BioC 3.6: CHECK report for CancerSubtypes on veracruz1

Package: CancerSubtypes

Version: 1.3.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.3.7.tar.gz

StartedAt: 2017-08-16 00:45:53 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:49:18 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 205.4 seconds

RetCode: 0

Status:  OK

CheckDir: CancerSubtypes.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.3.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.7’
* 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 loading without being on the library search path ... 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  44.205  3.484  48.638
ExecuteCNMF   25.791  1.576  12.566
ExecuteSNF.CC 17.461  0.531  18.284
ExecuteCC     10.252  0.903  11.324
survAnalysis  10.183  0.109  10.646
FSbyCox        5.231  0.045   5.424
drawHeatmap    4.955  0.091   5.142
* 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

* installing *source* package ‘CancerSubtypes’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CancerSubtypes)

name	user	system	elapsed
DiffExp.limma	1.449	0.047	1.522
ExecuteCC	10.252	0.903	11.324
ExecuteCNMF	25.791	1.576	12.566
ExecuteSNF.CC	17.461	0.531	18.284
ExecuteSNF	0.28	0.01	0.29
ExecuteWSNF	2.319	0.037	2.384
ExecuteiCluster	3.430	0.036	3.515
FSbyCox	5.231	0.045	5.424
FSbyMAD	0.195	0.006	0.202
FSbyPCA	0.119	0.009	0.128
FSbyVar	0.078	0.005	0.084
GeneExp	0.031	0.002	0.033
Ranking	0.023	0.001	0.024
data.checkDistribution	0.493	0.013	0.513
data.imputation	0.006	0.000	0.007
data.normalization	0.167	0.008	0.175
drawHeatmap	4.955	0.091	5.142
miRNAExp	0.004	0.001	0.004
saveFigure	1.573	0.038	1.636
sigclustTest	44.205	3.484	48.638
silhouette_SimilarityMatrix	0.300	0.016	0.339
spectralAlg	0.038	0.003	0.041
status	0.002	0.001	0.003
survAnalysis	10.183	0.109	10.646
time	0.002	0.003	0.004