BioC 3.5: CHECK report for CancerSubtypes on toluca2

Package: CancerSubtypes

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.1.0.tar.gz

StartedAt: 2017-04-23 01:21:58 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:25:59 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 241.1 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 --no-vignettes --timings CancerSubtypes_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CancerSubtypes.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.0’
* 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 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  52.678  4.926  57.723
ExecuteCNMF   27.376  1.784  14.136
ExecuteSNF.CC 22.206  0.690  22.914
ExecuteCC     11.889  1.198  13.113
survAnalysis  11.229  0.093  11.343
FSbyCox        7.025  0.074   7.110
drawHeatmap    5.223  0.093   5.321
* 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	1.849	0.063	1.913
ExecuteCC	11.889	1.198	13.113
ExecuteCNMF	27.376	1.784	14.136
ExecuteSNF.CC	22.206	0.690	22.914
ExecuteSNF	0.373	0.018	0.392
ExecuteiCluster	4.384	0.055	4.449
FSbyCox	7.025	0.074	7.110
FSbyMAD	0.280	0.009	0.289
FSbyPCA	0.139	0.010	0.149
FSbyVar	0.122	0.012	0.135
GeneExp	0.042	0.004	0.046
data.checkDistribution	0.326	0.010	0.338
data.imputation	0.010	0.001	0.009
data.normalization	0.175	0.009	0.184
drawHeatmap	5.223	0.093	5.321
miRNAExp	0.033	0.006	0.038
saveFigure	1.835	0.060	1.905
sigclustTest	52.678	4.926	57.723
silhouette_SimilarityMatrix	0.387	0.022	0.410
spectralAlg	0.069	0.004	0.072
status	0.002	0.002	0.005
survAnalysis	11.229	0.093	11.343
time	0.002	0.007	0.010