Jakob Willforss
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/NormalyzerDE |
| Branch: RELEASE_3_9 |
| Last Commit: 460392e |
| Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:16:03 -0400 (Wed, 16 Oct 2019).
| Package 1110/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NormalyzerDE 1.2.0 Jakob Willforss
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: NormalyzerDE |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings NormalyzerDE_1.2.0.tar.gz |
| StartedAt: 2019-10-16 03:35:00 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:40:14 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 314.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NormalyzerDE.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings NormalyzerDE_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/NormalyzerDE.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
generatePlots 19.252 0.127 19.414
NormalyzerEvaluationResults 5.828 0.064 5.893
analyzeNormalizations 5.455 0.003 5.460
writeNormalizedDatasets 5.197 0.008 5.206
generateStatsReport 5.113 0.088 5.217
* 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-3.9-bioc/meat/NormalyzerDE.Rcheck/00check.log’
for details.
NormalyzerDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL NormalyzerDE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)
NormalyzerDE.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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: 85 | SKIPPED: 0 | WARNINGS: 78 | FAILED: 0 ]
>
> proc.time()
user system elapsed
30.886 0.423 31.352
NormalyzerDE.Rcheck/NormalyzerDE-Ex.timings
| name | user | system | elapsed | |
| NormalyzerEvaluationResults | 5.828 | 0.064 | 5.893 | |
| NormalyzerResults | 0.065 | 0.004 | 0.070 | |
| NormalyzerStatistics | 0.018 | 0.000 | 0.018 | |
| analyzeNormalizations | 5.455 | 0.003 | 5.460 | |
| calculateContrasts | 0.090 | 0.000 | 0.091 | |
| generateAnnotatedMatrix | 0.054 | 0.000 | 0.054 | |
| generatePlots | 19.252 | 0.127 | 19.414 | |
| generateStatsReport | 5.113 | 0.088 | 5.217 | |
| getRTNormalizedMatrix | 2.444 | 0.004 | 2.448 | |
| getSmoothedRTNormalizedMatrix | 4.111 | 0.000 | 4.119 | |
| getVerifiedNormalyzerObject | 0.04 | 0.00 | 0.04 | |
| globalIntensityNormalization | 0.003 | 0.000 | 0.003 | |
| loadData | 0 | 0 | 0 | |
| loadDesign | 0 | 0 | 0 | |
| meanNormalization | 0.003 | 0.000 | 0.003 | |
| medianNormalization | 0.003 | 0.000 | 0.002 | |
| normMethods | 1.894 | 0.000 | 1.894 | |
| normalyzer | 0.000 | 0.001 | 0.000 | |
| normalyzerDE | 1.833 | 0.002 | 1.846 | |
| performCyclicLoessNormalization | 0.010 | 0.000 | 0.011 | |
| performGlobalRLRNormalization | 0.026 | 0.000 | 0.025 | |
| performQuantileNormalization | 0.002 | 0.001 | 0.002 | |
| performSMADNormalization | 0.000 | 0.002 | 0.002 | |
| performVSNNormalization | 0.024 | 0.000 | 0.024 | |
| reduceTechnicalReplicates | 0.112 | 0.000 | 0.112 | |
| setupJobDir | 0.000 | 0.000 | 0.001 | |
| setupRawContrastObject | 0.016 | 0.000 | 0.015 | |
| setupRawDataObject | 0.022 | 0.000 | 0.022 | |
| setupTestData | 0.003 | 0.000 | 0.003 | |
| writeNormalizedDatasets | 5.197 | 0.008 | 5.206 | |