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CHECK report for NormalyzerDE on malbec1

This page was generated on 2019-04-16 11:53:46 -0400 (Tue, 16 Apr 2019).

Package 1061/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormalyzerDE 1.0.0
Jakob Willforss
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/NormalyzerDE
Branch: RELEASE_3_8
Last Commit: 34d92b0
Last Changed Date: 2018-10-30 11:42:10 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NormalyzerDE
Version: 1.0.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings NormalyzerDE_1.0.0.tar.gz
StartedAt: 2019-04-16 01:47:32 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:51:50 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 257.9 seconds
RetCode: 0
Status:  OK 
CheckDir: NormalyzerDE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings NormalyzerDE_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/NormalyzerDE.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormalyzerDE/DESCRIPTION’ ... OK
* this is package ‘NormalyzerDE’ version ‘1.0.0’
* 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 ... OK
* 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 ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'NormalyzerDE'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* 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
generatePlots                 15.520  0.108  15.651
NormalyzerEvaluationResults    7.008  0.084   7.110
writeNormalizedDatasets        6.996  0.004   7.013
analyzeNormalizations          6.568  0.016   6.598
getSmoothedRTNormalizedMatrix  5.548  0.000   5.569
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/NormalyzerDE.Rcheck/00check.log’
for details.



Installation output

NormalyzerDE.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL NormalyzerDE
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output

NormalyzerDE.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> library(testthat)
> library(NormalyzerDE)
> test_check("NormalyzerDE")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 80 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 19.240   0.324  19.603 

Example timings

NormalyzerDE.Rcheck/NormalyzerDE-Ex.timings

nameusersystemelapsed
NormalyzerEvaluationResults7.0080.0847.110
NormalyzerStatistics0.0640.0040.071
analyzeNormalizations6.5680.0166.598
calculateContrasts0.1080.0000.107
generateAnnotatedMatrix0.0520.0040.054
generatePlots15.520 0.10815.651
generateStatsReport0.4400.0040.445
getRTNormalizedMatrix2.4520.0082.465
getSmoothedRTNormalizedMatrix5.5480.0005.569
getVerifiedNormalyzerObject0.0360.0000.038
globalIntensityNormalization0.0080.0000.006
loadData000
loadDesign000
meanNormalization0.0080.0000.006
medianNormalization0.0040.0000.005
normMethods2.8320.0002.876
normalyzer0.0000.0000.001
normalyzerDE0.3560.0000.355
performCyclicLoessNormalization0.0080.0000.006
performGlobalRLRNormalization0.0160.0000.017
performQuantileNormalization0.0040.0000.004
performSMADNormalization0.0000.0000.002
performVSNNormalization0.0160.0000.019
reduceDesignTechRep0.0040.0000.003
reduceTechnicalReplicates0.0040.0000.002
setupJobDir000
setupRawContrastObject0.0560.0000.055
setupRawDataObject0.0200.0000.018
setupTestData0.0040.0000.002
writeNormalizedDatasets6.9960.0047.013