BioC 2.14: CHECK report for viper on petty

Package: viper

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch viper_1.0.0.tar.gz

StartedAt: 2014-10-08 00:34:25 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:57:50 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 1405.0 seconds

RetCode: 0

Status:  OK

CheckDir: viper.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 --no-multiarch viper_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/viper.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.0.0’
* 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 ‘viper’ can be installed ... [5s/6s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22m/22m] OK
Examples with CPU or elapsed time > 5s
                          user  system elapsed
shadow                 462.986 124.285 587.301
msviperCombinatorial   180.282  18.477 209.008
msviperSynergy         151.737  21.056 172.886
viperSignature-methods  91.542  13.517 105.063
msviper                 81.504  11.106  92.777
plot.msviper            50.451  11.783  62.241
ledge                   14.864   0.490  15.375
bootstrapmsviper        12.929   1.758  14.698
bootstrapTtest-methods   9.485   1.392  10.892
msviperAnnot             8.888   0.530   9.549
ttestNull-methods        6.925   1.518   8.444
viper                    6.761   0.793   7.555
signatureDistance        6.835   0.289   7.124
aracne2regulon           6.469   0.642   7.141
* 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

* installing *source* package ‘viper’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (viper)

name	user	system	elapsed
aracne2regulon	6.469	0.642	7.141
bootstrapTtest-methods	9.485	1.392	10.892
bootstrapmsviper	12.929	1.758	14.698
distMode	1.892	0.080	1.973
fcvarna	1.826	0.049	1.875
filterCV-methods	2.070	0.084	2.155
frcv	1.897	0.062	1.961
frvarna	1.862	0.048	1.918
integrateSignatures	4.429	0.547	4.984
ledge	14.864	0.490	15.375
msviper	81.504	11.106	92.777
msviperAnnot	8.888	0.530	9.549
msviperCombinatorial	180.282	18.477	209.008
msviperSynergy	151.737	21.056	172.886
plot.msviper	50.451	11.783	62.241
pruneRegulon	1.534	0.067	1.602
rowTtest-methods	2.890	0.077	2.967
scaleGroups	1.535	0.057	1.593
shadow	462.986	124.285	587.301
signatureDistance	6.835	0.289	7.124
ttestNull-methods	6.925	1.518	8.444
viper	6.761	0.793	7.555
viperSignature-methods	91.542	13.517	105.063