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CHECK report for Autotuner on tokay1

This page was generated on 2020-08-13 11:45:45 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Autotuner PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 97/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Autotuner 1.3.0
Craig McLean
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/Autotuner
Branch: master
Last Commit: cd8f7af
Last Changed Date: 2020-05-07 22:13:18 -0400 (Thu, 07 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Autotuner
Version: 1.3.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Autotuner.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Autotuner_1.3.0.tar.gz
StartedAt: 2020-08-13 05:56:01 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 06:02:38 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 397.0 seconds
RetCode: 0
Status:  OK  
CheckDir: Autotuner.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Autotuner.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Autotuner_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Autotuner.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Autotuner/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Autotuner' version '1.3.0'
* 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 'Autotuner' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
createAutotuner 6.64   0.81   22.38
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
createAutotuner 10.18   0.66   11.97
* 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

Autotuner.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/Autotuner_1.3.0.tar.gz && rm -rf Autotuner.buildbin-libdir && mkdir Autotuner.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Autotuner.buildbin-libdir Autotuner_1.3.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Autotuner_1.3.0.zip && rm Autotuner_1.3.0.tar.gz Autotuner_1.3.0.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
100 3761k  100 3761k    0     0  42.9M      0 --:--:-- --:--:-- --:--:-- 44.8M

install for i386

* installing *source* package 'Autotuner' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Autotuner'
    finding HTML links ... done
    Autotuner-class                         html  
    EICparams                               html  
    TIC_params                              html  
    ThresholdingAlgo                        html  
    checkBounds                             html  
    checkEICPeaks                           html  
    createAutotuner                         html  
    dissectScans                            html  
    eicParamsEsts                           html  
    estimatePPM                             html  
    estimateSNThresh                        html  
    extract_peaks                           html  
    filterPeaksfromNoise                    html  
    filterPpmError                          html  
    findPeakWidth                           html  
    findTruePeaks                           html  
    getAutoFactorCol                        html  
    getAutoFile_col                         html  
    getAutoFile_paths                       html  
    getAutoIntensity                        html  
    getAutoMetadata                         html  
    getAutoPeak_difference                  html  
    getAutoPeak_table                       html  
    getAutoPeaks                            html  
    getAutoTime                             html  
    initialize-Autotuner-method             html  
    isolatePeaks                            html  
    mzDb                                    html  
    observedPeak                            html  
    peak_time_difference                    html  
    peakwidth_est                           html  
    peakwidth_table                         html  
    plot_peaks                              html  
    plot_signals                            html  
    returnParams                            html  
    setAutoFactorCol                        html  
    setAutoFile_col                         html  
    setAutoFile_paths                       html  
    setAutoIntensity                        html  
    setAutoMetadata                         html  
    setAutoPeak_difference                  html  
    setAutoPeak_table                       html  
    setAutoPeaks                            html  
    setAutoTime                             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 'Autotuner' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Autotuner' as Autotuner_1.3.0.zip
* DONE (Autotuner)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Autotuner' successfully unpacked and MD5 sums checked

Tests output

Autotuner.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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)
> 
> 
> test_check("Autotuner")
Loading required package: Autotuner
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.15.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws

     ____________________________________________________________
    / __  / / / /__  __/ _   /__  __/ / / /\     / / ____/ __   / 
   / / / / / / /  / / / / / /  / / / / / /  \   / / /___/ /_/  /  
  / /_/ / / / /  / / / / / /  / / / / / / /\ \ / / ____/  _   \ 
 / __  / /_/ /  / / / /_/ /  / / / /_/ / /  \   /  /__/  / /  /
/_/ /_/_____/  /_/ /_____/  /_/ /_____/_/    \ /_____/__/ /__/   v.1.3.0
https://github.com/crmclean/autotuner

== testthat results  ===========================================================
[ OK: 69 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  51.82    2.42   54.86 

Autotuner.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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)
> 
> 
> test_check("Autotuner")
Loading required package: Autotuner
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.15.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws

     ____________________________________________________________
    / __  / / / /__  __/ _   /__  __/ / / /\     / / ____/ __   / 
   / / / / / / /  / / / / / /  / / / / / /  \   / / /___/ /_/  /  
  / /_/ / / / /  / / / / / /  / / / / / / /\ \ / / ____/  _   \ 
 / __  / /_/ /  / / / /_/ /  / / / /_/ / /  \   /  /__/  / /  /
/_/ /_/_____/  /_/ /_____/  /_/ /_____/_/    \ /_____/__/ /__/   v.1.3.0
https://github.com/crmclean/autotuner

== testthat results  ===========================================================
[ OK: 69 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  95.00    2.67   97.62 

Example timings

Autotuner.Rcheck/examples_i386/Autotuner-Ex.timings

nameusersystemelapsed
ThresholdingAlgo0.100.000.09
createAutotuner 6.64 0.8122.38
getAutoFactorCol000
getAutoFile_col0.010.000.01
getAutoFile_paths000
getAutoIntensity000
getAutoMetadata0.010.000.01
getAutoPeak_difference000
getAutoPeak_table0.020.000.02
getAutoPeaks0.000.010.01
getAutoTime000
isolatePeaks0.580.020.82
plot_peaks0.010.000.01
plot_signals0.160.000.16
returnParams0.010.000.01
setAutoFactorCol000
setAutoFile_col000
setAutoFile_paths000
setAutoIntensity000
setAutoMetadata0.010.000.02
setAutoPeak_difference000
setAutoPeak_table0.020.000.01
setAutoPeaks0.000.000.09
setAutoTime000

Autotuner.Rcheck/examples_x64/Autotuner-Ex.timings

nameusersystemelapsed
ThresholdingAlgo0.130.000.12
createAutotuner10.18 0.6611.97
getAutoFactorCol000
getAutoFile_col0.020.000.01
getAutoFile_paths0.010.000.02
getAutoIntensity000
getAutoMetadata0.020.000.02
getAutoPeak_difference000
getAutoPeak_table0.010.000.01
getAutoPeaks0.020.000.02
getAutoTime000
isolatePeaks0.940.050.98
plot_peaks0.010.000.02
plot_signals0.260.000.27
returnParams000
setAutoFactorCol0.020.000.01
setAutoFile_col000
setAutoFile_paths0.010.000.02
setAutoIntensity000
setAutoMetadata000
setAutoPeak_difference0.020.000.02
setAutoPeak_table000
setAutoPeaks0.010.000.02
setAutoTime000