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This page was generated on 2023-04-12 11:06:19 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 lconway


To the developers/maintainers of the peakPantheR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1457/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.12.2  (landing page)
Arnaud Wolfer
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_16
git_last_commit: 8547bbd
git_last_commit_date: 2022-12-11 18:05:30 -0400 (Sun, 11 Dec 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: peakPantheR
Version: 1.12.2
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_1.12.2.tar.gz
StartedAt: 2023-04-10 21:48:12 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:02:21 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 849.5 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_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/peakPantheR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.12.2’
* 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 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                               15.388  0.153  15.579
peakPantheR_parallelAnnotation                          11.469  0.100  11.586
outputAnnotationResult-peakPantheRAnnotation-method     10.950  0.101  11.099
outputAnnotationDiagnostic-peakPantheRAnnotation-method 10.917  0.093  11.072
EICs-peakPantheRAnnotation-method                        7.268  0.326   7.630
retentionTimeCorrection-peakPantheRAnnotation-method     7.519  0.055   7.592
* 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/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 1.12.2 

> 
> test_check("peakPantheR")
2023-04-10 21:54:20.538 R[51274:1014715106] XType: com.apple.fonts is not accessible.
2023-04-10 21:54:20.538 R[51274:1014715106] XType: XTFontStaticRegistry is enabled.
2023-04-10 21:54:32.928 R[72252:1014779953] XType: com.apple.fonts is not accessible.
2023-04-10 21:54:32.928 R[72252:1014779953] XType: XTFontStaticRegistry is enabled.
2023-04-10 21:54:40.787 R[73319:1014874092] XType: com.apple.fonts is not accessible.
2023-04-10 21:54:40.787 R[73319:1014874092] XType: XTFontStaticRegistry is enabled.
2023-04-10 21:57:24.411 R[85110:1014909474] XType: com.apple.fonts is not accessible.
2023-04-10 21:57:24.411 R[85110:1014909474] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1438 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1438 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/private/tmp/Rtmp8Un393/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/Rtmp8Un393/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/Rtmp8Un393/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/Rtmp8Un393/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.2/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.2/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
> 
> proc.time()
   user  system elapsed 
565.371   4.947 704.316

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method7.2680.3267.630
FIR-peakPantheRAnnotation-method0.1730.0140.187
ROI-peakPantheRAnnotation-method0.7800.0170.801
TIC-peakPantheRAnnotation-method0.1700.0090.180
acquisitionTime-peakPantheRAnnotation-method0.1630.0150.186
annotationDiagnosticPlots-peakPantheRAnnotation-method0.1740.0110.185
annotationParamsDiagnostic-peakPantheRAnnotation-method0.1780.0110.189
annotationTable-peakPantheRAnnotation-method0.2010.0130.216
annotation_diagnostic_multiplot_UI_helper0.0960.0040.101
annotation_fit_summary_UI_helper0.0080.0010.008
annotation_showMethod_UI_helper0.0030.0000.004
annotation_showText_UI_helper0.0000.0000.001
cpdID-peakPantheRAnnotation-method0.1890.0110.200
cpdMetadata-peakPantheRAnnotation-method0.1990.0150.218
cpdName-peakPantheRAnnotation-method0.2040.0180.227
dataPoints-peakPantheRAnnotation-method0.2050.0140.220
filename-peakPantheRAnnotation-method0.1740.0100.185
filepath-peakPantheRAnnotation-method0.1990.0100.238
initialise_annotation_from_files_UI_helper0.0130.0010.014
isAnnotated-peakPantheRAnnotation-method0.1850.0120.197
load_annotation_from_file_UI_helper0.0050.0010.005
nbCompounds-peakPantheRAnnotation-method0.1910.0100.201
nbSamples-peakPantheRAnnotation-method0.1610.0090.169
outputAnnotationDiagnostic-peakPantheRAnnotation-method10.917 0.09311.072
outputAnnotationFeatureMetadata_UI_helper0.0040.0010.004
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0210.0010.022
outputAnnotationResult-peakPantheRAnnotation-method10.950 0.10111.099
outputAnnotationSpectraMetadata_UI_helper0.0060.0020.008
peakFit-peakPantheRAnnotation-method0.1830.0120.197
peakPantheRAnnotation0.1900.0160.211
peakPantheR_ROIStatistics15.388 0.15315.579
peakPantheR_loadAnnotationParamsCSV0.0070.0010.008
peakPantheR_parallelAnnotation11.469 0.10011.586
peakPantheR_plotEICFit0.2700.0030.274
peakPantheR_plotPeakwidth0.5000.0170.521
peakPantheR_singleFileSearch3.8650.0443.915
peakPantheR_start_GUI0.0000.0000.001
peakTables-peakPantheRAnnotation-method0.2230.0120.237
resetAnnotation-peakPantheRAnnotation-method0.2070.0130.222
resetFIR-peakPantheRAnnotation-method0.0040.0010.004
retentionTimeCorrection-peakPantheRAnnotation-method7.5190.0557.592
spectraMetadata-peakPantheRAnnotation-method0.1800.0090.189
spectraPaths_and_metadata_UI_helper0.0020.0010.003
spectra_metadata_colourScheme_UI_helper0.0040.0000.005
uROI-peakPantheRAnnotation-method0.2220.0120.236
uROIExist-peakPantheRAnnotation-method0.2140.0120.226
useFIR-peakPantheRAnnotation-method0.2110.0120.224
useUROI-peakPantheRAnnotation-method0.1890.0110.199