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This page was generated on 2022-01-21 11:06:20 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for NormalyzerDE on nebbiolo1


To the developers/maintainers of the NormalyzerDE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NormalyzerDE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1296/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormalyzerDE 1.13.1  (landing page)
Jakob Willforss
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/NormalyzerDE
git_branch: master
git_last_commit: 5d5c440
git_last_commit_date: 2021-11-21 00:39:00 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'vsn' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NormalyzerDE
Version: 1.13.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings NormalyzerDE_1.13.1.tar.gz
StartedAt: 2022-01-20 20:12:02 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:16:55 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 293.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: NormalyzerDE.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings NormalyzerDE_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/NormalyzerDE.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.13.1’
* 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 ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘direction’
  Warning: multiple methods tables found for ‘gridDistance’
See ‘/home/biocbuild/bbs-3.15-bioc/meat/NormalyzerDE.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 (user + system) or elapsed time > 5s
                user system elapsed
generatePlots 13.234  0.267  13.503
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/NormalyzerDE.Rcheck/00check.log’
for details.



Installation output

NormalyzerDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL NormalyzerDE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘NormalyzerDE’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: multiple methods tables found for ‘direction’
Warning: multiple methods tables found for ‘gridDistance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘direction’
Warning: multiple methods tables found for ‘gridDistance’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘direction’
Warning: multiple methods tables found for ‘gridDistance’
** testing if installed package keeps a record of temporary installation path
* DONE (NormalyzerDE)

Tests output

NormalyzerDE.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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)
Warning messages:
1: multiple methods tables found for 'direction' 
2: multiple methods tables found for 'gridDistance' 
> test_check("NormalyzerDE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
 26.173   0.939  27.098 

Example timings

NormalyzerDE.Rcheck/NormalyzerDE-Ex.timings

nameusersystemelapsed
NormalyzerEvaluationResults4.1180.1934.311
NormalyzerResults0.0820.0000.082
NormalyzerStatistics0.0140.0000.014
analyzeNormalizations3.8170.0273.846
calculateContrasts0.0760.0010.076
generateAnnotatedMatrix0.040.000.04
generatePlots13.234 0.26713.503
generateStatsReport1.8510.0161.866
getRTNormalizedMatrix1.4820.0241.506
getSmoothedRTNormalizedMatrix3.3540.1353.490
getVerifiedNormalyzerObject0.0490.0080.056
globalIntensityNormalization0.0030.0000.004
loadData0.0000.0000.001
loadDesign000
meanNormalization0.0010.0040.003
medianNormalization0.0000.0040.003
normMethods1.6530.0561.709
normalyzer0.0000.0000.001
normalyzerDE1.0320.0161.048
performCyclicLoessNormalization0.0030.0040.007
performGlobalRLRNormalization0.0160.0000.016
performQuantileNormalization0.0000.0020.002
performSMADNormalization0.0010.0000.003
performVSNNormalization0.0170.0000.018
reduceTechnicalReplicates0.0230.0040.028
setupJobDir0.0010.0000.000
setupRawContrastObject0.0130.0000.013
setupRawDataObject0.0160.0000.016
setupTestData0.0000.0020.002
writeNormalizedDatasets3.9850.0053.990