Package: perturbatr

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings perturbatr_1.4.0.tar.gz

StartedAt: 2019-10-16 05:29:55 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:43:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 839.2 seconds

RetCode: 0

Status:  OK

CheckDir: perturbatr.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings perturbatr_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/perturbatr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘perturbatr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘perturbatr’ version ‘1.4.0’
* 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 ‘perturbatr’ 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 or elapsed time > 5s
                                         user system elapsed
bootstrap                             106.872 53.437 160.341
HMAnalysedPerturbationData-class       11.791  8.954  20.748
rnaiscreen                             11.392  9.117  20.515
params-methods                         10.533  9.227  19.846
NetworkAnalysedPerturbationData-class  11.303  8.419  19.730
nestedGeneEffects-methods              10.486  9.053  19.735
graph-methods                          10.585  8.912  19.500
modelFit-methods                       10.373  9.054  19.511
diffuse-methods                        10.521  8.892  19.423
geneEffects-methods                    10.463  8.779  19.244
isBootstrapped-methods                 10.218  8.777  18.995
hm-methods                             10.109  8.731  18.842
inference-methods                      10.191  8.602  18.795
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL perturbatr
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘perturbatr’ ...
** 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 (perturbatr)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> # perturbatr: analysis of high-throughput gene perturbation screens
> #
> # Copyright (C) 2018 Simon Dirmeier
> #
> # This file is part of perturbatr
> #
> # perturbatr is free software: you can redistribute it and/or modify
> # it under the terms of the GNU General Public License as published by
> # the Free Software Foundation, either version 3 of the License, or
> # (at your option) any later version.
> #
> # perturbatr is distributed in the hope that it will be useful,
> # but WITHOUT ANY WARRANTY; without even the implied warranty of
> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> # GNU General Public License for more details.
> #
> # You should have received a copy of the GNU General Public License
> # along with perturbatr If not, see .
> 
> 
> library(testthat)
> library(perturbatr)

Attaching package: 'perturbatr'

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

    filter

> 
> test_check("perturbatr")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 41 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
208.708 109.527 318.538 

name	user	system	elapsed
HMAnalysedPerturbationData-class	11.791	8.954	20.748
NetworkAnalysedPerturbationData-class	11.303	8.419	19.730
PerturbationData-class	0.021	0.003	0.024
bootstrap	106.872	53.437	160.341
dataSet-methods	1.090	0.117	1.208
diffuse-methods	10.521	8.892	19.423
filter-methods	0.398	0.092	0.490
geneEffects-methods	10.463	8.779	19.244
graph-methods	10.585	8.912	19.500
hm-methods	10.109	8.731	18.842
inference-methods	10.191	8.602	18.795
isBootstrapped-methods	10.218	8.777	18.995
modelFit-methods	10.373	9.054	19.511
nestedGeneEffects-methods	10.486	9.053	19.735
params-methods	10.533	9.227	19.846
rbind.PerturbationData	0.622	0.152	0.775
rnaiscreen	11.392	9.117	20.515