Package: NormalyzerDE

Version: 1.1.15

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_1.1.15.tar.gz

StartedAt: 2019-04-09 02:32:22 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:37:44 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 321.6 seconds

RetCode: 0

Status:  OK

CheckDir: NormalyzerDE.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.1.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/NormalyzerDE.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.1.15’
* 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                 20.540  0.290  21.054
NormalyzerEvaluationResults    7.605  0.144   7.831
analyzeNormalizations          7.628  0.037   7.751
writeNormalizedDatasets        7.224  0.026   7.341
getSmoothedRTNormalizedMatrix  4.961  0.088   5.096
* 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-3.9-bioc/meat/NormalyzerDE.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NormalyzerDE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘NormalyzerDE’ ...
** 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
* DONE (NormalyzerDE)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 38.951   0.848  40.128 

name	user	system	elapsed
NormalyzerEvaluationResults	7.605	0.144	7.831
NormalyzerResults	0.107	0.001	0.110
NormalyzerStatistics	0.018	0.002	0.020
analyzeNormalizations	7.628	0.037	7.751
calculateContrasts	0.159	0.005	0.166
generateAnnotatedMatrix	0.080	0.004	0.084
generatePlots	20.540	0.290	21.054
generateStatsReport	3.346	0.017	3.409
getRTNormalizedMatrix	2.204	0.046	2.269
getSmoothedRTNormalizedMatrix	4.961	0.088	5.096
getVerifiedNormalyzerObject	0.066	0.002	0.069
globalIntensityNormalization	0.004	0.001	0.005
loadData	0	0	0
loadDesign	0	0	0
meanNormalization	0.006	0.001	0.007
medianNormalization	0.007	0.001	0.007
normMethods	2.720	0.016	2.760
normalyzer	0.000	0.000	0.001
normalyzerDE	1.822	0.011	1.859
performCyclicLoessNormalization	0.009	0.001	0.011
performGlobalRLRNormalization	0.021	0.001	0.023
performQuantileNormalization	0.002	0.001	0.002
performSMADNormalization	0.003	0.001	0.005
performVSNNormalization	0.018	0.001	0.019
reduceTechnicalReplicates	0.096	0.000	0.096
setupJobDir	0.000	0.001	0.001
setupRawContrastObject	0.012	0.000	0.012
setupRawDataObject	0.02	0.00	0.02
setupTestData	0.003	0.001	0.002
writeNormalizedDatasets	7.224	0.026	7.341