Package: CancerSubtypes

Version: 1.9.0

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_1.9.0.tar.gz

StartedAt: 2019-04-08 23:40:29 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:44:39 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 250.4 seconds

RetCode: 0

Status:  OK

CheckDir: CancerSubtypes.Rcheck

Warnings: 0

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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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CancerSubtypes.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.0’
* 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 or elapsed time > 5s
                  user system elapsed
sigclustTest    45.219  6.406  51.978
ExecuteCNMF     38.784  3.119  16.633
ExecuteSNF.CC   22.805  0.682  23.687
survAnalysis    17.005  0.178  17.322
ExecuteCC       11.121  1.662  12.949
FSbyCox         11.306  0.113  11.495
drawHeatmap      6.061  0.177   6.286
ExecuteiCluster  5.133  0.068   5.245
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CancerSubtypes
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CancerSubtypes’ ...
** 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
* DONE (CancerSubtypes)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isFALSE

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


RUNIT TEST PROTOCOL -- Mon Apr  8 23:44:34 2019 
*********************************************** 
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 
  3.786   0.282   4.058 

name	user	system	elapsed
DiffExp.limma	0.470	0.058	0.530
ExecuteCC	11.121	1.662	12.949
ExecuteCNMF	38.784	3.119	16.633
ExecuteSNF.CC	22.805	0.682	23.687
ExecuteSNF	0.342	0.022	0.366
ExecuteWSNF	2.965	0.050	3.068
ExecuteiCluster	5.133	0.068	5.245
FSbyCox	11.306	0.113	11.495
FSbyMAD	0.321	0.008	0.334
FSbyPCA	0.229	0.027	0.258
FSbyVar	0.188	0.006	0.196
GeneExp	0.047	0.004	0.051
Ranking	0.036	0.002	0.038
data.checkDistribution	0.613	0.014	0.631
data.imputation	0.011	0.000	0.011
data.normalization	0.178	0.005	0.184
drawHeatmap	6.061	0.177	6.286
miRNAExp	0.004	0.002	0.006
saveFigure	1.169	0.095	1.282
sigclustTest	45.219	6.406	51.978
silhouette_SimilarityMatrix	0.363	0.026	0.391
spectralAlg	0.037	0.002	0.038
status	0.002	0.002	0.004
survAnalysis	17.005	0.178	17.322
time	0.002	0.002	0.002