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This page was generated on 2024-05-04 11:38:16 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1536/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.18.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_19
git_last_commit: 80a6cae
git_last_commit_date: 2024-04-30 11:17:40 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for peakPantheR on palomino3


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: 1.18.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:peakPantheR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings peakPantheR_1.18.0.tar.gz
StartedAt: 2024-05-04 06:31:35 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 06:54:14 -0400 (Sat, 04 May 2024)
EllapsedTime: 1358.9 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:peakPantheR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings peakPantheR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/peakPantheR.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'peakPantheR/DESCRIPTION' ... OK
* this is package 'peakPantheR' version '1.18.0'
* 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 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 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                               23.26   0.32   23.59
peakPantheR_parallelAnnotation                          17.01   0.14   17.16
outputAnnotationResult-peakPantheRAnnotation-method     15.73   0.09   15.82
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.31   0.09   15.65
EICs-peakPantheRAnnotation-method                       11.15   0.64   12.21
retentionTimeCorrection-peakPantheRAnnotation-method    10.85   0.08   10.92
peakPantheR_singleFileSearch                             5.53   0.06    5.60
* 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 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:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL peakPantheR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 1.18.0 

> 
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1478 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpSgcbyu\notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpSgcbyu\notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpSgcbyu\notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpSgcbyu\notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (F:\biocbuild\bbs-3.19-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (F:\biocbuild\bbs-3.19-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
> 
> proc.time()
   user  system elapsed 
 836.06    9.04 1153.96 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method11.15 0.6412.21
FIR-peakPantheRAnnotation-method0.040.010.06
ROI-peakPantheRAnnotation-method0.050.000.04
TIC-peakPantheRAnnotation-method0.030.020.05
acquisitionTime-peakPantheRAnnotation-method0.050.000.04
annotationDiagnosticPlots-peakPantheRAnnotation-method0.060.000.07
annotationParamsDiagnostic-peakPantheRAnnotation-method0.030.020.04
annotationTable-peakPantheRAnnotation-method0.050.010.07
annotation_diagnostic_multiplot_UI_helper0.090.050.14
annotation_fit_summary_UI_helper000
annotation_showMethod_UI_helper0.000.010.01
annotation_showText_UI_helper000
cpdID-peakPantheRAnnotation-method0.040.020.05
cpdMetadata-peakPantheRAnnotation-method0.060.000.07
cpdName-peakPantheRAnnotation-method0.070.000.06
dataPoints-peakPantheRAnnotation-method0.040.010.06
filename-peakPantheRAnnotation-method0.10.00.1
filepath-peakPantheRAnnotation-method0.060.020.07
initialise_annotation_from_files_UI_helper0.010.000.03
isAnnotated-peakPantheRAnnotation-method0.060.000.06
load_annotation_from_file_UI_helper0.020.000.03
nbCompounds-peakPantheRAnnotation-method0.090.020.11
nbSamples-peakPantheRAnnotation-method0.10.00.1
outputAnnotationDiagnostic-peakPantheRAnnotation-method15.31 0.0915.65
outputAnnotationFeatureMetadata_UI_helper000
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.030.000.04
outputAnnotationResult-peakPantheRAnnotation-method15.73 0.0915.82
outputAnnotationSpectraMetadata_UI_helper0.040.000.03
peakFit-peakPantheRAnnotation-method0.060.000.07
peakPantheRAnnotation0.060.000.06
peakPantheR_ROIStatistics23.26 0.3223.59
peakPantheR_loadAnnotationParamsCSV0.020.000.03
peakPantheR_parallelAnnotation17.01 0.1417.16
peakPantheR_plotEICFit0.530.000.53
peakPantheR_plotPeakwidth0.720.010.73
peakPantheR_quickEIC4.560.104.65
peakPantheR_singleFileSearch5.530.065.60
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.060.000.07
resetAnnotation-peakPantheRAnnotation-method0.080.010.09
resetFIR-peakPantheRAnnotation-method0.010.000.02
retentionTimeCorrection-peakPantheRAnnotation-method10.85 0.0810.92
spectraMetadata-peakPantheRAnnotation-method0.070.020.08
spectraPaths_and_metadata_UI_helper0.000.010.02
spectra_metadata_colourScheme_UI_helper000
uROI-peakPantheRAnnotation-method0.10.00.1
uROIExist-peakPantheRAnnotation-method0.070.000.07
useFIR-peakPantheRAnnotation-method0.10.00.1
useUROI-peakPantheRAnnotation-method0.080.020.10