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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1536/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.18.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_19
git_last_commit: 80a6cae
git_last_commit_date: 2024-04-30 11:17:40 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped


CHECK results for peakPantheR on lconway

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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-06-09 22:09:59 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 22:31:19 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 1280.7 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/peakPantheR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.18.0’
* 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                               20.879  0.211  21.164
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.477  0.151  15.703
peakPantheR_parallelAnnotation                          15.143  0.110  15.322
outputAnnotationResult-peakPantheRAnnotation-method     14.922  0.248  15.446
EICs-peakPantheRAnnotation-method                       12.640  0.669  13.375
retentionTimeCorrection-peakPantheRAnnotation-method     9.997  0.057  10.073
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 1.18.0 

> 
> test_check("peakPantheR")
2024-06-09 22:18:23.823 R[10757:34220378] XType: com.apple.fonts is not accessible.
2024-06-09 22:18:23.823 R[10757:34220378] XType: XTFontStaticRegistry is enabled.
2024-06-09 22:18:39.246 R[41621:34396323] XType: com.apple.fonts is not accessible.
2024-06-09 22:18:39.246 R[41621:34396323] XType: XTFontStaticRegistry is enabled.
2024-06-09 22:18:49.070 R[42192:34397875] XType: com.apple.fonts is not accessible.
2024-06-09 22:18:49.070 R[42192:34397875] XType: XTFontStaticRegistry is enabled.
2024-06-09 22:22:52.028 R[65190:34443656] XType: com.apple.fonts is not accessible.
2024-06-09 22:22:52.029 R[65190:34443656] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1478 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/private/tmp/RtmphCsslG/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/RtmphCsslG/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/RtmphCsslG/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/RtmphCsslG/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 
 791.036    7.072 1086.942 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method12.640 0.66913.375
FIR-peakPantheRAnnotation-method0.0850.0040.089
ROI-peakPantheRAnnotation-method0.0750.0050.081
TIC-peakPantheRAnnotation-method0.0650.0050.070
acquisitionTime-peakPantheRAnnotation-method0.0800.0070.087
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0720.0050.077
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0730.0060.079
annotationTable-peakPantheRAnnotation-method0.0650.0050.070
annotation_diagnostic_multiplot_UI_helper0.1310.0160.147
annotation_fit_summary_UI_helper0.0100.0010.011
annotation_showMethod_UI_helper0.0040.0010.005
annotation_showText_UI_helper0.0000.0010.001
cpdID-peakPantheRAnnotation-method0.0600.0060.067
cpdMetadata-peakPantheRAnnotation-method0.0630.0050.068
cpdName-peakPantheRAnnotation-method0.0580.0040.063
dataPoints-peakPantheRAnnotation-method0.0720.0060.077
filename-peakPantheRAnnotation-method0.0650.0060.071
filepath-peakPantheRAnnotation-method0.1020.0070.108
initialise_annotation_from_files_UI_helper0.0140.0010.015
isAnnotated-peakPantheRAnnotation-method0.0700.0040.074
load_annotation_from_file_UI_helper0.0070.0010.007
nbCompounds-peakPantheRAnnotation-method0.0750.0040.079
nbSamples-peakPantheRAnnotation-method0.0740.0040.079
outputAnnotationDiagnostic-peakPantheRAnnotation-method15.477 0.15115.703
outputAnnotationFeatureMetadata_UI_helper0.0080.0000.008
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0300.0010.030
outputAnnotationResult-peakPantheRAnnotation-method14.922 0.24815.446
outputAnnotationSpectraMetadata_UI_helper0.0060.0010.007
peakFit-peakPantheRAnnotation-method0.0710.0040.075
peakPantheRAnnotation0.0740.0050.079
peakPantheR_ROIStatistics20.879 0.21121.164
peakPantheR_loadAnnotationParamsCSV0.0090.0020.011
peakPantheR_parallelAnnotation15.143 0.11015.322
peakPantheR_plotEICFit0.2900.0050.296
peakPantheR_plotPeakwidth0.5530.0100.565
peakPantheR_quickEIC4.2200.0484.274
peakPantheR_singleFileSearch4.9270.0404.975
peakPantheR_start_GUI0.0010.0010.001
peakTables-peakPantheRAnnotation-method0.0540.0030.057
resetAnnotation-peakPantheRAnnotation-method0.0790.0050.084
resetFIR-peakPantheRAnnotation-method0.0070.0010.008
retentionTimeCorrection-peakPantheRAnnotation-method 9.997 0.05710.073
spectraMetadata-peakPantheRAnnotation-method0.0680.0040.073
spectraPaths_and_metadata_UI_helper0.0020.0010.003
spectra_metadata_colourScheme_UI_helper0.0040.0010.004
uROI-peakPantheRAnnotation-method0.0520.0030.055
uROIExist-peakPantheRAnnotation-method0.0530.0030.056
useFIR-peakPantheRAnnotation-method0.0540.0040.058
useUROI-peakPantheRAnnotation-method0.0700.0050.075