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This page was generated on 2025-10-20 12:04 -0400 (Mon, 20 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1133/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
limpca 1.5.1  (landing page)
Manon Martin
Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 2025)
git_url: https://git.bioconductor.org/packages/limpca
git_branch: devel
git_last_commit: a949790
git_last_commit_date: 2025-09-23 07:42:54 -0400 (Tue, 23 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for limpca on nebbiolo2

To the developers/maintainers of the limpca package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/limpca.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: limpca
Version: 1.5.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:limpca.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings limpca_1.5.1.tar.gz
StartedAt: 2025-10-20 01:21:24 -0400 (Mon, 20 Oct 2025)
EndedAt: 2025-10-20 01:27:15 -0400 (Mon, 20 Oct 2025)
EllapsedTime: 351.4 seconds
RetCode: 0
Status:   OK  
CheckDir: limpca.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:limpca.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings limpca_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/limpca.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘limpca/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘limpca’ version ‘1.5.1’
* 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 ‘limpca’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
lmpBootstrapTests 14.441  3.195  11.969
lmpLoading1dPlot   5.050  0.184   5.234
* 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: OK


Installation output

limpca.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL limpca
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘limpca’ ...
** this is package ‘limpca’ version ‘1.5.1’
** 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 (limpca)

Tests output

limpca.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(limpca)
> 
> test_check("limpca")
| dim outcomes: 10x3
| formula: ~ factA + factB
| design variables (2): 
* factA (factor)
* factB (factor)
| dim outcomes: 10x3
| formula: ~ factA + factB
| design variables (2): 
* factA (factor)
* factB (factor)
| dim outcomes: 10x3
| formula: ~ factA + factB
| design variables (2): 
* factA (factor)
* factB (factor)
| dim outcomes: 10x3
| formula: ~ factA + factB
| design variables (2): 
* factA (factor)
* factB (factor)
| dim outcomes: 10x3
| formula: 
| design variables (2): 
* factA (factor)
* factB (factor)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
> 
> proc.time()
   user  system elapsed 
  9.062   1.545   9.761 

Example timings

limpca.Rcheck/limpca-Ex.timings

nameusersystemelapsed
UCH0.0110.0020.013
data2lmpDataList0.2470.0050.252
lmpBootstrapTests14.441 3.19511.969
lmpContributions2.1360.8591.723
lmpEffectMatrices0.8570.0070.864
lmpEffectPlot2.0350.1682.205
lmpLoading1dPlot5.0500.1845.234
lmpLoading2dPlot3.8390.3174.156
lmpModelMatrix0.0060.0000.006
lmpPcaEffects0.7450.0060.751
lmpScorePlot1.3990.0401.439
lmpScoreScatterPlotM1.5600.1081.669
lmpScreePlot0.9810.0201.001
pcaBySvd0.0170.0010.018
pcaLoading1dPlot0.3600.0120.372
pcaLoading2dPlot1.9860.0572.044
pcaScorePlot0.6220.0090.632
pcaScreePlot0.2000.0040.204
plotDesign3.9010.0503.954
plotLine3.8190.0403.860
plotMeans1.7970.0041.802
plotScatter3.1990.0473.248
plotScatterM0.0570.0020.060
trout0.0000.0010.001