Package: NormalyzerDE

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NormalyzerDE_1.4.0.tar.gz

StartedAt: 2020-04-15 04:15:50 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:21:51 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 361.5 seconds

RetCode: 0

Status:  OK

CheckDir: NormalyzerDE.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NormalyzerDE_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/NormalyzerDE.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormalyzerDE/DESCRIPTION’ ... OK
* this is package ‘NormalyzerDE’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘NormalyzerDE’ 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
Missing or unexported object: ‘SummarizedExperiment::metadata’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
generatePlots                 24.344  0.393  24.952
NormalyzerEvaluationResults    7.927  0.248   8.250
writeNormalizedDatasets        6.659  0.049   6.769
analyzeNormalizations          6.552  0.041   6.662
getSmoothedRTNormalizedMatrix  4.865  0.103   5.004
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/NormalyzerDE.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NormalyzerDE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘NormalyzerDE’ ...
** using staged installation
** R
** data
** 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 (NormalyzerDE)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> library(testthat)
> library(NormalyzerDE)
> test_check("NormalyzerDE")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 85 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 37.361   1.059  38.695 

name	user	system	elapsed
NormalyzerEvaluationResults	7.927	0.248	8.250
NormalyzerResults	0.124	0.002	0.127
NormalyzerStatistics	0.034	0.008	0.042
analyzeNormalizations	6.552	0.041	6.662
calculateContrasts	0.15	0.01	0.16
generateAnnotatedMatrix	0.082	0.009	0.092
generatePlots	24.344	0.393	24.952
generateStatsReport	3.528	0.059	3.614
getRTNormalizedMatrix	2.228	0.069	2.305
getSmoothedRTNormalizedMatrix	4.865	0.103	5.004
getVerifiedNormalyzerObject	0.057	0.002	0.059
globalIntensityNormalization	0.004	0.001	0.004
loadData	0.000	0.000	0.001
loadDesign	0	0	0
meanNormalization	0.004	0.001	0.005
medianNormalization	0.003	0.001	0.004
normMethods	2.470	0.030	2.521
normalyzer	0.000	0.000	0.001
normalyzerDE	1.819	0.019	1.858
performCyclicLoessNormalization	0.010	0.001	0.011
performGlobalRLRNormalization	0.021	0.000	0.022
performQuantileNormalization	0.002	0.002	0.003
performSMADNormalization	0.003	0.001	0.004
performVSNNormalization	0.016	0.001	0.017
reduceTechnicalReplicates	0.020	0.001	0.020
setupJobDir	0	0	0
setupRawContrastObject	0.01	0.00	0.01
setupRawDataObject	0.013	0.000	0.013
setupTestData	0.002	0.000	0.002
writeNormalizedDatasets	6.659	0.049	6.769