Package: perturbatr

Version: 1.2.1

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_1.2.1.tar.gz

StartedAt: 2019-04-16 01:51:54 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:04:32 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 758.0 seconds

RetCode: 0

Status:  OK

CheckDir: perturbatr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/perturbatr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.1’
* 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                             77.037 27.155 105.008
HMAnalysedPerturbationData-class      13.606  8.907  22.673
NetworkAnalysedPerturbationData-class 13.412  8.965  22.505
nestedGeneEffects-methods             12.714  9.298  22.288
geneEffects-methods                   12.596  9.394  22.088
isBootstrapped-methods                12.706  9.277  22.162
params-methods                        12.586  9.281  22.042
modelFit-methods                      12.540  9.196  22.192
hm-methods                            12.349  9.331  21.788
inference-methods                     12.351  9.070  21.632
diffuse-methods                       12.232  9.051  21.352
rnaiscreen                            12.381  8.798  21.245
graph-methods                         11.819  8.761  20.657
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL perturbatr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘perturbatr’ ...
** 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
* DONE (perturbatr)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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: 44 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
200.537 100.982 303.080 

name	user	system	elapsed
HMAnalysedPerturbationData-class	13.606	8.907	22.673
NetworkAnalysedPerturbationData-class	13.412	8.965	22.505
PerturbationData-class	0.015	0.001	0.016
bootstrap	77.037	27.155	105.008
dataSet-methods	0.822	0.045	0.869
diffuse-methods	12.232	9.051	21.352
filter-methods	0.516	0.066	0.585
geneEffects-methods	12.596	9.394	22.088
graph-methods	11.819	8.761	20.657
hm-methods	12.349	9.331	21.788
inference-methods	12.351	9.070	21.632
isBootstrapped-methods	12.706	9.277	22.162
modelFit-methods	12.540	9.196	22.192
nestedGeneEffects-methods	12.714	9.298	22.288
params-methods	12.586	9.281	22.042
rbind.PerturbationData	0.707	0.098	0.809
rnaiscreen	12.381	8.798	21.245