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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DAPAR_1.20.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DAPAR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.20.3’
* 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 ‘DAPAR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Package in Depends field not imported from: ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
boxPlotD: warning in axis(side = 1, at = 1:ncol(qData), label =
  legend): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = labCol, las = 2, line =
  -0.5 + offsetCol, tick = 0, cex.axis = cexCol, hadj = NA, padj = 0):
  partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = rep("", nc), las = 2,
  tick = 0): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = labRow, las = 5, line =
  -0.5 + offsetRow, tick = 0, cex.axis = cexRow, hadj = 0, padj = NA):
  partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = rep("", nr), las = 2,
  line = -0.5, tick = 0): partial argument match of 'label' to 'labels'
violinPlotD: warning in axis(side = 1, at = 1:ncol(qData), label = if
  (is.vector(legend)) {: partial argument match of 'label' to 'labels'
violinPlotD: warning in legend: partial argument match of 'label' to
  'labels'
violinPlotD: warning in } else {: partial argument match of 'label' to
  'labels'
violinPlotD: warning in legend[, i]: partial argument match of 'label'
  to 'labels'
violinPlotD: warning in }, line = 2 * i - 1): partial argument match of
  'label' to 'labels'
aggregateIterParallel: no visible binding for global variable ‘cond’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘x’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘y’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘g’
display.CC.visNet: no visible binding for global variable
  ‘layout_nicely’
getTextForGOAnalysis: no visible binding for global variable
  ‘textGOParams’
getTextForGOAnalysis: no visible binding for global variable ‘input’
Undefined global functions or variables:
  cond g input layout_nicely textGOParams x y
* checking Rd files ... NOTE
prepare_Rd: plotJitter_rCharts.Rd:20-23: Dropping empty section \examples
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
CVDistD_HC               4.506  2.957   7.214
wrapper.CVDistD_HC       4.387  2.839   6.841
compareNormalizationD_HC 4.563  1.855   6.235
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DAPAR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘DAPAR’ ...
** using staged installation
** R
** 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 (DAPAR)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> library(testthat)
> library(DAPAR)
Loading required package: foreach
Loading required package: parallel
Loading required package: doParallel
Loading required package: iterators
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


> 
> test_check("DAPAR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 16.740   1.266  18.013