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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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    ERROR  


CHECK results for mixOmics on teran2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mixOmics_6.30.0.tar.gz
StartedAt: 2024-11-20 05:53:21 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 06:04:00 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 639.1 seconds
RetCode: 0
Status:   OK  
CheckDir: mixOmics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mixOmics_6.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/mixOmics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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  6.3Mb
  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 loading without being on the library search path ... 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 11.317  0.012  11.342
* 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: 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/mixOmics.Rcheck/00check.log’
for details.


Installation output

mixOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL mixOmics
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 6.30.0
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")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ]
Warning messages:
1: In forceAndCall(1, FUN, newX[, i], ...) :
  closing unused connection 6 (<-localhost:11119)
2: In forceAndCall(1, FUN, newX[, i], ...) :
  closing unused connection 5 (<-localhost:11119)
> 
> proc.time()
   user  system elapsed 
 72.626   1.885  86.120 

Example timings

mixOmics.Rcheck/mixOmics-Ex.timings

nameusersystemelapsed
S3methods-print0.0110.0010.012
auroc0.7310.0390.771
background.predict4.2250.0474.276
biplot11.317 0.01211.342
block.pls0.3330.0080.341
block.plsda0.4470.0020.448
block.spls3.6690.0183.689
block.splsda4.3170.0174.336
cim0.0230.0020.025
cimDiablo0.1980.0020.200
circosPlot4.1290.0094.139
colors0.0200.0010.020
explained_variance0.0800.0030.082
get.confusion_matrix0.3580.0030.360
image.tune.rcc1.3770.0031.380
imgCor0.0380.0020.040
impute.nipals0.0150.0000.014
ipca0.5020.0130.515
logratio-transformations0.0450.0020.047
map0.0020.0010.003
mat.rank0.0000.0010.001
mint.block.pls0.0880.0030.091
mint.block.plsda0.0840.0010.085
mint.block.spls0.1020.0030.105
mint.block.splsda0.0870.0020.090
mint.pca0.2650.0010.266
mint.pls0.3300.0010.331
mint.plsda0.4000.0010.402
mint.spls0.3360.0010.337
mint.splsda0.4100.0000.409
mixOmics0.1840.0120.196
nearZeroVar0.4620.0040.466
network0.0100.0000.009
pca3.3320.0183.350
perf1.7690.0181.787
plot.rcc0.010.000.01
plot.tune0.0010.0000.001
plotArrow2.3180.0072.325
plotDiablo0.1280.0030.131
plotIndiv0.2070.0010.208
plotLoadings0.0650.0010.065
plotMarkers000
plotVar0.3760.0020.377
pls0.0040.0010.005
plsda0.2270.0000.228
predict0.1200.0010.121
rcc0.0020.0010.002
selectVar0.2430.0010.244
sipca0.3510.0000.351
spca2.1790.0052.185
spls0.1220.0010.123
splsda0.2220.0010.223
study_split0.0020.0020.004
summary0.0110.0000.011
tune2.6140.0092.621
tune.block.splsda000
tune.mint.splsda1.5130.0031.515
tune.pca0.1320.0010.134
tune.rcc1.3970.0011.398
tune.spca0.4290.0000.429
tune.spls000
tune.splsda2.5990.0072.605
tune.splslevel0.5770.0030.579
unmap0.0030.0000.004
vip0.0050.0010.006
withinVariation0.5890.0060.595
wrapper.rgcca0.0430.0010.044
wrapper.sgcca0.0830.0000.083