BioC 3.4: CHECK report for CancerSubtypes on morelia

Package: CancerSubtypes

Version: 0.99.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CancerSubtypes_0.99.10.tar.gz

StartedAt: 2016-09-20 04:01:19 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:04:20 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 181.4 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_0.99.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘0.99.10’
* 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  42.729  3.964  46.711
ExecuteCNMF   23.972  1.295   9.677
ExecuteSNF.CC 16.803  0.324  17.130
ExecuteCC     12.597  0.453  13.062
survAnalysis   8.251  0.079   8.334
FSbyCox        5.644  0.067   5.713
* 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	0.542	0.021	0.563
ExecuteCC	12.597	0.453	13.062
ExecuteCNMF	23.972	1.295	9.677
ExecuteSNF.CC	16.803	0.324	17.130
ExecuteSNF	0.328	0.021	0.350
ExecuteiCluster	3.497	0.044	3.544
FSbyCox	5.644	0.067	5.713
FSbyMAD	0.188	0.009	0.198
FSbyPCA	0.134	0.010	0.144
FSbyVar	0.095	0.013	0.108
GeneExp	0.042	0.006	0.048
data.checkDistribution	0.264	0.015	0.279
data.imputation	0.006	0.000	0.006
data.normalization	0.111	0.005	0.116
drawHeatmap	4.371	0.114	4.522
miRNAExp	0.028	0.004	0.032
saveFigure	1.166	0.073	1.284
sigclustTest	42.729	3.964	46.711
silhouette_SimilarityMatrix	0.356	0.028	0.386
spectralAlg	0.065	0.004	0.070
status	0.001	0.002	0.003
survAnalysis	8.251	0.079	8.334
time	0.002	0.002	0.003