Package: perturbatr

Version: 1.4.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings perturbatr_1.4.0.tar.gz

StartedAt: 2019-10-16 03:52:07 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:57:58 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 350.9 seconds

RetCode: 0

Status:  OK

CheckDir: perturbatr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:perturbatr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings perturbatr_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/perturbatr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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                        69.467  0.051  70.016
inference-methods                 6.268  0.040   6.309
params-methods                    5.778  0.032   5.896
diffuse-methods                   5.732  0.024   5.873
HMAnalysedPerturbationData-class  5.524  0.080   5.604
rnaiscreen                        5.501  0.048   5.549
graph-methods                     5.469  0.036   5.509
hm-methods                        5.142  0.032   5.286
geneEffects-methods               5.091  0.004   5.095
* 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-3.9-bioc/R/bin/R CMD INSTALL perturbatr
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-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 .
> 
> 
> 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: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
128.888   0.327 129.943 

name	user	system	elapsed
HMAnalysedPerturbationData-class	5.524	0.080	5.604
NetworkAnalysedPerturbationData-class	4.764	0.024	4.794
PerturbationData-class	0.010	0.000	0.009
bootstrap	69.467	0.051	70.016
dataSet-methods	0.987	0.020	1.017
diffuse-methods	5.732	0.024	5.873
filter-methods	0.440	0.016	0.457
geneEffects-methods	5.091	0.004	5.095
graph-methods	5.469	0.036	5.509
hm-methods	5.142	0.032	5.286
inference-methods	6.268	0.040	6.309
isBootstrapped-methods	4.340	0.028	4.561
modelFit-methods	4.670	0.024	4.694
nestedGeneEffects-methods	4.466	0.020	4.490
params-methods	5.778	0.032	5.896
rbind.PerturbationData	0.718	0.032	0.750
rnaiscreen	5.501	0.048	5.549