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This page was generated on 2023-10-16 11:37:19 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 1392/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormalyzerDE 1.18.1  (landing page)
Jakob Willforss
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/NormalyzerDE
git_branch: RELEASE_3_17
git_last_commit: 2b9deb3
git_last_commit_date: 2023-09-12 14:48:33 -0400 (Tue, 12 Sep 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for NormalyzerDE on merida1


To the developers/maintainers of the NormalyzerDE package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: NormalyzerDE
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NormalyzerDE_1.18.1.tar.gz
StartedAt: 2023-10-16 04:41:53 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 04:57:07 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 913.3 seconds
RetCode: 0
Status:   OK  
CheckDir: NormalyzerDE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NormalyzerDE_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/NormalyzerDE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormalyzerDE/DESCRIPTION’ ... OK
* this is package ‘NormalyzerDE’ version ‘1.18.1’
* 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 ... 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
generatePlots                 29.510  1.304  39.940
NormalyzerEvaluationResults    9.229  0.427  12.207
analyzeNormalizations          8.507  0.142  11.144
writeNormalizedDatasets        8.274  0.061  10.371
getSmoothedRTNormalizedMatrix  7.799  0.281  10.323
generateStatsReport            5.113  0.056   6.514
normMethods                    4.036  0.050   5.183
getRTNormalizedMatrix          3.311  0.101   5.043
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/NormalyzerDE.Rcheck/00check.log’
for details.



Installation output

NormalyzerDE.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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)

Tests output

NormalyzerDE.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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)
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, were retired in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
> test_check("NormalyzerDE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
 58.999   2.142  77.697 

Example timings

NormalyzerDE.Rcheck/NormalyzerDE-Ex.timings

nameusersystemelapsed
NormalyzerEvaluationResults 9.229 0.42712.207
NormalyzerResults0.1980.0040.256
NormalyzerStatistics0.0300.0020.041
analyzeNormalizations 8.507 0.14211.144
calculateContrasts0.2080.0040.267
generateAnnotatedMatrix0.1090.0040.137
generatePlots29.510 1.30439.940
generateStatsReport5.1130.0566.514
getRTNormalizedMatrix3.3110.1015.043
getSmoothedRTNormalizedMatrix 7.799 0.28110.323
getVerifiedNormalyzerObject0.0960.0030.124
globalIntensityNormalization0.0090.0030.012
loadData000
loadDesign000
meanNormalization0.0080.0020.013
medianNormalization0.0090.0020.014
normMethods4.0360.0505.183
normalyzer0.0000.0010.001
normalyzerDE2.3650.0253.095
performCyclicLoessNormalization0.0130.0030.022
performGlobalRLRNormalization0.0340.0030.050
performQuantileNormalization0.0030.0030.012
performSMADNormalization0.0030.0020.006
performVSNNormalization0.0390.0030.055
reduceTechnicalReplicates0.0650.0020.084
setupJobDir0.0000.0010.004
setupRawContrastObject0.0300.0020.039
setupRawDataObject0.0380.0020.051
setupTestData0.0020.0000.005
writeNormalizedDatasets 8.274 0.06110.371