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This page was generated on 2024-04-17 11:38:03 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1520/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.16.1  (landing page)
Arnaud Wolfer
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_18
git_last_commit: 8a9ba02
git_last_commit_date: 2024-02-26 17:51:10 -0400 (Mon, 26 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.16.1
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_1.16.1.tar.gz
StartedAt: 2024-04-16 06:48:41 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 07:16:46 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 1685.1 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_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/peakPantheR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.16.1’
* 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 ‘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 R 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 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                               26.198  0.475  28.923
EICs-peakPantheRAnnotation-method                       22.217  1.041  26.443
peakPantheR_parallelAnnotation                          18.233  0.166  19.247
outputAnnotationDiagnostic-peakPantheRAnnotation-method 17.318  0.166  17.949
outputAnnotationResult-peakPantheRAnnotation-method     17.334  0.148  18.869
retentionTimeCorrection-peakPantheRAnnotation-method    11.781  0.084  12.409
peakPantheR_singleFileSearch                             6.057  0.086   6.433
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 1.16.1 

> 
> test_check("peakPantheR")
2024-04-16 07:00:44.413 R[7738:2549023575] XType: com.apple.fonts is not accessible.
2024-04-16 07:00:44.414 R[7738:2549023575] XType: XTFontStaticRegistry is enabled.
2024-04-16 07:01:16.339 R[62417:2549170441] XType: com.apple.fonts is not accessible.
2024-04-16 07:01:16.339 R[62417:2549170441] XType: XTFontStaticRegistry is enabled.
2024-04-16 07:01:36.986 R[65859:2549179867] XType: com.apple.fonts is not accessible.
2024-04-16 07:01:36.986 R[65859:2549179867] XType: XTFontStaticRegistry is enabled.
2024-04-16 07:07:14.714 R[14128:2549373729] XType: com.apple.fonts is not accessible.
2024-04-16 07:07:14.714 R[14128:2549373729] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1458 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/private/tmp/RtmpirG4MA/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/RtmpirG4MA/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/RtmpirG4MA/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/RtmpirG4MA/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
> 
> proc.time()
    user   system  elapsed 
 991.067   10.833 1380.490

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method22.217 1.04126.443
FIR-peakPantheRAnnotation-method0.3290.0330.378
ROI-peakPantheRAnnotation-method0.3170.0330.365
TIC-peakPantheRAnnotation-method0.2970.0310.341
acquisitionTime-peakPantheRAnnotation-method0.3100.0340.360
annotationDiagnosticPlots-peakPantheRAnnotation-method0.3120.0330.359
annotationParamsDiagnostic-peakPantheRAnnotation-method0.3140.0340.364
annotationTable-peakPantheRAnnotation-method0.3080.0340.368
annotation_diagnostic_multiplot_UI_helper0.2480.0370.311
annotation_fit_summary_UI_helper0.0190.0050.024
annotation_showMethod_UI_helper0.0090.0020.012
annotation_showText_UI_helper0.0010.0020.002
cpdID-peakPantheRAnnotation-method0.3130.0330.374
cpdMetadata-peakPantheRAnnotation-method0.3390.0320.375
cpdName-peakPantheRAnnotation-method0.2970.0200.322
dataPoints-peakPantheRAnnotation-method0.3000.0190.326
filename-peakPantheRAnnotation-method0.3160.0190.349
filepath-peakPantheRAnnotation-method0.3100.0200.357
initialise_annotation_from_files_UI_helper0.0260.0020.029
isAnnotated-peakPantheRAnnotation-method0.2950.0190.338
load_annotation_from_file_UI_helper0.0140.0030.016
nbCompounds-peakPantheRAnnotation-method0.3120.0200.335
nbSamples-peakPantheRAnnotation-method0.3090.0200.333
outputAnnotationDiagnostic-peakPantheRAnnotation-method17.318 0.16617.949
outputAnnotationFeatureMetadata_UI_helper0.0110.0010.012
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0530.0020.055
outputAnnotationResult-peakPantheRAnnotation-method17.334 0.14818.869
outputAnnotationSpectraMetadata_UI_helper0.0150.0020.023
peakFit-peakPantheRAnnotation-method0.3170.0220.393
peakPantheRAnnotation0.3250.0240.452
peakPantheR_ROIStatistics26.198 0.47528.923
peakPantheR_loadAnnotationParamsCSV0.0140.0030.017
peakPantheR_parallelAnnotation18.233 0.16619.247
peakPantheR_plotEICFit0.7720.0070.829
peakPantheR_plotPeakwidth1.1910.0201.303
peakPantheR_singleFileSearch6.0570.0866.433
peakPantheR_start_GUI0.0000.0000.001
peakTables-peakPantheRAnnotation-method0.3080.0190.338
resetAnnotation-peakPantheRAnnotation-method0.3490.0220.385
resetFIR-peakPantheRAnnotation-method0.0110.0010.013
retentionTimeCorrection-peakPantheRAnnotation-method11.781 0.08412.409
spectraMetadata-peakPantheRAnnotation-method0.3110.0200.346
spectraPaths_and_metadata_UI_helper0.0040.0020.006
spectra_metadata_colourScheme_UI_helper0.0110.0010.013
uROI-peakPantheRAnnotation-method0.3140.0210.347
uROIExist-peakPantheRAnnotation-method0.3130.0200.360
useFIR-peakPantheRAnnotation-method0.3110.0200.364
useUROI-peakPantheRAnnotation-method0.3050.0200.361