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This page was generated on 2021-09-17 15:06:16 -0400 (Fri, 17 Sep 2021).

CHECK results for peakPantheR on tokay2

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
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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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:peakPantheR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings peakPantheR_1.6.1.tar.gz
StartedAt: 2021-09-17 03:22:03 -0400 (Fri, 17 Sep 2021)
EndedAt: 2021-09-17 03:49:03 -0400 (Fri, 17 Sep 2021)
EllapsedTime: 1619.5 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:peakPantheR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings peakPantheR_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/peakPantheR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                         user system elapsed
peakPantheR_ROIStatistics                               14.47   0.36   14.83
outputAnnotationDiagnostic-peakPantheRAnnotation-method 10.71   0.10   11.13
peakPantheR_parallelAnnotation                          10.51   0.08   10.59
outputAnnotationResult-peakPantheRAnnotation-method     10.21   0.01   10.21
EICs-peakPantheRAnnotation-method                        7.44   0.73    8.24
retentionTimeCorrection-peakPantheRAnnotation-method     7.87   0.00    7.87
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                         user system elapsed
peakPantheR_ROIStatistics                               16.48   0.11   16.60
peakPantheR_parallelAnnotation                          13.81   0.08   13.91
outputAnnotationResult-peakPantheRAnnotation-method     12.42   0.04   12.47
outputAnnotationDiagnostic-peakPantheRAnnotation-method 12.33   0.07   12.39
EICs-peakPantheRAnnotation-method                        9.29   0.30    9.58
retentionTimeCorrection-peakPantheRAnnotation-method     8.58   0.03    8.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/peakPantheR_1.6.1.tar.gz && rm -rf peakPantheR.buildbin-libdir && mkdir peakPantheR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=peakPantheR.buildbin-libdir peakPantheR_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL peakPantheR_1.6.1.zip && rm peakPantheR_1.6.1.tar.gz peakPantheR_1.6.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 58 1763k   58 1024k    0     0  1832k      0 --:--:-- --:--:-- --:--:-- 1832k
100 1763k  100 1763k    0     0  2159k      0 --:--:-- --:--:-- --:--:-- 2158k

install for i386

* installing *source* package 'peakPantheR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'peakPantheR'
    finding HTML links ... done
    EICs-peakPantheRAnnotation-method       html  
    FIR-peakPantheRAnnotation-method        html  
    ROI-peakPantheRAnnotation-method        html  
    TIC-peakPantheRAnnotation-method        html  
    acquisitionTime-peakPantheRAnnotation-method
                                            html  
    annotationDiagnosticMultiplot           html  
    annotationDiagnosticPlots-peakPantheRAnnotation-method
                                            html  
    annotationParamsDiagnostic-peakPantheRAnnotation-method
                                            html  
    annotationTable-peakPantheRAnnotation-method
                                            html  
    annotation_diagnostic_multiplot_UI_helper
                                            html  
    annotation_fit_summary_UI_helper        html  
    annotation_showMethod_UI_helper         html  
    annotation_showText_UI_helper           html  
    cpdID-peakPantheRAnnotation-method      html  
    cpdMetadata-peakPantheRAnnotation-method
                                            html  
    cpdName-peakPantheRAnnotation-method    html  
    dataPoints-peakPantheRAnnotation-method
                                            html  
    emgGaussian_guess                       html  
    emgGaussian_minpack.lm                  html  
    emgGaussian_minpack.lm_objectiveFun     html  
    extractSignalRawData                    html  
    filename-peakPantheRAnnotation-method   html  
    filepath-peakPantheRAnnotation-method   html  
    findTargetFeatures                      html  
    fitCurve                                html  
    gaussian_cerf                           html  
    gaussian_erf                            html  
    generateIonChromatogram                 html  
    getAcquisitionDatemzML                  html  
    getTargetFeatureStatistic               html  
    initialise_annotation_from_files_UI_helper
                                            html  
    integrateFIR                            html  
    is.peakPantheR_curveFit                 html  
    isAnnotated-peakPantheRAnnotation-method
                                            html  
    load_annotation_from_file_UI_helper     html  
    nbCompounds-peakPantheRAnnotation-method
                                            html  
    nbSamples-peakPantheRAnnotation-method
                                            html  
    outputAnnotationDiagnostic-peakPantheRAnnotation-method
                                            html  
    outputAnnotationFeatureMetadata_UI_helper
                                            html  
    outputAnnotationParamsCSV-peakPantheRAnnotation-method
                                            html  
    outputAnnotationResult-peakPantheRAnnotation-method
                                            html  
    outputAnnotationSpectraMetadata_UI_helper
                                            html  
    peakFit-peakPantheRAnnotation-method    html  
    peakPantheR                             html  
    peakPantheRAnnotation                   html  
    peakPantheR_ROIStatistics               html  
    peakPantheR_applyRTCorrection           html  
    peakPantheR_loadAnnotationParamsCSV     html  
    peakPantheR_parallelAnnotation          html  
    peakPantheR_plotEICFit                  html  
    peakPantheR_plotPeakwidth               html  
    peakPantheR_singleFileSearch            html  
    peakPantheR_start_GUI                   html  
    peakTables-peakPantheRAnnotation-method
                                            html  
    plotEICDetectedPeakwidth                html  
    plotHistogram                           html  
    predictCurve                            html  
    prepare_advanced_target_parameters      html  
    prepare_basic_target_parameters         html  
    resetAnnotation-peakPantheRAnnotation-method
                                            html  
    resetFIR-peakPantheRAnnotation-method   html  
    retentionTimeCorrection-peakPantheRAnnotation-method
                                            html  
    saveSingleFileMultiEIC                  html  
    skewedGaussian_guess                    html  
    skewedGaussian_minpack.lm               html  
    skewedGaussian_minpack.lm_objectiveFun
                                            html  
    spectraMetadata-peakPantheRAnnotation-method
                                            html  
    spectraPaths_and_metadata_UI_helper     html  
    spectra_metadata_colourScheme_UI_helper
                                            html  
    sub-peakPantheRAnnotation-ANY-ANY-ANY-method
                                            html  
    uROI-peakPantheRAnnotation-method       html  
    uROIExist-peakPantheRAnnotation-method
                                            html  
    useFIR-peakPantheRAnnotation-method     html  
    useUROI-peakPantheRAnnotation-method    html  
*** 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

