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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:perturbatr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings perturbatr_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/perturbatr.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'perturbatr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'perturbatr' version '1.15.0'
* 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 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 LazyData ... 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 319.75   6.23  325.98
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("perturbatr")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ]
  
  == Failed tests ================================================================
  -- Failure (test_util.R:29:3): data plots --------------------------------------
  `s <- plot(rnaiscreen)` produced warnings.
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  'D:/biocbuild/bbs-3.15-bioc/meat/perturbatr.Rcheck/00check.log'
for details.

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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL perturbatr
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'perturbatr'
    finding HTML links ... done
    HMAnalysedPerturbationData-class        html  
    NetworkAnalysedPerturbationData-class   html  
    PerturbationData-class                  html  
    bootstrap                               html  
    dataSet-methods                         html  
    diffuse-methods                         html  
    filter-methods                          html  
    geneEffects-methods                     html  
    graph-methods                           html  
    hm-methods                              html  
    inference-methods                       html  
    isBootstrapped-methods                  html  
    modelFit-methods                        html  
    nestedGeneEffects-methods               html  
    params-methods                          html  
    perturbatr-package                      html  
    plot.NetworkAnalysedPerturbationData    html  
    plot.PerturbationData                   html  
    rbind.PerturbationData                  html  
    rnaiscreen                              html  
    setModelData-methods                    html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'DIAlignR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'GGPA' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'SeqSQC' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ]

== Failed tests ================================================================
-- Failure (test_util.R:29:3): data plots --------------------------------------
`s <- plot(rnaiscreen)` produced warnings.

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ]
Error: Test failures
Execution halted