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This page was generated on 2024-05-04 11:36:50 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1299/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.28.0  (landing page)
Max Bladen
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/mixOmics
git_branch: RELEASE_3_19
git_last_commit: 69f1322
git_last_commit_date: 2024-04-30 11:10:54 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for mixOmics on nebbiolo1


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: 6.28.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings mixOmics_6.28.0.tar.gz
StartedAt: 2024-05-04 01:10:23 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:23:42 -0400 (Sat, 04 May 2024)
EllapsedTime: 799.4 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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  7.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.4Mb
    doc    1.7Mb
* 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             14.398  0.112  14.511
background.predict  7.391  0.395   7.787
block.splsda        6.630  0.055   6.688
circosPlot          5.526  0.041   5.567
block.spls          5.256  0.056   5.311
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.19-bioc/R/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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: x86_64-pc-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 (ijk.keepA in 1:nrow(keepA[[comp]])) { :
  closing unused connection 6 (<-localhost:11575)
2: In for (ijk.keepA in 1:nrow(keepA[[comp]])) { :
  closing unused connection 5 (<-localhost:11575)
> 
> proc.time()
   user  system elapsed 
102.199   2.776 119.676 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0190.0000.020
auroc1.4120.0521.465
background.predict7.3910.3957.787
biplot14.398 0.11214.511
block.pls0.5100.0080.518
block.plsda0.6710.0080.679
block.spls5.2560.0565.311
block.splsda6.6300.0556.688
cim0.0350.0040.039
cimDiablo0.2440.0000.244
circosPlot5.5260.0415.567
colors0.0280.0000.028
explained_variance0.0850.0070.093
get.confusion_matrix0.1330.0080.140
image.tune.rcc2.0790.0242.103
imgCor0.0770.0000.077
impute.nipals0.0080.0040.012
ipca0.7780.0040.783
logratio-transformations0.0650.0000.065
map0.0040.0000.005
mat.rank0.0020.0000.003
mint.block.pls0.1470.0000.148
mint.block.plsda0.1400.0040.144
mint.block.spls0.1640.0020.166
mint.block.splsda0.1360.0010.137
mint.pca0.3750.0000.376
mint.pls0.5170.0000.517
mint.plsda0.5880.0000.589
mint.spls0.5230.0000.524
mint.splsda0.6130.0000.614
mixOmics0.6220.0120.634
nearZeroVar0.6800.0000.681
network0.0130.0000.014
pca4.2800.0364.317
perf2.2710.0042.276
plot.rcc0.0120.0040.016
plot.tune0.0000.0020.002
plotArrow3.4870.0703.557
plotDiablo0.1650.0080.174
plotIndiv0.2760.0040.280
plotLoadings0.1270.0040.132
plotMarkers000
plotVar0.5390.0000.539
pls0.0060.0000.007
plsda0.3300.0000.331
predict0.1950.0020.196
rcc0.0020.0010.004
selectVar0.5840.0230.607
sipca0.4160.0010.417
spca2.7440.0122.755
spls0.4580.0040.461
splsda0.3150.0000.315
study_split0.0060.0000.005
summary0.0160.0000.016
tune4.3060.0224.349
tune.block.splsda000
tune.mint.splsda2.4010.0042.406
tune.pca0.1770.0000.177
tune.rcc2.3870.0032.392
tune.spca0.5930.0000.594
tune.spls0.0010.0000.000
tune.splsda3.7600.0683.848
tune.splslevel0.8170.0120.830
unmap0.0060.0000.006
vip0.0070.0040.010
withinVariation0.8260.0000.826
wrapper.rgcca0.0560.0070.062
wrapper.sgcca0.1030.0060.109