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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:12:26 -0400 (Tue, 16 Apr 2019).
| Package 1061/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NormalyzerDE 1.0.0 Jakob Willforss
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: NormalyzerDE |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2019-04-16 01:36:19 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:41:20 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 301.3 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/NormalyzerDE.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.0’
* 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 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 22.229 0.306 22.792
writeNormalizedDatasets 7.121 0.031 7.241
NormalyzerEvaluationResults 7.005 0.133 7.200
analyzeNormalizations 6.874 0.028 7.008
getSmoothedRTNormalizedMatrix 5.101 0.081 5.242
* 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-3.8-bioc/meat/NormalyzerDE.Rcheck/00check.log’
for details.
NormalyzerDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NormalyzerDE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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)
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-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: 80 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
21.892 0.688 22.762
NormalyzerDE.Rcheck/NormalyzerDE-Ex.timings
| name | user | system | elapsed | |
| NormalyzerEvaluationResults | 7.005 | 0.133 | 7.200 | |
| NormalyzerStatistics | 0.106 | 0.002 | 0.111 | |
| analyzeNormalizations | 6.874 | 0.028 | 7.008 | |
| calculateContrasts | 0.130 | 0.004 | 0.138 | |
| generateAnnotatedMatrix | 0.105 | 0.004 | 0.113 | |
| generatePlots | 22.229 | 0.306 | 22.792 | |
| generateStatsReport | 0.736 | 0.007 | 0.754 | |
| getRTNormalizedMatrix | 2.364 | 0.056 | 2.445 | |
| getSmoothedRTNormalizedMatrix | 5.101 | 0.081 | 5.242 | |
| getVerifiedNormalyzerObject | 0.037 | 0.001 | 0.039 | |
| globalIntensityNormalization | 0.007 | 0.001 | 0.008 | |
| loadData | 0.000 | 0.000 | 0.001 | |
| loadDesign | 0 | 0 | 0 | |
| meanNormalization | 0.008 | 0.001 | 0.009 | |
| medianNormalization | 0.006 | 0.001 | 0.008 | |
| normMethods | 2.718 | 0.016 | 2.765 | |
| normalyzer | 0.001 | 0.001 | 0.000 | |
| normalyzerDE | 0.475 | 0.004 | 0.483 | |
| performCyclicLoessNormalization | 0.008 | 0.000 | 0.008 | |
| performGlobalRLRNormalization | 0.025 | 0.001 | 0.028 | |
| performQuantileNormalization | 0.001 | 0.001 | 0.003 | |
| performSMADNormalization | 0.003 | 0.001 | 0.004 | |
| performVSNNormalization | 0.022 | 0.001 | 0.023 | |
| reduceDesignTechRep | 0.006 | 0.000 | 0.006 | |
| reduceTechnicalReplicates | 0.003 | 0.001 | 0.003 | |
| setupJobDir | 0.001 | 0.000 | 0.001 | |
| setupRawContrastObject | 0.057 | 0.001 | 0.058 | |
| setupRawDataObject | 0.017 | 0.001 | 0.016 | |
| setupTestData | 0.002 | 0.000 | 0.002 | |
| writeNormalizedDatasets | 7.121 | 0.031 | 7.241 | |