Multiple platform build/check report for BioC 3.11 - CHECK report for pulsedSilac on tokay2

Package: pulsedSilac

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pulsedSilac.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pulsedSilac_1.2.0.tar.gz

StartedAt: 2020-10-17 07:09:20 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 07:16:03 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 403.8 seconds

RetCode: 0

Status: OK

CheckDir: pulsedSilac.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pulsedSilac.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pulsedSilac_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pulsedSilac.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pulsedSilac/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pulsedSilac' version '1.2.0'
* 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 'pulsedSilac' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pulsedSilac_1.2.0.tar.gz && rm -rf pulsedSilac.buildbin-libdir && mkdir pulsedSilac.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pulsedSilac.buildbin-libdir pulsedSilac_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pulsedSilac_1.2.0.zip && rm pulsedSilac_1.2.0.tar.gz pulsedSilac_1.2.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1370k  100 1370k    0     0  18.5M      0 --:--:-- --:--:-- --:--:-- 20.5M

install for i386

* installing *source* package 'pulsedSilac' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
in method for 'addMisscleavedPeptides' with signature '"SilacProteinExperiment"': no definition for class "SilacProteinExperiment"
in method for 'addMisscleavedPeptides' with signature '"SilacPeptideExperiment"': no definition for class "SilacPeptideExperiment"
in method for 'addMisscleavedPeptides' with signature '"SilacProteomicsExperiment"': no definition for class "SilacProteomicsExperiment"
** help
*** installing help indices
  converting help for package 'pulsedSilac'
    finding HTML links ... done
    SilacPeptideExperiment-class            html  
    finding level-2 HTML links ... done

    SilacPeptideExperiment-constructor      html  
    SilacProteinExperiment-class            html  
    SilacProteinExperiment-constructor      html  
    SilacProteinPeptideExperiment-accessors
                                            html  
    SilacProteomicsExperiment-accessors     html  
    SilacProteomicsExperiment-class         html  
    SilacProteomicsExperiment-constructor   html  
    addMisscleavedPeptides                  html  
    barplotCounts                           html  
    barplotTimeCoverage                     html  
    buildLinkerDf                           html  
    calculateAIC                            html  
    calculateIsotopeFraction                html  
    calculateIsotopeRatio                   html  
    calculateOldIsotopePool                 html  
    compareAIC                              html  
    filterByMissingTimepoints               html  
    mefPE                                   html  
    merge                                   html  
    mergeModelsLists                        html  
    modelTurnover                           html  
    mostStable                              html  
    plotDistributionAssay                   html  
    plotDistributionModel                   html  
    plotIndividualModel                     html  
    recycleLightLysine                      html  
    scatterCompareAssays                    html  
    scatterCompareModels                    html  
    upsetTimeCoverage                       html  
    wormsPE                                 html  
** 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 'pulsedSilac' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pulsedSilac' as pulsedSilac_1.2.0.zip
* DONE (pulsedSilac)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pulsedSilac' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(pulsedSilac)
> 
> test_check("pulsedSilac")
== testthat results  ===========================================================
[ OK: 1018 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  46.14    1.18   48.62


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(pulsedSilac)
> 
> test_check("pulsedSilac")
== testthat results  ===========================================================
[ OK: 1018 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  51.53    0.60   52.12

name	user	system	elapsed
SilacPeptideExperiment-constructor	0.07	0.05	0.12
SilacProteinExperiment-constructor	0.02	0.01	0.03
SilacProteinPeptideExperiment-accessors	0.66	0.11	0.77
SilacProteomicsExperiment-accessors	0.97	0.20	1.17
SilacProteomicsExperiment-constructor	0.06	0.00	0.06
addMisscleavedPeptides	0.77	0.13	0.89
barplotCounts	0.61	0.08	0.69
barplotTimeCoverage	1.11	0.04	1.15
buildLinkerDf	0.01	0.00	0.02
calculateAIC	0.46	0.05	0.50
calculateIsotopeFraction	0.32	0.08	0.42
calculateIsotopeRatio	0.30	0.09	0.39
calculateOldIsotopePool	0.73	0.16	0.89
compareAIC	0.50	0.09	0.60
filterByMissingTimepoints	0.35	0.07	0.40
merge	0.61	0.09	0.71
mergeModelsLists	0.45	0.03	0.48
modelTurnover	0.33	0.08	0.41
mostStable	0.30	0.00	0.29
plotDistributionAssay	0.50	0.06	0.57
plotDistributionModel	0.48	0.13	0.61
plotIndividualModel	0.56	0.06	0.62
scatterCompareAssays	0.85	0.12	0.97
scatterCompareModels	0.48	0.11	0.59
upsetTimeCoverage	0.66	0.07	0.72

name	user	system	elapsed
SilacPeptideExperiment-constructor	0.21	0.00	0.20
SilacProteinExperiment-constructor	0.04	0.00	0.05
SilacProteinPeptideExperiment-accessors	0.77	0.15	0.92
SilacProteomicsExperiment-accessors	1.14	0.08	1.22
SilacProteomicsExperiment-constructor	0.07	0.00	0.08
addMisscleavedPeptides	1.08	0.11	1.19
barplotCounts	0.71	0.09	0.80
barplotTimeCoverage	0.93	0.12	1.06
buildLinkerDf	0	0	0
calculateAIC	0.80	0.13	0.92
calculateIsotopeFraction	0.47	0.11	0.58
calculateIsotopeRatio	0.39	0.11	0.51
calculateOldIsotopePool	1.70	0.19	1.89
compareAIC	0.91	0.12	1.04
filterByMissingTimepoints	0.36	0.14	0.50
merge	0.69	0.06	0.75
mergeModelsLists	0.43	0.08	0.51
modelTurnover	0.44	0.03	0.47
mostStable	0.28	0.02	0.30
plotDistributionAssay	0.88	0.03	0.90
plotDistributionModel	0.90	0.11	1.02
plotIndividualModel	0.93	0.16	1.08
scatterCompareAssays	1.29	0.07	1.37
scatterCompareModels	0.83	0.13	0.95
upsetTimeCoverage	1.11	0.17	1.28

CHECK report for pulsedSilac on tokay2

Summary

Command output

Installation output

Tests output

Example timings