Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-05-15 13:46:37 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 1259/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.29.0  (landing page)
Max Bladen
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/mixOmics
git_branch: devel
git_last_commit: 3eefa3c
git_last_commit_date: 2024-04-30 11:10:54 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for mixOmics on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: mixOmics
Version: 6.28.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings mixOmics_6.28.0.tar.gz
StartedAt: 2024-05-09 09:33:36 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 09:45:16 -0000 (Thu, 09 May 2024)
EllapsedTime: 700.2 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings mixOmics_6.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/mixOmics.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘6.28.0’
* 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  8.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.3Mb
    doc    1.9Mb
* 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
biplot             19.071  0.132  19.237
image.tune.rcc     14.534  0.028  14.579
tune.rcc           14.502  0.040  14.562
background.predict 11.856  0.259  12.139
block.splsda       10.491  0.096  10.609
circosPlot          9.882  0.084   9.987
block.spls          8.576  0.024   8.618
tune                6.755  0.009   6.777
pca                 6.503  0.028   6.543
tune.splsda         6.315  0.028   6.355
perf                6.277  0.004   6.293
plotArrow           5.812  0.044   5.868
tune.mint.splsda    5.153  0.004   5.167
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/mixOmics.Rcheck/00check.log’
for details.


Installation output

mixOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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)

Tests output

mixOmics.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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 6.28.0
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 0 | WARN 4 | SKIP 0 | PASS 236 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 236 ]
Warning messages:
1: In for (h in 1:ncomp) { :
  closing unused connection 6 (<-localhost:11541)
2: In for (h in 1:ncomp) { :
  closing unused connection 5 (<-localhost:11541)
> 
> proc.time()
   user  system elapsed 
354.418   3.297 378.573 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0710.0040.075
auroc1.5240.0281.555
background.predict11.856 0.25912.139
biplot19.071 0.13219.237
block.pls0.8530.0080.863
block.plsda1.0720.0081.082
block.spls8.5760.0248.618
block.splsda10.491 0.09610.609
cim0.0470.0040.051
cimDiablo0.4450.0120.458
circosPlot9.8820.0849.987
colors0.0320.0000.032
explained_variance0.2360.0000.237
get.confusion_matrix0.3240.0000.325
image.tune.rcc14.534 0.02814.579
imgCor0.1800.0040.185
impute.nipals0.0210.0040.025
ipca1.3280.0311.362
logratio-transformations0.0980.0040.101
map0.0040.0000.004
mat.rank0.0030.0000.003
mint.block.pls0.2210.0000.223
mint.block.plsda0.1760.0000.176
mint.block.spls0.2770.0000.277
mint.block.splsda0.1930.0000.193
mint.pca0.5490.0000.549
mint.pls0.7960.0000.798
mint.plsda0.9490.0000.951
mint.spls0.8070.0000.809
mint.splsda1.0000.0001.002
mixOmics0.8560.0000.857
nearZeroVar1.2910.0121.306
network0.0690.0000.069
pca6.5030.0286.543
perf6.2770.0046.293
plot.rcc0.0660.0040.070
plot.tune0.0010.0000.000
plotArrow5.8120.0445.868
plotDiablo0.2520.0080.261
plotIndiv0.5150.0000.517
plotLoadings0.2360.0040.240
plotMarkers000
plotVar0.9540.0000.956
pls0.0090.0000.009
plsda0.5480.0000.549
predict0.3500.0000.351
rcc0.0030.0000.003
selectVar0.9140.0200.936
sipca0.7150.0040.720
spca4.8400.0284.877
spls0.5420.0040.547
splsda0.5520.0000.553
study_split0.0050.0000.005
summary0.1010.0000.102
tune6.7550.0096.777
tune.block.splsda0.0010.0000.001
tune.mint.splsda5.1530.0045.167
tune.pca0.2520.0000.252
tune.rcc14.502 0.04014.562
tune.spca1.0370.0321.071
tune.spls000
tune.splsda6.3150.0286.355
tune.splslevel2.1130.0042.121
unmap0.0040.0000.004
vip0.0140.0000.014
withinVariation1.4250.0001.428
wrapper.rgcca0.1100.0000.111
wrapper.sgcca0.2120.0040.217