Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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: 2024-06-12 14:00 -0400 (Wed, 12 Jun 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


CHECK results for peakPantheR on nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings peakPantheR_1.18.0.tar.gz
StartedAt: 2024-06-13 02:10:00 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 02:33:21 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 1401.2 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings peakPantheR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/peakPantheR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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                               20.393  0.320  20.718
peakPantheR_parallelAnnotation                          16.074  0.180  16.256
outputAnnotationResult-peakPantheRAnnotation-method     14.666  0.200  14.866
outputAnnotationDiagnostic-peakPantheRAnnotation-method 14.512  0.308  14.844
EICs-peakPantheRAnnotation-method                       12.009  0.704  12.726
retentionTimeCorrection-peakPantheRAnnotation-method    10.349  0.080  10.429
peakPantheR_singleFileSearch                             5.572  0.064   5.636
* 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-3.19-bioc/R/bin/R CMD INSTALL peakPantheR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 1.18.0 

> 
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1478 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/tmp/RtmpBp7HC1/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/tmp/RtmpBp7HC1/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/tmp/RtmpBp7HC1/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/tmp/RtmpBp7HC1/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/home/biocbuild/bbs-3.19-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/home/biocbuild/bbs-3.19-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
> 
> proc.time()
    user   system  elapsed 
 798.026   21.435 1092.369 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method12.009 0.70412.726
FIR-peakPantheRAnnotation-method0.0600.0040.064
ROI-peakPantheRAnnotation-method0.0490.0000.050
TIC-peakPantheRAnnotation-method0.0400.0040.043
acquisitionTime-peakPantheRAnnotation-method0.0440.0000.043
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0440.0030.047
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0470.0040.051
annotationTable-peakPantheRAnnotation-method0.0420.0070.051
annotation_diagnostic_multiplot_UI_helper0.1090.0200.130
annotation_fit_summary_UI_helper0.0050.0040.008
annotation_showMethod_UI_helper0.0000.0030.004
annotation_showText_UI_helper0.0010.0000.000
cpdID-peakPantheRAnnotation-method0.0460.0040.050
cpdMetadata-peakPantheRAnnotation-method0.0470.0000.048
cpdName-peakPantheRAnnotation-method0.0370.0080.044
dataPoints-peakPantheRAnnotation-method0.0450.0080.053
filename-peakPantheRAnnotation-method0.0400.0070.046
filepath-peakPantheRAnnotation-method0.0690.0000.068
initialise_annotation_from_files_UI_helper0.0130.0000.013
isAnnotated-peakPantheRAnnotation-method0.0360.0030.040
load_annotation_from_file_UI_helper0.0060.0000.006
nbCompounds-peakPantheRAnnotation-method0.0370.0030.041
nbSamples-peakPantheRAnnotation-method0.0400.0000.041
outputAnnotationDiagnostic-peakPantheRAnnotation-method14.512 0.30814.844
outputAnnotationFeatureMetadata_UI_helper0.0050.0000.005
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0210.0000.021
outputAnnotationResult-peakPantheRAnnotation-method14.666 0.20014.866
outputAnnotationSpectraMetadata_UI_helper0.0020.0040.005
peakFit-peakPantheRAnnotation-method0.0470.0000.047
peakPantheRAnnotation0.0510.0040.055
peakPantheR_ROIStatistics20.393 0.32020.718
peakPantheR_loadAnnotationParamsCSV0.0060.0000.007
peakPantheR_parallelAnnotation16.074 0.18016.256
peakPantheR_plotEICFit0.2870.0000.288
peakPantheR_plotPeakwidth0.4990.0040.503
peakPantheR_quickEIC4.2500.0244.275
peakPantheR_singleFileSearch5.5720.0645.636
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.0450.0010.046
resetAnnotation-peakPantheRAnnotation-method0.0510.0000.051
resetFIR-peakPantheRAnnotation-method0.0040.0000.004
retentionTimeCorrection-peakPantheRAnnotation-method10.349 0.08010.429
spectraMetadata-peakPantheRAnnotation-method0.0520.0040.056
spectraPaths_and_metadata_UI_helper0.0030.0000.003
spectra_metadata_colourScheme_UI_helper0.0050.0000.005
uROI-peakPantheRAnnotation-method0.0570.0000.057
uROIExist-peakPantheRAnnotation-method0.0540.0000.054
useFIR-peakPantheRAnnotation-method0.0450.0040.049
useUROI-peakPantheRAnnotation-method0.0550.0000.055