install for x64

* installing *source* package 'peakPantheR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'peakPantheR' as peakPantheR_1.6.1.zip
* DONE (peakPantheR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'peakPantheR' successfully unpacked and MD5 sums checked

Tests output

peakPantheR.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 1417 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpMdwfe3\notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpMdwfe3\notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (C:\Users\biocbuild\bbs-3.13-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (C:\Users\biocbuild\bbs-3.13-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
> 
> proc.time()
   user  system elapsed 
 468.10    4.01  614.37 

peakPantheR.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 (C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpeegGjW\notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpeegGjW\notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (C:\Users\biocbuild\bbs-3.13-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (C:\Users\biocbuild\bbs-3.13-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
> 
> proc.time()
   user  system elapsed 
 599.64    3.04  748.92 

Example timings

peakPantheR.Rcheck/examples_i386/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method7.440.738.24
FIR-peakPantheRAnnotation-method0.220.020.23
ROI-peakPantheRAnnotation-method0.170.010.19
TIC-peakPantheRAnnotation-method0.160.020.17
acquisitionTime-peakPantheRAnnotation-method0.150.010.17
annotationDiagnosticPlots-peakPantheRAnnotation-method0.140.030.17
annotationParamsDiagnostic-peakPantheRAnnotation-method0.190.020.20
annotationTable-peakPantheRAnnotation-method0.170.000.17
annotation_diagnostic_multiplot_UI_helper0.080.000.08
annotation_fit_summary_UI_helper0.000.020.02
annotation_showMethod_UI_helper000
annotation_showText_UI_helper000
cpdID-peakPantheRAnnotation-method0.150.010.17
cpdMetadata-peakPantheRAnnotation-method0.170.000.17
cpdName-peakPantheRAnnotation-method0.190.000.19
dataPoints-peakPantheRAnnotation-method0.140.030.17
filename-peakPantheRAnnotation-method0.140.020.16
filepath-peakPantheRAnnotation-method0.170.000.17
initialise_annotation_from_files_UI_helper0.020.000.01
isAnnotated-peakPantheRAnnotation-method0.140.010.16
load_annotation_from_file_UI_helper000
nbCompounds-peakPantheRAnnotation-method0.280.000.28
nbSamples-peakPantheRAnnotation-method0.170.000.17
outputAnnotationDiagnostic-peakPantheRAnnotation-method10.71 0.1011.13
outputAnnotationFeatureMetadata_UI_helper000
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.030.000.04
outputAnnotationResult-peakPantheRAnnotation-method10.21 0.0110.21
outputAnnotationSpectraMetadata_UI_helper0.010.000.02
peakFit-peakPantheRAnnotation-method0.140.020.16
peakPantheRAnnotation0.190.000.19
peakPantheR_ROIStatistics14.47 0.3614.83
peakPantheR_loadAnnotationParamsCSV000
peakPantheR_parallelAnnotation10.51 0.0810.59
peakPantheR_plotEICFit0.490.000.49
peakPantheR_plotPeakwidth0.470.000.47
peakPantheR_singleFileSearch3.960.003.96
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.160.010.18
resetAnnotation-peakPantheRAnnotation-method0.200.030.23
resetFIR-peakPantheRAnnotation-method000
retentionTimeCorrection-peakPantheRAnnotation-method7.870.007.87
spectraMetadata-peakPantheRAnnotation-method0.170.020.18
spectraPaths_and_metadata_UI_helper0.020.000.02
spectra_metadata_colourScheme_UI_helper000
uROI-peakPantheRAnnotation-method0.150.010.17
uROIExist-peakPantheRAnnotation-method0.170.000.17
useFIR-peakPantheRAnnotation-method0.150.000.16
useUROI-peakPantheRAnnotation-method0.220.040.25

