Package: perturbatr

Version: 1.7.0

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_1.7.0.tar.gz

StartedAt: 2020-01-16 07:23:05 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:38:11 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 906.4 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/perturbatr.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.7.0’
* 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 (user + system) or elapsed time > 5s
                                         user system elapsed
bootstrap                             106.873 52.654 159.545
NetworkAnalysedPerturbationData-class  12.090  8.735  20.829
rnaiscreen                             11.447  9.276  20.777
HMAnalysedPerturbationData-class       12.427  7.973  20.401
isBootstrapped-methods                 11.150  9.197  20.379
inference-methods                      10.933  9.349  20.290
params-methods                         10.961  9.196  20.161
geneEffects-methods                    10.989  9.131  20.125
modelFit-methods                       10.879  9.123  20.007
nestedGeneEffects-methods              10.803  9.099  19.902
graph-methods                          10.696  9.083  19.796
hm-methods                             10.741  9.007  19.753
diffuse-methods                        10.671  8.911  19.584
* 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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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 <http://www.gnu.org/licenses/>.
> 
> 
> 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: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
246.394 121.671 368.834 

name	user	system	elapsed
HMAnalysedPerturbationData-class	12.427	7.973	20.401
NetworkAnalysedPerturbationData-class	12.090	8.735	20.829
PerturbationData-class	0.012	0.000	0.013
bootstrap	106.873	52.654	159.545
dataSet-methods	0.908	0.110	1.017
diffuse-methods	10.671	8.911	19.584
filter-methods	0.577	0.118	0.696
geneEffects-methods	10.989	9.131	20.125
graph-methods	10.696	9.083	19.796
hm-methods	10.741	9.007	19.753
inference-methods	10.933	9.349	20.290
isBootstrapped-methods	11.150	9.197	20.379
modelFit-methods	10.879	9.123	20.007
nestedGeneEffects-methods	10.803	9.099	19.902
params-methods	10.961	9.196	20.161
rbind.PerturbationData	0.704	0.181	0.885
rnaiscreen	11.447	9.276	20.777