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This page was generated on 2023-06-03 14:38:20 -0400 (Sat, 03 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" 4623
palomino3Windows Server 2022 Datacenterx644.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" 4374
merida1macOS 12.6.4 Montereyx86_644.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" 4332
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

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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1490/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.14.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2023-06-02 14:00:14 -0400 (Fri, 02 Jun 2023)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_17
git_last_commit: 3478dbc
git_last_commit_date: 2023-04-25 11:12:38 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: peakPantheR
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2023-06-03 05:30:36 -0400 (Sat, 03 Jun 2023)
EndedAt: 2023-06-03 06:01:52 -0400 (Sat, 03 Jun 2023)
EllapsedTime: 1876.5 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/peakPantheR.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84257)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.14.0’
* 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 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                               23.966  0.334  30.610
EICs-peakPantheRAnnotation-method                       17.834  0.848  24.002
peakPantheR_parallelAnnotation                          16.316  0.151  21.524
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.585  0.170  20.327
outputAnnotationResult-peakPantheRAnnotation-method     15.339  0.155  19.722
retentionTimeCorrection-peakPantheRAnnotation-method    10.467  0.088  14.087
peakPantheR_singleFileSearch                             5.468  0.072   7.572
* 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 4.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow"
Copyright (C) 2023 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 1.14.0 

> 
> test_check("peakPantheR")
2023-06-03 05:44:06.434 R[64792:370864009] XType: com.apple.fonts is not accessible.
2023-06-03 05:44:06.434 R[64792:370864009] XType: XTFontStaticRegistry is enabled.
2023-06-03 05:44:43.586 R[87193:370914484] XType: com.apple.fonts is not accessible.
2023-06-03 05:44:43.586 R[87193:370914484] XType: XTFontStaticRegistry is enabled.
2023-06-03 05:45:05.765 R[87775:370916250] XType: com.apple.fonts is not accessible.
2023-06-03 05:45:05.765 R[87775:370916250] XType: XTFontStaticRegistry is enabled.
2023-06-03 05:51:15.013 R[99724:370999547] XType: com.apple.fonts is not accessible.
2023-06-03 05:51:15.013 R[99724:370999547] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1438 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/private/tmp/Rtmp7aHt4Q/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/Rtmp7aHt4Q/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/Rtmp7aHt4Q/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/Rtmp7aHt4Q/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 
 886.028    9.161 1548.987

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method17.834 0.84824.002
FIR-peakPantheRAnnotation-method0.3160.0350.439
ROI-peakPantheRAnnotation-method0.3120.0340.441
TIC-peakPantheRAnnotation-method0.2920.0330.414
acquisitionTime-peakPantheRAnnotation-method0.3040.0350.432
annotationDiagnosticPlots-peakPantheRAnnotation-method0.3030.0340.425
annotationParamsDiagnostic-peakPantheRAnnotation-method0.3070.0340.468
annotationTable-peakPantheRAnnotation-method0.3090.0340.471
annotation_diagnostic_multiplot_UI_helper0.2430.0150.347
annotation_fit_summary_UI_helper0.0160.0010.023
annotation_showMethod_UI_helper0.0080.0010.010
annotation_showText_UI_helper0.0010.0010.002
cpdID-peakPantheRAnnotation-method0.3120.0200.433
cpdMetadata-peakPantheRAnnotation-method0.3090.0190.442
cpdName-peakPantheRAnnotation-method0.3060.0210.447
dataPoints-peakPantheRAnnotation-method0.2980.0200.435
filename-peakPantheRAnnotation-method0.2950.0200.427
filepath-peakPantheRAnnotation-method0.3030.0200.449
initialise_annotation_from_files_UI_helper0.0250.0030.040
isAnnotated-peakPantheRAnnotation-method0.3080.0220.439
load_annotation_from_file_UI_helper0.0140.0030.027
nbCompounds-peakPantheRAnnotation-method0.3110.0230.424
nbSamples-peakPantheRAnnotation-method0.3270.0240.445
outputAnnotationDiagnostic-peakPantheRAnnotation-method15.585 0.17020.327
outputAnnotationFeatureMetadata_UI_helper0.0110.0020.016
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0570.0030.075
outputAnnotationResult-peakPantheRAnnotation-method15.339 0.15519.722
outputAnnotationSpectraMetadata_UI_helper0.0130.0020.021
peakFit-peakPantheRAnnotation-method0.3290.0220.445
peakPantheRAnnotation0.3420.0240.461
peakPantheR_ROIStatistics23.966 0.33430.610
peakPantheR_loadAnnotationParamsCSV0.0140.0040.022
peakPantheR_parallelAnnotation16.316 0.15121.524
peakPantheR_plotEICFit0.7950.0081.061
peakPantheR_plotPeakwidth1.2530.0331.883
peakPantheR_singleFileSearch5.4680.0727.572
peakPantheR_start_GUI0.0000.0000.001
peakTables-peakPantheRAnnotation-method0.3120.0210.450
resetAnnotation-peakPantheRAnnotation-method0.3200.0230.454
resetFIR-peakPantheRAnnotation-method0.0110.0010.017
retentionTimeCorrection-peakPantheRAnnotation-method10.467 0.08814.087
spectraMetadata-peakPantheRAnnotation-method0.3190.0200.432
spectraPaths_and_metadata_UI_helper0.0050.0020.010
spectra_metadata_colourScheme_UI_helper0.0120.0020.018
uROI-peakPantheRAnnotation-method0.3140.0210.425
uROIExist-peakPantheRAnnotation-method0.3090.0200.429
useFIR-peakPantheRAnnotation-method0.3070.0200.423
useUROI-peakPantheRAnnotation-method0.3070.0190.417