca                 6.275  0.076   6.114
tune.splsda         6.085  0.042   6.137
plotArrow           5.539  0.016   5.273
spca                5.397  0.000   4.127
* 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:
  ── Failure ('test-plotIndiv.R:83:3'): plotIndiv works for sgcca and rgcca ──────
  round(numeric_value, digits = digits) not equal to round(expected, digits = digits).
  1/1 mismatches
  [1] 0.11 - 3.32 == -3.21
  Backtrace:
      ▆
   1. └─mixOmics:::.expect_numerically_close(...) at test-plotIndiv.R:83:3
   2.   └─testthat::expect_equal(...) at tests/testthat/helpers.R:25:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 235 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (k in 1:J) { : closing unused connection 6 (<-localhost:11985)
  2: In for (k in 1:J) { : closing unused connection 5 (<-localhost:11985)
  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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/mixOmics.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 6.30.0
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")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 235 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotIndiv.R:83:3'): plotIndiv works for sgcca and rgcca ──────
round(numeric_value, digits = digits) not equal to round(expected, digits = digits).
1/1 mismatches
[1] 0.11 - 3.32 == -3.21
Backtrace:
    ▆
 1. └─mixOmics:::.expect_numerically_close(...) at test-plotIndiv.R:83:3
 2.   └─testthat::expect_equal(...) at tests/testthat/helpers.R:25:5

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 235 ]
Error: Test failures
In addition: Warning messages:
1: In for (k in 1:J) { : closing unused connection 6 (<-localhost:11985)
2: In for (k in 1:J) { : closing unused connection 5 (<-localhost:11985)
Execution halted