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CHECK report for CancerSubtypes on malbec1

This page was generated on 2021-02-22 12:28:50 -0500 (Mon, 22 Feb 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: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 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)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CancerSubtypes_1.16.0.tar.gz
StartedAt: 2021-02-22 00:12:49 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 00:16:11 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 202.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CancerSubtypes.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CancerSubtypes_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CancerSubtypes.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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   31.308  2.228  13.924
sigclustTest  27.820  0.028  27.889
ExecuteSNF.CC 26.872  0.360  16.679
survAnalysis  14.428  0.012  14.455
FSbyCox        8.536  0.000   8.544
ExecuteCC      7.572  0.060   7.724
drawHeatmap    6.076  0.032   6.125
* 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:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CancerSubtypes
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-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.

> BiocGenerics:::testPackage("CancerSubtypes")
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 19/20
  To enable shared memory capabilities, try: install.extras('
NMF
')


RUNIT TEST PROTOCOL -- Mon Feb 22 00:16:07 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 
  4.452   0.148   4.696 

Example timings

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.3160.0080.322
ExecuteCC7.5720.0607.724
ExecuteCNMF31.308 2.22813.924
ExecuteSNF.CC26.872 0.36016.679
ExecuteSNF0.3360.0000.334
ExecuteWSNF2.9560.0082.988
ExecuteiCluster3.7800.0163.799
FSbyCox8.5360.0008.544
FSbyMAD0.2000.0000.203
FSbyPCA0.1200.0000.122
FSbyVar0.0560.0000.056
GeneExp0.0120.0040.014
Ranking0.0240.0000.025
data.checkDistribution0.4840.0000.485
data.imputation0.0040.0000.006
data.normalization0.0920.0000.093
drawHeatmap6.0760.0326.125
miRNAExp0.0040.0000.005
saveFigure1.0960.0081.104
sigclustTest27.820 0.02827.889
silhouette_SimilarityMatrix0.2240.0000.225
spectralAlg0.0360.0000.033
status0.0000.0000.001
survAnalysis14.428 0.01214.455
time0.0000.0000.001