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This page was generated on 2025-08-04 11:46 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1127/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
limpca 1.4.0  (landing page)
Manon Martin
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/limpca
git_branch: RELEASE_3_21
git_last_commit: 4fbe988
git_last_commit_date: 2025-04-15 13:35:42 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for limpca on kjohnson1

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: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:limpca.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings limpca_1.4.0.tar.gz
StartedAt: 2025-08-02 00:26:12 -0400 (Sat, 02 Aug 2025)
EndedAt: 2025-08-02 00:30:13 -0400 (Sat, 02 Aug 2025)
EllapsedTime: 241.2 seconds
RetCode: 0
Status:   OK  
CheckDir: limpca.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:limpca.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings limpca_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/limpca.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limpca/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘limpca’ version ‘1.4.0’
* 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 ‘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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  data2lmpDataList.Rd: SummarizedExperiment, colData
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 17.291  3.658  13.128
* 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-3.21-bioc/meat/limpca.Rcheck/00check.log’
for details.


Installation output

limpca.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL limpca
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘limpca’ ...
** this is package ‘limpca’ version ‘1.4.0’
** 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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 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.

> # 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 
  9.164   1.026   9.947 

Example timings

limpca.Rcheck/limpca-Ex.timings

nameusersystemelapsed
UCH0.0160.0030.019
data2lmpDataList0.3010.0180.320
lmpBootstrapTests17.291 3.65813.128
lmpContributions1.1420.2111.353
lmpEffectMatrices0.7880.0500.839
lmpEffectPlot1.4480.0471.498
lmpLoading1dPlot3.5910.0743.671
lmpLoading2dPlot2.5600.0352.598
lmpModelMatrix0.0080.0020.010
lmpPcaEffects0.7800.0180.799
lmpScorePlot1.2490.0271.277
lmpScoreScatterPlotM0.9830.0281.012
lmpScreePlot1.9460.1632.112
pcaBySvd0.0240.0030.027
pcaLoading1dPlot0.2710.0100.285
pcaLoading2dPlot1.5560.0131.571
pcaScorePlot0.3960.0070.402
pcaScreePlot0.1230.0040.132
plotDesign3.1490.0473.234
plotLine2.7660.0312.800
plotMeans1.1740.0111.187
plotScatter2.1250.0242.153
plotScatterM0.0680.0060.074
trout0.0010.0010.002