Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:05:32 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 nebbiolo2


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: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
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 20.04.4 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings peakPantheR_1.8.0.tar.gz
StartedAt: 2022-01-20 08:51:28 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 09:06:37 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 909.2 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings peakPantheR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/peakPantheR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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                               17.519  0.276  17.795
peakPantheR_parallelAnnotation                          13.698  0.956  14.654
outputAnnotationResult-peakPantheRAnnotation-method     12.141  0.140  12.281
outputAnnotationDiagnostic-peakPantheRAnnotation-method 12.090  0.125  12.226
EICs-peakPantheRAnnotation-method                        7.905  0.252   8.170
retentionTimeCorrection-peakPantheRAnnotation-method     7.926  0.064   7.990
* 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:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL peakPantheR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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 
633.605  11.610 774.356 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method7.9050.2528.170
FIR-peakPantheRAnnotation-method0.1540.0190.173
ROI-peakPantheRAnnotation-method0.1390.0070.147
TIC-peakPantheRAnnotation-method0.1470.0040.151
acquisitionTime-peakPantheRAnnotation-method0.1470.0070.154
annotationDiagnosticPlots-peakPantheRAnnotation-method0.1650.0000.164
annotationParamsDiagnostic-peakPantheRAnnotation-method0.1530.0000.154
annotationTable-peakPantheRAnnotation-method0.1360.0030.140
annotation_diagnostic_multiplot_UI_helper0.0710.0000.072
annotation_fit_summary_UI_helper0.0060.0000.006
annotation_showMethod_UI_helper0.0030.0000.003
annotation_showText_UI_helper0.0010.0000.000
cpdID-peakPantheRAnnotation-method0.1220.0040.125
cpdMetadata-peakPantheRAnnotation-method0.1960.0030.199
cpdName-peakPantheRAnnotation-method0.1220.0000.122
dataPoints-peakPantheRAnnotation-method0.1200.0000.121
filename-peakPantheRAnnotation-method0.1170.0000.117
filepath-peakPantheRAnnotation-method0.1140.0030.118
initialise_annotation_from_files_UI_helper0.0110.0000.012
isAnnotated-peakPantheRAnnotation-method0.1200.0000.121
load_annotation_from_file_UI_helper0.0050.0000.006
nbCompounds-peakPantheRAnnotation-method0.7810.0070.788
nbSamples-peakPantheRAnnotation-method0.1340.0030.138
outputAnnotationDiagnostic-peakPantheRAnnotation-method12.090 0.12512.226
outputAnnotationFeatureMetadata_UI_helper0.0050.0000.004
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0220.0000.021
outputAnnotationResult-peakPantheRAnnotation-method12.141 0.14012.281
outputAnnotationSpectraMetadata_UI_helper0.0050.0000.005
peakFit-peakPantheRAnnotation-method0.1720.0000.173
peakPantheRAnnotation0.1810.0000.181
peakPantheR_ROIStatistics17.519 0.27617.795
peakPantheR_loadAnnotationParamsCSV0.0070.0000.006
peakPantheR_parallelAnnotation13.698 0.95614.654
peakPantheR_plotEICFit0.2420.0040.246
peakPantheR_plotPeakwidth0.3610.0400.401
peakPantheR_singleFileSearch4.0710.0804.151
peakPantheR_start_GUI0.0000.0000.001
peakTables-peakPantheRAnnotation-method0.1560.0160.172
resetAnnotation-peakPantheRAnnotation-method0.1610.0000.162
resetFIR-peakPantheRAnnotation-method0.0040.0000.004
retentionTimeCorrection-peakPantheRAnnotation-method7.9260.0647.990
spectraMetadata-peakPantheRAnnotation-method0.1500.0080.158
spectraPaths_and_metadata_UI_helper0.0020.0000.002
spectra_metadata_colourScheme_UI_helper0.0040.0000.004
uROI-peakPantheRAnnotation-method0.1570.0000.157
uROIExist-peakPantheRAnnotation-method0.1720.0000.172
useFIR-peakPantheRAnnotation-method0.1630.0000.163
useUROI-peakPantheRAnnotation-method0.1560.0000.156