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This page was generated on 2021-11-29 15:06:05 -0500 (Mon, 29 Nov 2021).

CHECK results for peakPantheR on machv2

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? here 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 1391/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.8.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_14
git_last_commit: eb2c999
git_last_commit_date: 2021-10-26 12:54:33 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: peakPantheR
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2021-11-28 19:34:08 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 19:51:44 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 1056.2 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_1.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/peakPantheR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.8.0’
* 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 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                               16.655  0.155  16.827
EICs-peakPantheRAnnotation-method                       12.671  0.496  13.182
peakPantheR_parallelAnnotation                          12.745  0.100  12.862
outputAnnotationDiagnostic-peakPantheRAnnotation-method 12.566  0.121  12.711
outputAnnotationResult-peakPantheRAnnotation-method     11.732  0.091  11.837
retentionTimeCorrection-peakPantheRAnnotation-method     8.198  0.043   8.248
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 1.8.0 

> 
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1434 ]
> 
> proc.time()
   user  system elapsed 
666.713   4.902 871.809 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method12.671 0.49613.182
FIR-peakPantheRAnnotation-method0.2640.0180.283
ROI-peakPantheRAnnotation-method0.3770.0170.394
TIC-peakPantheRAnnotation-method0.2650.0130.278
acquisitionTime-peakPantheRAnnotation-method0.2590.0130.272
annotationDiagnosticPlots-peakPantheRAnnotation-method0.2510.0130.264
annotationParamsDiagnostic-peakPantheRAnnotation-method0.1900.0120.202
annotationTable-peakPantheRAnnotation-method0.2020.0130.214
annotation_diagnostic_multiplot_UI_helper0.7990.0050.804
annotation_fit_summary_UI_helper0.0140.0020.015
annotation_showMethod_UI_helper0.0060.0010.007
annotation_showText_UI_helper0.0010.0010.002
cpdID-peakPantheRAnnotation-method0.2470.0110.258
cpdMetadata-peakPantheRAnnotation-method0.2730.0120.286
cpdName-peakPantheRAnnotation-method0.2540.0110.266
dataPoints-peakPantheRAnnotation-method0.2520.0120.264
filename-peakPantheRAnnotation-method0.2480.0100.258
filepath-peakPantheRAnnotation-method0.2260.0100.235
initialise_annotation_from_files_UI_helper0.0210.0010.023
isAnnotated-peakPantheRAnnotation-method0.2700.0180.288
load_annotation_from_file_UI_helper0.0080.0020.011
nbCompounds-peakPantheRAnnotation-method0.2640.0190.283
nbSamples-peakPantheRAnnotation-method0.2700.0220.292
outputAnnotationDiagnostic-peakPantheRAnnotation-method12.566 0.12112.711
outputAnnotationFeatureMetadata_UI_helper0.0090.0010.009
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0450.0010.046
outputAnnotationResult-peakPantheRAnnotation-method11.732 0.09111.837
outputAnnotationSpectraMetadata_UI_helper0.0120.0020.013
peakFit-peakPantheRAnnotation-method0.2640.0140.278
peakPantheRAnnotation0.2550.0140.269
peakPantheR_ROIStatistics16.655 0.15516.827
peakPantheR_loadAnnotationParamsCSV0.0080.0020.009
peakPantheR_parallelAnnotation12.745 0.10012.862
peakPantheR_plotEICFit0.5190.0050.525
peakPantheR_plotPeakwidth0.6340.0140.651
peakPantheR_singleFileSearch4.3940.0524.455
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.2330.0100.243
resetAnnotation-peakPantheRAnnotation-method0.2240.0100.233
resetFIR-peakPantheRAnnotation-method0.0080.0010.009
retentionTimeCorrection-peakPantheRAnnotation-method8.1980.0438.248
spectraMetadata-peakPantheRAnnotation-method0.2620.0100.272
spectraPaths_and_metadata_UI_helper0.0040.0010.005
spectra_metadata_colourScheme_UI_helper0.0100.0010.011
uROI-peakPantheRAnnotation-method0.2580.0110.269
uROIExist-peakPantheRAnnotation-method0.2890.0120.300
useFIR-peakPantheRAnnotation-method0.2810.0120.292
useUROI-peakPantheRAnnotation-method0.250.010.26