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CHECK report for CancerSubtypes on machv2

This page was generated on 2020-10-17 11:58:09 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CancerSubtypes PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 228/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.14.0
Taosheng Xu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CancerSubtypes
Branch: RELEASE_3_11
Last Commit: 49fb18d
Last Changed Date: 2020-04-27 15:00:39 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerSubtypes
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CancerSubtypes_1.14.0.tar.gz
StartedAt: 2020-10-16 23:22:06 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:26:39 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 273.6 seconds
RetCode: 0
Status:  OK 
CheckDir: CancerSubtypes.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CancerSubtypes_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CancerSubtypes.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CancerSubtypes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CancerSubtypes’ version ‘1.14.0’
* 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 ‘CancerSubtypes’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
ExecuteCNMF   49.982  3.578  16.260
sigclustTest  37.555  2.076  39.733
ExecuteSNF.CC 26.808  0.808  27.778
survAnalysis  21.199  0.137  21.387
FSbyCox       12.873  0.102  13.006
ExecuteCC     10.249  1.463  12.091
drawHeatmap    5.921  0.206   6.136
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK


Installation output

CancerSubtypes.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CancerSubtypes
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CancerSubtypes’ ...
** 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 (CancerSubtypes)

Tests output

CancerSubtypes.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> BiocGenerics:::testPackage("CancerSubtypes")
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 23/24
  To enable shared memory capabilities, try: install.extras('
NMF
')


RUNIT TEST PROTOCOL -- Fri Oct 16 23:26:30 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CancerSubtypes RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  5.320   0.310   5.627 

Example timings

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.4560.0450.500
ExecuteCC10.249 1.46312.091
ExecuteCNMF49.982 3.57816.260
ExecuteSNF.CC26.808 0.80827.778
ExecuteSNF0.3320.0190.351
ExecuteWSNF3.0880.0543.147
ExecuteiCluster4.6090.0584.684
FSbyCox12.873 0.10213.006
FSbyMAD0.3690.0030.374
FSbyPCA0.1610.0050.166
FSbyVar0.0700.0030.074
GeneExp0.2590.0150.275
Ranking0.0570.0020.060
data.checkDistribution0.5370.0130.551
data.imputation0.0120.0010.014
data.normalization0.2470.0220.269
drawHeatmap5.9210.2066.136
miRNAExp0.0060.0020.008
saveFigure1.2140.0381.262
sigclustTest37.555 2.07639.733
silhouette_SimilarityMatrix0.3920.0220.415
spectralAlg0.0550.0020.058
status0.0020.0030.005
survAnalysis21.199 0.13721.387
time0.0010.0040.006