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CHECK report for CancerSubtypes on merida1

This page was generated on 2021-01-24 11:56:46 -0500 (Sun, 24 Jan 2021).

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 231/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.16.0
Taosheng Xu
Snapshot Date: 2021-01-23 14:40:16 -0500 (Sat, 23 Jan 2021)
URL: https://git.bioconductor.org/packages/CancerSubtypes
Branch: RELEASE_3_12
Last Commit: 5228b58
Last Changed Date: 2020-10-27 11:16:57 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerSubtypes
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2021-01-23 23:47:53 -0500 (Sat, 23 Jan 2021)
EndedAt: 2021-01-23 23:52:10 -0500 (Sat, 23 Jan 2021)
EllapsedTime: 257.6 seconds
RetCode: 0
Status:  OK 
CheckDir: CancerSubtypes.Rcheck
Warnings: 0

Command output

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### Running 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-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 ‘1.16.0’
* 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   48.411  3.637  15.624
sigclustTest  34.801  1.433  36.270
ExecuteSNF.CC 24.458  0.604  25.268
survAnalysis  18.548  0.121  18.690
FSbyCox       12.617  0.078  12.705
ExecuteCC      9.331  1.618  11.357
drawHeatmap    5.703  0.204   5.918
* 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 -- Sat Jan 23 23:52:01 2021 
*********************************************** 
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 
  4.814   0.295   5.100 

Example timings

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.4180.0480.467
ExecuteCC 9.331 1.61811.357
ExecuteCNMF48.411 3.63715.624
ExecuteSNF.CC24.458 0.60425.268
ExecuteSNF0.5340.0240.560
ExecuteWSNF2.6090.0492.663
ExecuteiCluster4.3720.0524.431
FSbyCox12.617 0.07812.705
FSbyMAD0.3660.0060.372
FSbyPCA0.1920.0050.198
FSbyVar0.0880.0040.093
GeneExp0.0170.0030.021
Ranking0.0480.0030.050
data.checkDistribution0.4720.0110.485
data.imputation0.0080.0000.008
data.normalization0.4220.0240.446
drawHeatmap5.7030.2045.918
miRNAExp0.0060.0030.009
saveFigure1.2560.0481.311
sigclustTest34.801 1.43336.270
silhouette_SimilarityMatrix0.3620.0170.380
spectralAlg0.0520.0040.056
status0.0020.0040.006
survAnalysis18.548 0.12118.690
time0.0010.0020.003