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This page was generated on 2024-05-04 11:39:33 -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 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: 2024-05-03 23:17:39 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 23:24:41 -0400 (Fri, 03 May 2024)
EllapsedTime: 422.7 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 beta (2024-04-14 r86421)
* 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  8.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    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             11.970  0.127  12.179
background.predict  7.728  1.468   9.303
circosPlot          7.710  0.152   7.943
block.splsda        7.595  0.143   7.830
block.spls          6.560  0.118   6.752
tune                4.580  0.465   5.108
* 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 beta (2024-04-14 r86421) -- "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")
2024-05-03 23:21:55.830 R[55965:1726162845] XType: com.apple.fonts is not accessible.
2024-05-03 23:21:55.830 R[55965:1726162845] 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:11135)
2: In for (h in 1:ncomp) { :
  closing unused connection 5 (<-localhost:11135)
> 
> proc.time()
   user  system elapsed 
120.476   5.720 162.003 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0200.0040.024
auroc1.1870.0571.255
background.predict7.7281.4689.303
biplot11.970 0.12712.179
block.pls0.5750.0150.596
block.plsda0.8350.0160.860
block.spls6.5600.1186.752
block.splsda7.5950.1437.830
cim0.0390.0070.047
cimDiablo0.3230.0150.345
circosPlot7.7100.1527.943
colors0.0310.0020.033
explained_variance0.1100.0070.120
get.confusion_matrix0.2190.0170.239
image.tune.rcc2.5180.0812.622
imgCor0.0960.0200.118
impute.nipals0.0150.0040.018
ipca1.2370.0381.287
logratio-transformations0.0660.0050.073
map0.0050.0030.008
mat.rank0.0020.0000.002
mint.block.pls0.1570.0090.169
mint.block.plsda0.1190.0050.126
mint.block.spls0.1780.0120.190
mint.block.splsda0.1320.0060.139
mint.pca0.4110.0070.421
mint.pls0.5940.0110.611
mint.plsda0.6780.0110.696
mint.spls0.6190.0130.639
mint.splsda0.7130.0140.735
mixOmics0.3700.0340.408
nearZeroVar0.7300.0160.754
network0.0160.0040.020
pca4.6500.0674.750
perf2.8990.1613.092
plot.rcc0.0150.0050.020
plot.tune0.0000.0020.002
plotArrow4.1650.0994.301
plotDiablo0.1750.0080.186
plotIndiv0.3570.0140.373
plotLoadings0.1200.0090.131
plotMarkers000
plotVar0.7290.0180.757
pls0.0080.0010.010
plsda0.4080.0140.426
predict0.1830.0120.196
rcc0.0020.0020.003
selectVar0.4440.0610.510
sipca0.5060.0190.529
spca3.5340.1433.706
spls0.2050.0150.221
splsda0.3510.0130.364
study_split0.0040.0020.005
summary0.0200.0040.023
tune4.5800.4655.108
tune.block.splsda0.0000.0010.001
tune.mint.splsda2.5890.1382.751
tune.pca0.1980.0160.214
tune.rcc2.2970.0762.392
tune.spca0.7830.0170.807
tune.spls0.0010.0000.000
tune.splsda4.2270.3764.658
tune.splslevel1.2430.0721.326
unmap0.0050.0050.009
vip0.0100.0030.013
withinVariation0.9440.0160.966
wrapper.rgcca0.0820.0030.086
wrapper.sgcca0.1330.0090.143