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This page was generated on 2025-03-17 11:40 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1301/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.31.4  (landing page)
Eva Hamrud
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/mixOmics
git_branch: devel
git_last_commit: c667e77
git_last_commit_date: 2025-03-13 00:05:55 -0400 (Thu, 13 Mar 2025)
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for mixOmics on kjohnson3

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.

raw results


Summary

Package: mixOmics
Version: 6.31.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.31.4.tar.gz
StartedAt: 2025-03-16 20:18:05 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 20:24:46 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 401.5 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.31.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* 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 ... 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 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
perf.assess.sgccda: no visible binding for global variable
  ‘signif.threshold’
Undefined global functions or variables:
  signif.threshold
* 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         75.966  4.728  80.974
tune.splsda       30.954  2.696  33.756
tune.plsda        13.975  0.979  15.027
tune.pls          11.620  0.735  12.367
tune.block.plsda   9.096  0.159   9.282
perf.assess        8.379  0.540   9.000
tune.block.splsda  3.709  0.076  13.604
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck/00check.log’
for details.


Installation output

mixOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘mixOmics’ ...
** this is package ‘mixOmics’ version ‘6.31.4’
** 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)

Tests output

mixOmics.Rcheck/tests/testthat.Rout

R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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")
2025-03-16 20:22:17.498 R[73992:736780026] XType: Using static font registry.
[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 0 | PASS 616 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 616 ]
> 
> proc.time()
   user  system elapsed 
 86.106   8.798 148.144 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0060.0010.008
auroc0.3630.0130.377
background.predict3.2360.9344.193
biplot4.2210.0334.257
block.pls0.1690.0060.180
block.plsda0.2060.0020.208
block.spls1.6530.0401.782
block.splsda1.9760.0492.050
cim0.0160.0010.018
cimDiablo0.0840.0020.087
circosPlot2.0600.0272.095
colors0.0110.0010.012
explained_variance0.0360.0030.040
get.confusion_matrix0.0560.0040.060
image.tune.rcc0.6010.0290.670
imgCor0.0240.0030.028
impute.nipals0.0040.0020.006
ipca0.2540.0150.274
logratio-transformations0.0260.0040.030
map0.0010.0010.003
mat.rank000
mint.block.pls0.0630.0030.065
mint.block.plsda0.0520.0020.059
mint.block.spls0.0680.0040.073
mint.block.splsda0.0550.0030.059
mint.pca0.1170.0020.121
mint.pls0.1480.0040.153
mint.plsda0.1810.0030.188
mint.spls0.1600.0030.165
mint.splsda0.1850.0030.189
mixOmics0.1320.0100.141
nearZeroVar0.3280.0100.338
network0.0050.0010.005
pca1.6660.0301.701
perf0.8840.0720.961
perf.assess8.3790.5409.000
plot.rcc0.0050.0010.007
plot.tune000
plotArrow1.1030.0241.127
plotDiablo0.0760.0050.080
plotIndiv0.0950.0050.107
plotLoadings0.0380.0040.043
plotMarkers000
plotVar0.1960.0080.206
pls0.0020.0000.003
plsda0.1140.0040.135
predict0.0570.0060.074
rcc0.0010.0010.001
selectVar0.1550.0300.191
sipca0.1700.0160.193
spca1.1620.0591.266
spls0.0760.0110.092
splsda0.1180.0050.132
study_split0.0030.0010.003
summary0.0050.0010.013
tune2.0080.2302.327
tune.block.plsda9.0960.1599.282
tune.block.splsda 3.709 0.07613.604
tune.mint.plsda0.2640.0160.281
tune.mint.splsda1.0740.0801.172
tune.pca0.2980.0150.313
tune.pls11.620 0.73512.367
tune.plsda13.975 0.97915.027
tune.rcc0.5950.0420.636
tune.spca0.1890.0070.197
tune.spls75.966 4.72880.974
tune.splsda30.954 2.69633.756
unmap0.0010.0020.003
vip0.0030.0010.004
withinVariation0.2790.0050.284
wrapper.rgcca0.0160.0030.018
wrapper.sgcca0.0400.0040.044