BioC 3.6: CHECK report for CancerSubtypes on malbec1

Package: CancerSubtypes

Version: 1.3.7

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.3.7.tar.gz

StartedAt: 2017-08-15 21:44:20 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:47:34 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 193.5 seconds

RetCode: 0

Status:  OK

CheckDir: CancerSubtypes.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.3.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.7’
* 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  44.780  0.020  44.829
ExecuteCNMF   25.588  1.020  10.945
ExecuteSNF.CC 16.292  0.024  16.328
survAnalysis  11.044  0.004  11.068
ExecuteCC      8.752  0.020   8.776
drawHeatmap    5.476  0.028   5.522
FSbyCox        5.348  0.000   5.353
* 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	1.132	0.020	1.150
ExecuteCC	8.752	0.020	8.776
ExecuteCNMF	25.588	1.020	10.945
ExecuteSNF.CC	16.292	0.024	16.328
ExecuteSNF	0.264	0.004	0.265
ExecuteWSNF	1.948	0.008	1.962
ExecuteiCluster	3.688	0.000	3.686
FSbyCox	5.348	0.000	5.353
FSbyMAD	0.216	0.000	0.216
FSbyPCA	0.136	0.000	0.133
FSbyVar	0.088	0.000	0.089
GeneExp	0.04	0.00	0.04
Ranking	0.024	0.000	0.025
data.checkDistribution	0.336	0.000	0.333
data.imputation	0.004	0.000	0.006
data.normalization	0.128	0.000	0.126
drawHeatmap	5.476	0.028	5.522
miRNAExp	0.004	0.000	0.006
saveFigure	1.704	0.012	1.717
sigclustTest	44.780	0.020	44.829
silhouette_SimilarityMatrix	0.304	0.000	0.303
spectralAlg	0.028	0.000	0.029
status	0.000	0.000	0.003
survAnalysis	11.044	0.004	11.068
time	0.000	0.000	0.002