BioC 3.2: CHECK report for viper on perceval

Package: viper

Version: 1.5.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings viper_1.5.2.tar.gz

StartedAt: 2015-08-24 06:06:08 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 06:36:41 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 1833.3 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_1.5.2.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 (2015-08-14 r69078)
* 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 ‘1.5.2’
* 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 ... [4s/4s] 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                 553.936 194.467 748.690
viperSignature-methods 249.968  62.168 312.152
bootstrapViper         166.617  15.297 182.078
msviperSynergy         113.868  25.023 139.826
msviperCombinatorial   104.919  21.984 127.114
plot.msviper            65.784  21.160  87.946
msviper                 67.344  19.122  86.495
bootstrapmsviper         8.877   2.066  10.946
viperRPT                 9.009   1.455  10.464
viper                    8.066   1.509   9.576
ledge                    8.686   0.875   9.562
ttestNull-methods        6.928   2.078   9.008
bootstrapTtest-methods   6.593   1.562   8.166
signatureDistance        5.208   0.345   5.554
msviperAnnot             4.879   0.466   5.351
* 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	0.243	0.017	0.259
aracne2regulon	4.242	0.663	4.996
aracne2regulon4cnv	3.770	0.508	4.656
bootstrapTtest-methods	6.593	1.562	8.166
bootstrapViper	166.617	15.297	182.078
bootstrapmsviper	8.877	2.066	10.946
distMode	1.210	0.067	1.278
fcvarna	1.164	0.045	1.209
filterCV-methods	1.309	0.086	1.396
frcv	1.227	0.062	1.290
frvarna	1.166	0.035	1.202
integrateSignatures	3.306	0.810	4.117
ledge	8.686	0.875	9.562
msviper	67.344	19.122	86.495
msviperAnnot	4.879	0.466	5.351
msviperClass	3.041	0.228	3.278
msviperCombinatorial	104.919	21.984	127.114
msviperSynergy	113.868	25.023	139.826
plot.msviper	65.784	21.160	87.946
pruneRegulon	1.247	0.086	1.352
rowTtest-methods	2.355	0.101	2.492
scaleGroups	1.228	0.067	1.302
shadow	553.936	194.467	748.690
signatureDistance	5.208	0.345	5.554
ttestNull-methods	6.928	2.078	9.008
viper	8.066	1.509	9.576
viperRPT	9.009	1.455	10.464
viperSignature-methods	249.968	62.168	312.152