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This page was generated on 2021-09-17 15:05:48 -0400 (Fri, 17 Sep 2021).

CHECK results for peakPantheR on nebbiolo1

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/peakPantheR.git to
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raw results

Package 1366/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.6.1  (landing page)
Arnaud Wolfer
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_13
git_last_commit: 3308eac
git_last_commit_date: 2021-06-23 16:02:41 -0400 (Wed, 23 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.6.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings peakPantheR_1.6.1.tar.gz
StartedAt: 2021-09-16 10:57:08 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 11:14:01 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 1013.5 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings peakPantheR_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/peakPantheR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.6.1’
* 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                               17.299  0.172  17.472
peakPantheR_parallelAnnotation                          13.966  0.052  14.020
outputAnnotationDiagnostic-peakPantheRAnnotation-method 13.776  0.085  13.874
outputAnnotationResult-peakPantheRAnnotation-method     12.730  0.072  12.803
retentionTimeCorrection-peakPantheRAnnotation-method     9.403  0.048   9.452
EICs-peakPantheRAnnotation-method                        8.264  0.692   8.967
peakPantheR_singleFileSearch                             5.003  0.036   5.039
* 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:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL peakPantheR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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 1.6.1 

> 
> test_check("peakPantheR")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 1434 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/tmp/RtmpTmHHLi/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/tmp/RtmpTmHHLi/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/home/biocbuild/bbs-3.13-bioc/R/library/peakPantheR/extdata/test_fakemzML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/home/biocbuild/bbs-3.13-bioc/R/library/peakPantheR/extdata/test_fakemzML.mzML)
> 
> proc.time()
   user  system elapsed 
665.800  13.677 819.952 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method8.2640.6928.967
FIR-peakPantheRAnnotation-method0.1680.0120.180
ROI-peakPantheRAnnotation-method0.1410.0240.164
TIC-peakPantheRAnnotation-method0.1570.0120.169
acquisitionTime-peakPantheRAnnotation-method0.1500.0040.154
annotationDiagnosticPlots-peakPantheRAnnotation-method0.1520.0040.156
annotationParamsDiagnostic-peakPantheRAnnotation-method0.1690.0050.175
annotationTable-peakPantheRAnnotation-method0.1460.0080.154
annotation_diagnostic_multiplot_UI_helper0.0750.0040.080
annotation_fit_summary_UI_helper0.0070.0000.007
annotation_showMethod_UI_helper0.0030.0000.004
annotation_showText_UI_helper0.0000.0010.001
cpdID-peakPantheRAnnotation-method0.1730.0020.175
cpdMetadata-peakPantheRAnnotation-method0.1750.0040.180
cpdName-peakPantheRAnnotation-method0.1490.0000.149
dataPoints-peakPantheRAnnotation-method0.1480.0040.151
filename-peakPantheRAnnotation-method0.1630.0000.162
filepath-peakPantheRAnnotation-method0.1590.0000.159
initialise_annotation_from_files_UI_helper0.0130.0000.013
isAnnotated-peakPantheRAnnotation-method0.1570.0000.157
load_annotation_from_file_UI_helper0.010.000.01
nbCompounds-peakPantheRAnnotation-method0.2080.0080.216
nbSamples-peakPantheRAnnotation-method0.1660.0040.170
outputAnnotationDiagnostic-peakPantheRAnnotation-method13.776 0.08513.874
outputAnnotationFeatureMetadata_UI_helper0.0050.0000.005
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0220.0000.022
outputAnnotationResult-peakPantheRAnnotation-method12.730 0.07212.803
outputAnnotationSpectraMetadata_UI_helper0.0060.0000.006
peakFit-peakPantheRAnnotation-method0.2080.0080.215
peakPantheRAnnotation0.2210.0040.225
peakPantheR_ROIStatistics17.299 0.17217.472
peakPantheR_loadAnnotationParamsCSV0.0070.0000.008
peakPantheR_parallelAnnotation13.966 0.05214.020
peakPantheR_plotEICFit0.2650.0000.265
peakPantheR_plotPeakwidth0.3740.0000.373
peakPantheR_singleFileSearch5.0030.0365.039
peakPantheR_start_GUI0.0010.0000.000
peakTables-peakPantheRAnnotation-method0.2080.0000.207
resetAnnotation-peakPantheRAnnotation-method0.2000.0040.204
resetFIR-peakPantheRAnnotation-method0.0050.0000.005
retentionTimeCorrection-peakPantheRAnnotation-method9.4030.0489.452
spectraMetadata-peakPantheRAnnotation-method0.2100.0010.210
spectraPaths_and_metadata_UI_helper0.0030.0000.003
spectra_metadata_colourScheme_UI_helper0.0050.0000.005
uROI-peakPantheRAnnotation-method0.1830.0040.187
uROIExist-peakPantheRAnnotation-method0.1630.0040.167
useFIR-peakPantheRAnnotation-method0.1810.0000.182
useUROI-peakPantheRAnnotation-method0.1650.0160.180