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This page was generated on 2024-06-07 20:27 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for mixOmics on lconway

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: /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_6.28.0.tar.gz
StartedAt: 2024-06-05 21:39:56 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 21:46:32 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 396.0 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_6.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mixOmics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mixOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mixOmics’ version ‘6.28.0’
* 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  8.1Mb
  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 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             10.329  0.069  10.420
background.predict  7.561  1.544   9.203
block.splsda        7.202  0.111   7.365
circosPlot          6.740  0.108   6.869
block.spls          5.790  0.065   5.872
tune                4.584  0.495   5.142
* 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
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/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 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 6.28.0
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")
2024-06-05 21:43:56.183 R[27752:20910208] XType: com.apple.fonts is not accessible.
2024-06-05 21:43:56.183 R[27752:20910208] XType: XTFontStaticRegistry is enabled.
[ 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:11224)
2: In for (h in 1:ncomp) { :
  closing unused connection 5 (<-localhost:11224)
> 
> proc.time()
   user  system elapsed 
112.514   5.431 152.109 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0210.0050.025
auroc1.1110.0471.161
background.predict7.5611.5449.203
biplot10.329 0.06910.420
block.pls0.5200.0090.530
block.plsda0.6810.0080.692
block.spls5.7900.0655.872
block.splsda7.2020.1117.365
cim0.0380.0080.047
cimDiablo0.2530.0130.267
circosPlot6.7400.1086.869
colors0.0280.0030.031
explained_variance0.0790.0030.082
get.confusion_matrix0.1250.0090.133
image.tune.rcc2.3980.0542.461
imgCor0.0690.0100.080
impute.nipals0.0110.0040.015
ipca0.8750.0460.938
logratio-transformations0.0720.0060.079
map0.0050.0030.008
mat.rank0.0020.0010.002
mint.block.pls0.1560.0180.176
mint.block.plsda0.1290.0040.134
mint.block.spls0.1740.0070.181
mint.block.splsda0.1370.0050.141
mint.pca0.3540.0070.361
mint.pls0.5790.0080.589
mint.plsda0.7280.0130.751
mint.spls0.6330.0190.659
mint.splsda0.7320.0050.741
mixOmics0.3370.0220.361
nearZeroVar0.8910.0280.921
network0.0310.0130.045
pca4.4340.0414.488
perf2.7600.1532.920
plot.rcc0.0160.0040.020
plot.tune0.0000.0000.001
plotArrow3.8920.0784.006
plotDiablo0.1690.0060.177
plotIndiv0.2830.0120.296
plotLoadings0.0970.0080.105
plotMarkers000
plotVar0.5870.0150.603
pls0.0050.0010.006
plsda0.3660.0050.372
predict0.1920.0080.202
rcc0.0020.0020.003
selectVar0.4440.0520.498
sipca0.5420.0170.561
spca3.4220.1533.607
spls0.2080.0100.220
splsda0.4050.0100.416
study_split0.0040.0010.005
summary0.0180.0040.023
tune4.5840.4955.142
tune.block.splsda0.0010.0000.001
tune.mint.splsda2.4540.1482.609
tune.pca0.1860.0240.210
tune.rcc2.3100.0552.369
tune.spca0.7470.0170.765
tune.spls0.0000.0010.000
tune.splsda4.0620.3864.493
tune.splslevel0.9510.0621.019
unmap0.0040.0030.006
vip0.0110.0020.012
withinVariation1.2710.0311.307
wrapper.rgcca0.0610.0040.065
wrapper.sgcca0.1100.0050.116