Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-04-13 12:07:08 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for pulsedSilac on tokay2


To the developers/maintainers of the pulsedSilac package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pulsedSilac.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1485/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pulsedSilac 1.8.0  (landing page)
Marc Pagès-Gallego
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/pulsedSilac
git_branch: RELEASE_3_14
git_last_commit: 69698be
git_last_commit_date: 2021-10-26 12:54:42 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: pulsedSilac
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pulsedSilac.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pulsedSilac_1.8.0.tar.gz
StartedAt: 2022-04-13 00:58:47 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:05:19 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 392.3 seconds
RetCode: 0
Status:   OK  
CheckDir: pulsedSilac.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pulsedSilac.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pulsedSilac_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/pulsedSilac.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.8.0'
* 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


Installation output

pulsedSilac.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/pulsedSilac_1.8.0.tar.gz && rm -rf pulsedSilac.buildbin-libdir && mkdir pulsedSilac.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pulsedSilac.buildbin-libdir pulsedSilac_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL pulsedSilac_1.8.0.zip && rm pulsedSilac_1.8.0.tar.gz pulsedSilac_1.8.0.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
 47 1322k   47  624k    0     0   669k      0  0:00:01 --:--:--  0:00:01  669k
100 1322k  100 1322k    0     0   911k      0  0:00:01  0:00:01 --:--:--  911k

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_1.8.0.zip
* DONE (pulsedSilac)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'pulsedSilac' successfully unpacked and MD5 sums checked

Tests output

pulsedSilac.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1018 ]
> 
> proc.time()
   user  system elapsed 
  68.70    1.10   69.85 

pulsedSilac.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1018 ]
> 
> proc.time()
   user  system elapsed 
  73.35    0.62   74.04 

Example timings

pulsedSilac.Rcheck/examples_i386/pulsedSilac-Ex.timings

nameusersystemelapsed
SilacPeptideExperiment-constructor0.230.000.24
SilacProteinExperiment-constructor0.050.000.04
SilacProteinPeptideExperiment-accessors0.690.140.83
SilacProteomicsExperiment-accessors1.400.221.62
SilacProteomicsExperiment-constructor0.160.000.15
addMisscleavedPeptides0.890.221.11
barplotCounts0.700.070.78
barplotTimeCoverage0.550.100.64
buildLinkerDf0.010.000.02
calculateAIC0.500.010.52
calculateIsotopeFraction0.810.040.84
calculateIsotopeRatio0.250.040.30
calculateOldIsotopePool0.940.221.15
compareAIC0.610.080.69
filterByMissingTimepoints0.280.030.31
merge0.660.060.72
mergeModelsLists0.360.080.44
modelTurnover0.340.050.39
mostStable0.240.010.25
plotDistributionAssay0.420.070.48
plotDistributionModel0.420.120.55
plotIndividualModel0.440.080.52
scatterCompareAssays0.610.030.64
scatterCompareModels0.480.030.51
upsetTimeCoverage0.550.100.64

pulsedSilac.Rcheck/examples_x64/pulsedSilac-Ex.timings

nameusersystemelapsed
SilacPeptideExperiment-constructor0.180.000.17
SilacProteinExperiment-constructor0.040.000.05
SilacProteinPeptideExperiment-accessors0.780.090.88
SilacProteomicsExperiment-accessors1.110.081.19
SilacProteomicsExperiment-constructor0.140.000.14
addMisscleavedPeptides1.280.111.39
barplotCounts0.560.060.62
barplotTimeCoverage0.500.050.55
buildLinkerDf000
calculateAIC0.390.110.50
calculateIsotopeFraction0.220.070.30
calculateIsotopeRatio0.270.070.32
calculateOldIsotopePool0.730.090.83
compareAIC0.550.090.64
filterByMissingTimepoints0.220.080.30
merge0.730.080.81
mergeModelsLists0.630.130.75
modelTurnover0.370.090.47
mostStable0.350.000.35
plotDistributionAssay0.500.080.57
plotDistributionModel0.730.110.85
plotIndividualModel0.610.060.67
scatterCompareAssays0.640.060.70
scatterCompareModels0.490.080.56
upsetTimeCoverage0.570.080.66