BioC 3.5: CHECK report for CancerSubtypes on malbec2

Package: CancerSubtypes

Version: 1.2.5

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.2.5.tar.gz

StartedAt: 2017-10-17 21:45:04 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:48:10 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 186.3 seconds

RetCode: 0

Status:  OK

CheckDir: CancerSubtypes.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.2.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.5’
* 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  42.588  0.048  42.668
ExecuteCNMF   23.868  1.080  10.689
ExecuteSNF.CC 16.004  0.020  16.035
ExecuteCC      9.076  0.048   9.316
survAnalysis   8.160  0.012   8.179
drawHeatmap    6.600  0.008   6.832
FSbyCox        5.696  0.004   5.705
* 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	1.020	0.016	1.037
ExecuteCC	9.076	0.048	9.316
ExecuteCNMF	23.868	1.080	10.689
ExecuteSNF.CC	16.004	0.020	16.035
ExecuteSNF	0.280	0.004	0.285
ExecuteiCluster	4.444	0.036	4.484
FSbyCox	5.696	0.004	5.705
FSbyMAD	0.216	0.000	0.217
FSbyPCA	0.136	0.000	0.137
FSbyVar	0.084	0.000	0.087
GeneExp	0.036	0.000	0.040
data.checkDistribution	0.292	0.000	0.292
data.imputation	0.020	0.000	0.022
data.normalization	0.176	0.000	0.178
drawHeatmap	6.600	0.008	6.832
miRNAExp	0.040	0.004	0.042
saveFigure	1.552	0.004	1.557
sigclustTest	42.588	0.048	42.668
silhouette_SimilarityMatrix	0.284	0.000	0.282
spectralAlg	0.076	0.000	0.076
status	0.004	0.000	0.001
survAnalysis	8.160	0.012	8.179
time	0.000	0.000	0.002