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This page was generated on 2025-02-06 12:08 -0500 (Thu, 06 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4753
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4501
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4524
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4476
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4407
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 1522/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.20.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 2025)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_20
git_last_commit: 89aef90
git_last_commit_date: 2024-10-29 10:40:22 -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    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for peakPantheR on merida1

To the developers/maintainers of the peakPantheR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/peakPantheR.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: peakPantheR
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings peakPantheR_1.20.0.tar.gz
StartedAt: 2025-02-04 07:51:01 -0500 (Tue, 04 Feb 2025)
EndedAt: 2025-02-04 08:24:09 -0500 (Tue, 04 Feb 2025)
EllapsedTime: 1988.6 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings peakPantheR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/peakPantheR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.20.0’
* 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 ‘peakPantheR’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                          user system elapsed
peakPantheR_ROIStatistics                               27.393  0.453  29.782
EICs-peakPantheRAnnotation-method                       22.589  1.189  24.136
peakPantheR_parallelAnnotation                          18.526  0.126  19.178
outputAnnotationDiagnostic-peakPantheRAnnotation-method 17.723  0.183  18.176
outputAnnotationResult-peakPantheRAnnotation-method     17.405  0.151  17.733
retentionTimeCorrection-peakPantheRAnnotation-method    11.921  0.086  12.675
peakPantheR_singleFileSearch                             6.262  0.074   6.592
peakPantheR_quickEIC                                     5.217  0.050   5.572
* 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: OK


Installation output

peakPantheR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘peakPantheR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (peakPantheR)

Tests output

peakPantheR.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-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(peakPantheR)

This is peakPantheR version 1.20.0 

> 
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1478 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/private/tmp/Rtmpz7oJTm/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/Rtmpz7oJTm/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/Rtmpz7oJTm/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/Rtmpz7oJTm/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
> 
> proc.time()
    user   system  elapsed 
1064.875   13.973 1687.136 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method22.589 1.18924.136
FIR-peakPantheRAnnotation-method0.1060.0060.112
ROI-peakPantheRAnnotation-method0.0900.0050.095
TIC-peakPantheRAnnotation-method0.0900.0060.096
acquisitionTime-peakPantheRAnnotation-method0.0860.0070.093
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0860.0060.092
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0900.0060.095
annotationTable-peakPantheRAnnotation-method0.0880.0040.093
annotation_diagnostic_multiplot_UI_helper0.2340.0070.242
annotation_fit_summary_UI_helper0.0180.0010.020
annotation_showMethod_UI_helper0.0080.0020.009
annotation_showText_UI_helper0.0010.0010.003
cpdID-peakPantheRAnnotation-method0.0880.0060.094
cpdMetadata-peakPantheRAnnotation-method0.0900.0050.096
cpdName-peakPantheRAnnotation-method0.0840.0050.090
dataPoints-peakPantheRAnnotation-method0.0890.0050.094
filename-peakPantheRAnnotation-method0.0860.0050.091
filepath-peakPantheRAnnotation-method0.0890.0060.095
initialise_annotation_from_files_UI_helper0.0310.0030.035
isAnnotated-peakPantheRAnnotation-method0.1030.0060.108
load_annotation_from_file_UI_helper0.0150.0030.017
nbCompounds-peakPantheRAnnotation-method0.0890.0060.095
nbSamples-peakPantheRAnnotation-method0.0780.0060.084
outputAnnotationDiagnostic-peakPantheRAnnotation-method17.723 0.18318.176
outputAnnotationFeatureMetadata_UI_helper0.0120.0010.015
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0600.0020.062
outputAnnotationResult-peakPantheRAnnotation-method17.405 0.15117.733
outputAnnotationSpectraMetadata_UI_helper0.0150.0010.016
peakFit-peakPantheRAnnotation-method0.0940.0060.101
peakPantheRAnnotation0.1070.0070.115
peakPantheR_ROIStatistics27.393 0.45329.782
peakPantheR_loadAnnotationParamsCSV0.0150.0030.018
peakPantheR_parallelAnnotation18.526 0.12619.178
peakPantheR_plotEICFit0.8280.0080.872
peakPantheR_plotPeakwidth1.2930.0201.397
peakPantheR_quickEIC5.2170.0505.572
peakPantheR_singleFileSearch6.2620.0746.592
peakPantheR_start_GUI0.0000.0000.001
peakTables-peakPantheRAnnotation-method0.1020.0070.114
resetAnnotation-peakPantheRAnnotation-method0.1080.0080.117
resetFIR-peakPantheRAnnotation-method0.0130.0020.014
retentionTimeCorrection-peakPantheRAnnotation-method11.921 0.08612.675
spectraMetadata-peakPantheRAnnotation-method0.0930.0060.101
spectraPaths_and_metadata_UI_helper0.0050.0020.007
spectra_metadata_colourScheme_UI_helper0.0120.0020.014
uROI-peakPantheRAnnotation-method0.1000.0070.106
uROIExist-peakPantheRAnnotation-method0.0930.0060.102
useFIR-peakPantheRAnnotation-method0.0870.0060.093
useUROI-peakPantheRAnnotation-method0.0900.0060.100