BioC 3.2: CHECK report for viper on perceval

Package: viper

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings viper_1.6.0.tar.gz

StartedAt: 2015-11-10 10:29:42 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 11:00:01 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 1818.9 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 viper_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/viper.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.6.0’
* 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 ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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 ... [30m/30m] OK
Examples with CPU or elapsed time > 5s
                          user  system elapsed
shadow                 583.274 149.283 732.622
viperSignature-methods 283.214  57.462 340.689
msviperSynergy         125.988  23.122 149.126
msviperCombinatorial   118.088  20.800 138.895
msviper                 84.166  18.475 102.645
bootstrapViper          90.235  11.114 101.354
plot.msviper            81.846  19.300 101.235
viperRPT                13.565   2.315  15.881
viper                   12.659   2.353  15.013
bootstrapmsviper        10.290   1.944  12.236
ledge                    8.517   0.500   9.019
ttestNull-methods        6.941   1.542   8.482
bootstrapTtest-methods   6.541   0.886   7.679
signatureDistance        4.793   0.328   5.121
msviperAnnot             4.683   0.278   5.015
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/viper.Rcheck/00check.log’
for details.

* 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
approxk2d	0.217	0.012	0.228
aracne2regulon	4.002	0.415	4.471
aracne2regulon4cnv	3.728	0.310	4.064
bootstrapTtest-methods	6.541	0.886	7.679
bootstrapViper	90.235	11.114	101.354
bootstrapmsviper	10.290	1.944	12.236
distMode	1.401	0.045	1.448
fcvarna	1.351	0.032	1.384
filterCV-methods	1.472	0.053	1.526
frcv	1.369	0.031	1.400
frvarna	1.371	0.032	1.402
integrateSignatures	2.978	0.470	3.448
ledge	8.517	0.500	9.019
msviper	84.166	18.475	102.645
msviperAnnot	4.683	0.278	5.015
msviperClass	3.035	0.137	3.174
msviperCombinatorial	118.088	20.800	138.895
msviperSynergy	125.988	23.122	149.126
plot.msviper	81.846	19.300	101.235
pruneRegulon	1.499	0.047	1.546
rowTtest-methods	2.893	0.076	2.970
scaleGroups	1.536	0.063	1.600
shadow	583.274	149.283	732.622
signatureDistance	4.793	0.328	5.121
ttestNull-methods	6.941	1.542	8.482
viper	12.659	2.353	15.013
viperRPT	13.565	2.315	15.881
viperSignature-methods	283.214	57.462	340.689