peakPantheR.Rcheck/examples_x64/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method9.290.309.58
FIR-peakPantheRAnnotation-method0.230.030.27
ROI-peakPantheRAnnotation-method0.240.020.25
TIC-peakPantheRAnnotation-method0.260.000.26
acquisitionTime-peakPantheRAnnotation-method0.200.050.25
annotationDiagnosticPlots-peakPantheRAnnotation-method0.20.00.2
annotationParamsDiagnostic-peakPantheRAnnotation-method0.190.000.19
annotationTable-peakPantheRAnnotation-method0.200.030.23
annotation_diagnostic_multiplot_UI_helper0.130.000.13
annotation_fit_summary_UI_helper000
annotation_showMethod_UI_helper0.010.000.02
annotation_showText_UI_helper000
cpdID-peakPantheRAnnotation-method0.210.010.21
cpdMetadata-peakPantheRAnnotation-method0.180.020.19
cpdName-peakPantheRAnnotation-method0.190.000.19
dataPoints-peakPantheRAnnotation-method0.250.000.25
filename-peakPantheRAnnotation-method0.220.000.22
filepath-peakPantheRAnnotation-method0.170.030.20
initialise_annotation_from_files_UI_helper0.010.000.02
isAnnotated-peakPantheRAnnotation-method0.190.050.23
load_annotation_from_file_UI_helper0.020.000.14
nbCompounds-peakPantheRAnnotation-method0.220.030.25
nbSamples-peakPantheRAnnotation-method0.220.010.23
outputAnnotationDiagnostic-peakPantheRAnnotation-method12.33 0.0712.39
outputAnnotationFeatureMetadata_UI_helper0.010.000.02
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.040.000.03
outputAnnotationResult-peakPantheRAnnotation-method12.42 0.0412.47
outputAnnotationSpectraMetadata_UI_helper000
peakFit-peakPantheRAnnotation-method0.160.020.18
peakPantheRAnnotation0.190.000.18
peakPantheR_ROIStatistics16.48 0.1116.60
peakPantheR_loadAnnotationParamsCSV0.020.000.01
peakPantheR_parallelAnnotation13.81 0.0813.91
peakPantheR_plotEICFit0.390.000.39
peakPantheR_plotPeakwidth0.450.000.45
peakPantheR_singleFileSearch4.390.004.39
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.160.010.18
resetAnnotation-peakPantheRAnnotation-method0.190.000.18
resetFIR-peakPantheRAnnotation-method000
retentionTimeCorrection-peakPantheRAnnotation-method8.580.038.61
spectraMetadata-peakPantheRAnnotation-method0.210.020.24
spectraPaths_and_metadata_UI_helper000
spectra_metadata_colourScheme_UI_helper000
uROI-peakPantheRAnnotation-method0.220.030.25
uROIExist-peakPantheRAnnotation-method0.230.010.25
useFIR-peakPantheRAnnotation-method0.180.000.17
useUROI-peakPantheRAnnotation-method0.180.000.19