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

This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1288/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mixOmics 6.30.0  (landing page)
Eva Hamrud
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/mixOmics
git_branch: RELEASE_3_20
git_last_commit: 39e7eb5
git_last_commit_date: 2024-10-29 10:33:04 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for mixOmics on kjohnson1

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: 6.30.0
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_6.30.0.tar.gz
StartedAt: 2024-12-21 01:40:30 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 01:46:34 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 364.1 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_6.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mixOmics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 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 ‘6.30.0’
* 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  6.2Mb
  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 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
biplot             12.535  0.093  12.649
background.predict  8.264  2.009  10.327
block.splsda        6.180  0.118   6.304
circosPlot          5.793  0.089   5.890
block.spls          5.282  0.118   5.403
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 6.30.0
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")
2024-12-21 01:44:10.614 R[45372:80585732] XType: Using static font registry.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ]
Warning messages:
1: In name : closing unused connection 6 (<-localhost:11423)
2: In name : closing unused connection 5 (<-localhost:11423)
> 
> proc.time()
   user  system elapsed 
103.812   5.302 140.834 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0200.0050.025
auroc1.0910.0361.127
background.predict 8.264 2.00910.327
biplot12.535 0.09312.649
block.pls0.3740.0080.384
block.plsda0.4060.0060.416
block.spls5.2820.1185.403
block.splsda6.1800.1186.304
cim0.0520.0070.059
cimDiablo0.2660.0110.278
circosPlot5.7930.0895.890
colors0.0370.0020.038
explained_variance0.1480.0070.155
get.confusion_matrix0.1820.0080.190
image.tune.rcc2.3680.0642.432
imgCor0.0730.0080.082
impute.nipals0.0120.0020.015
ipca1.0960.0351.132
logratio-transformations0.0760.0070.082
map0.0060.0020.007
mat.rank0.0020.0010.002
mint.block.pls0.2140.0150.228
mint.block.plsda0.1590.0070.166
mint.block.spls0.2050.0110.216
mint.block.splsda0.1690.0060.175
mint.pca0.3730.0160.390
mint.pls0.4700.0070.479
mint.plsda0.5550.0090.564
mint.spls0.4670.0100.476
mint.splsda0.5630.0080.572
mixOmics0.3690.0260.395
nearZeroVar0.6710.0260.698
network0.0170.0030.020
pca4.4640.0644.530
perf2.6950.1472.842
plot.rcc0.0180.0040.021
plot.tune0.0010.0000.002
plotArrow3.6180.0693.691
plotDiablo0.2140.0100.224
plotIndiv0.2790.0080.288
plotLoadings0.1220.0110.134
plotMarkers000
plotVar0.5090.0110.519
pls0.0050.0020.007
plsda0.3270.0100.337
predict0.1750.0110.187
rcc0.0020.0020.004
selectVar0.4910.0490.540
sipca0.4850.0240.510
spca3.6590.1233.789
spls0.2240.0350.259
splsda0.3260.0140.341
study_split0.0080.0020.011
summary0.0290.0050.034
tune4.4620.3404.826
tune.block.splsda0.0000.0010.001
tune.mint.splsda2.2560.1422.398
tune.pca0.2210.0160.238
tune.rcc2.1750.0412.215
tune.spca0.5940.0110.604
tune.spls000
tune.splsda4.1930.3154.509
tune.splslevel0.9160.0550.988
unmap0.0050.0050.010
vip0.0090.0030.012
withinVariation0.8540.0220.876
wrapper.rgcca0.0590.0030.062
wrapper.sgcca0.1030.0080.111