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CHECK report for Autotuner on merida1

This page was generated on 2020-10-29 12:36:12 -0400 (Thu, 29 Oct 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 103/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Autotuner 1.4.0
Craig McLean
Snapshot Date: 2020-10-28 14:42:40 -0400 (Wed, 28 Oct 2020)
URL: https://git.bioconductor.org/packages/Autotuner
Branch: RELEASE_3_12
Last Commit: 9d402d7
Last Changed Date: 2020-10-27 11:47:39 -0400 (Tue, 27 Oct 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: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Autotuner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Autotuner_1.4.0.tar.gz
StartedAt: 2020-10-28 23:19:22 -0400 (Wed, 28 Oct 2020)
EndedAt: 2020-10-28 23:27:32 -0400 (Wed, 28 Oct 2020)
EllapsedTime: 489.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Autotuner.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Autotuner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Autotuner_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/Autotuner.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Autotuner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Autotuner’ version ‘1.4.0’
* 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 ‘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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
createAutotuner 7.711  0.471   8.214
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Autotuner
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Autotuner’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (Autotuner)

Tests output

Autotuner.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 2.16.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    trimws

     ____________________________________________________________
    / __  / / / /__  __/ _   /__  __/ / / /\     / / ____/ __   / 
   / / / / / / /  / / / / / /  / / / / / /  \   / / /___/ /_/  /  
  / /_/ / / / /  / / / / / /  / / / / / / /\ \ / / ____/  _   \ 
 / __  / /_/ /  / / / /_/ /  / / / /_/ / /  \   /  /__/  / /  /
/_/ /_/_____/  /_/ /_____/  /_/ /_____/_/    \ /_____/__/ /__/   v.1.4.0
https://github.com/crmclean/autotuner

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 69 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 80.175   1.913  82.227 

Example timings

Autotuner.Rcheck/Autotuner-Ex.timings

nameusersystemelapsed
ThresholdingAlgo0.1960.0130.209
createAutotuner7.7110.4718.214
getAutoFactorCol0.0080.0010.008
getAutoFile_col0.0080.0010.009
getAutoFile_paths0.0060.0010.006
getAutoIntensity0.0080.0010.009
getAutoMetadata0.0050.0010.005
getAutoPeak_difference0.0080.0010.009
getAutoPeak_table0.0050.0010.005
getAutoPeaks0.0050.0000.005
getAutoTime0.0050.0000.005
isolatePeaks0.7610.1110.874
plot_peaks0.0160.0010.017
plot_signals0.2590.0240.284
returnParams0.0110.0020.012
setAutoFactorCol0.0060.0010.007
setAutoFile_col0.0050.0010.005
setAutoFile_paths0.0050.0000.005
setAutoIntensity0.0050.0010.006
setAutoMetadata0.0060.0010.008
setAutoPeak_difference0.0060.0010.006
setAutoPeak_table0.0070.0010.008
setAutoPeaks0.0070.0010.008
setAutoTime0.0060.0010.007