BioC 3.5: CHECK report for CancerSubtypes on veracruz2

Package: CancerSubtypes

Version: 1.2.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.2.5.tar.gz

StartedAt: 2017-10-18 01:20:03 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:23:55 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 231.4 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 --no-vignettes --timings CancerSubtypes_1.2.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.5’
* 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  47.916  4.427  54.126
ExecuteCNMF   26.218  1.777  13.046
ExecuteSNF.CC 21.082  0.323  22.329
ExecuteCC     10.514  0.850  11.960
survAnalysis   9.540  0.106   9.956
FSbyCox        6.120  0.078   6.485
drawHeatmap    5.946  0.122   6.438
* 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	1.496	0.055	1.598
ExecuteCC	10.514	0.850	11.960
ExecuteCNMF	26.218	1.777	13.046
ExecuteSNF.CC	21.082	0.323	22.329
ExecuteSNF	0.373	0.014	0.398
ExecuteiCluster	4.097	0.060	4.411
FSbyCox	6.120	0.078	6.485
FSbyMAD	0.302	0.009	0.322
FSbyPCA	0.167	0.014	0.210
FSbyVar	0.107	0.006	0.138
GeneExp	0.046	0.006	0.053
data.checkDistribution	0.390	0.021	0.447
data.imputation	0.025	0.001	0.027
data.normalization	0.158	0.009	0.175
drawHeatmap	5.946	0.122	6.438
miRNAExp	0.028	0.004	0.033
saveFigure	2.070	0.069	2.324
sigclustTest	47.916	4.427	54.126
silhouette_SimilarityMatrix	0.401	0.026	0.446
spectralAlg	0.058	0.003	0.063
status	0.002	0.002	0.004
survAnalysis	9.540	0.106	9.956
time	0.002	0.002	0.003