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This page was generated on 2025-01-02 12:04 -0500 (Thu, 02 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1522/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.20.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_20
git_last_commit: 89aef90
git_last_commit_date: 2024-10-29 10:40:22 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for peakPantheR on nebbiolo2

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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: peakPantheR
Version: 1.20.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings peakPantheR_1.20.0.tar.gz
StartedAt: 2024-12-31 00:46:17 -0500 (Tue, 31 Dec 2024)
EndedAt: 2024-12-31 01:07:37 -0500 (Tue, 31 Dec 2024)
EllapsedTime: 1279.4 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings peakPantheR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/peakPantheR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.20.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether 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                               20.286  0.182  20.474
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.784  0.283  16.095
peakPantheR_parallelAnnotation                          15.212  0.064  15.279
outputAnnotationResult-peakPantheRAnnotation-method     14.877  0.076  14.954
EICs-peakPantheRAnnotation-method                       10.547  0.487  11.050
retentionTimeCorrection-peakPantheRAnnotation-method     9.653  0.049   9.703
peakPantheR_singleFileSearch                             5.116  0.028   5.144
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

peakPantheR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL peakPantheR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 1.20.0 

> 
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1478 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpQqdfBq/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpQqdfBq/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpQqdfBq/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpQqdfBq/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/home/biocbuild/bbs-3.20-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/home/biocbuild/bbs-3.20-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
> 
> proc.time()
   user  system elapsed 
725.964  12.298 985.235

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method10.547 0.48711.050
FIR-peakPantheRAnnotation-method0.0420.0010.043
ROI-peakPantheRAnnotation-method0.0340.0030.038
TIC-peakPantheRAnnotation-method0.0370.0000.037
acquisitionTime-peakPantheRAnnotation-method0.0360.0020.038
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0380.0000.038
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0380.0010.039
annotationTable-peakPantheRAnnotation-method0.0370.0010.038
annotation_diagnostic_multiplot_UI_helper0.1040.0090.112
annotation_fit_summary_UI_helper0.0060.0020.008
annotation_showMethod_UI_helper0.0040.0000.004
annotation_showText_UI_helper000
cpdID-peakPantheRAnnotation-method0.0400.0030.043
cpdMetadata-peakPantheRAnnotation-method0.0400.0020.042
cpdName-peakPantheRAnnotation-method0.0400.0030.043
dataPoints-peakPantheRAnnotation-method0.0420.0010.044
filename-peakPantheRAnnotation-method0.0430.0010.044
filepath-peakPantheRAnnotation-method0.0440.0030.046
initialise_annotation_from_files_UI_helper0.0130.0000.013
isAnnotated-peakPantheRAnnotation-method0.0390.0030.041
load_annotation_from_file_UI_helper0.0070.0000.006
nbCompounds-peakPantheRAnnotation-method0.0380.0050.042
nbSamples-peakPantheRAnnotation-method0.0390.0020.041
outputAnnotationDiagnostic-peakPantheRAnnotation-method15.784 0.28316.095
outputAnnotationFeatureMetadata_UI_helper0.0040.0000.004
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0210.0000.021
outputAnnotationResult-peakPantheRAnnotation-method14.877 0.07614.954
outputAnnotationSpectraMetadata_UI_helper0.0060.0000.005
peakFit-peakPantheRAnnotation-method0.0520.0000.052
peakPantheRAnnotation0.0520.0010.052
peakPantheR_ROIStatistics20.286 0.18220.474
peakPantheR_loadAnnotationParamsCSV0.0050.0000.006
peakPantheR_parallelAnnotation15.212 0.06415.279
peakPantheR_plotEICFit0.2920.0000.292
peakPantheR_plotPeakwidth0.4930.0010.495
peakPantheR_quickEIC4.0710.0254.096
peakPantheR_singleFileSearch5.1160.0285.144
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.0480.0000.048
resetAnnotation-peakPantheRAnnotation-method0.0500.0010.051
resetFIR-peakPantheRAnnotation-method0.0050.0000.005
retentionTimeCorrection-peakPantheRAnnotation-method9.6530.0499.703
spectraMetadata-peakPantheRAnnotation-method0.0380.0010.039
spectraPaths_and_metadata_UI_helper0.0020.0000.002
spectra_metadata_colourScheme_UI_helper0.0040.0000.005
uROI-peakPantheRAnnotation-method0.0390.0020.042
uROIExist-peakPantheRAnnotation-method0.0370.0010.038
useFIR-peakPantheRAnnotation-method0.0380.0000.038
useUROI-peakPantheRAnnotation-method0.0380.0010.038