Package: perturbatr

Version: 1.2.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings perturbatr_1.2.1.tar.gz

StartedAt: 2019-04-16 02:03:15 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:09:28 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 373.3 seconds

RetCode: 0

Status:  OK

CheckDir: perturbatr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings perturbatr_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/perturbatr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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                             62.792  0.072  62.922
HMAnalysedPerturbationData-class       8.812  0.104   8.929
NetworkAnalysedPerturbationData-class  8.564  0.028   8.618
graph-methods                          8.068  0.036   8.113
hm-methods                             7.976  0.052   8.045
rnaiscreen                             7.856  0.032   7.891
geneEffects-methods                    7.504  0.048   7.561
diffuse-methods                        7.296  0.032   7.346
modelFit-methods                       7.096  0.020   7.126
isBootstrapped-methods                 7.000  0.028   7.040
params-methods                         6.996  0.028   7.032
nestedGeneEffects-methods              6.760  0.012   6.775
inference-methods                      6.112  0.016   6.136
* 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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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL perturbatr
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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-pc-linux-gnu (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: 42 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
145.136   0.320 145.918 

name	user	system	elapsed
HMAnalysedPerturbationData-class	8.812	0.104	8.929
NetworkAnalysedPerturbationData-class	8.564	0.028	8.618
PerturbationData-class	0.008	0.000	0.009
bootstrap	62.792	0.072	62.922
dataSet-methods	0.848	0.016	0.865
diffuse-methods	7.296	0.032	7.346
filter-methods	0.416	0.016	0.433
geneEffects-methods	7.504	0.048	7.561
graph-methods	8.068	0.036	8.113
hm-methods	7.976	0.052	8.045
inference-methods	6.112	0.016	6.136
isBootstrapped-methods	7.000	0.028	7.040
modelFit-methods	7.096	0.020	7.126
nestedGeneEffects-methods	6.760	0.012	6.775
params-methods	6.996	0.028	7.032
rbind.PerturbationData	0.776	0.004	0.780
rnaiscreen	7.856	0.032	7.891