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: 2015-10-27 13:14:51 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 10:45:17 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 1826.1 seconds

RetCode: 0

Status:  OK

CheckDir: viper.Rcheck

Warnings: 0

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


* 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 ... [4s/5s] 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                 570.796 146.137 716.959
viperSignature-methods 278.469  56.003 334.485
msviperSynergy         132.319  24.388 156.878
msviperCombinatorial   122.581  22.211 144.881
msviper                 86.161  19.428 105.594
bootstrapViper          93.650  11.210 105.037
plot.msviper            83.821  19.906 104.546
viperRPT                13.343   2.311  15.654
viper                   12.280   2.242  14.522
bootstrapmsviper        10.151   2.139  12.291
ledge                    8.965   0.629   9.595
ttestNull-methods        6.993   1.510   8.503
bootstrapTtest-methods   6.875   1.035   7.911
msviperAnnot             4.858   0.269   5.130
signatureDistance        4.657   0.344   5.001
* 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	0.223	0.012	0.236
aracne2regulon	4.169	0.428	4.742
aracne2regulon4cnv	3.880	0.468	4.348
bootstrapTtest-methods	6.875	1.035	7.911
bootstrapViper	93.650	11.210	105.037
bootstrapmsviper	10.151	2.139	12.291
distMode	1.475	0.051	1.527
fcvarna	1.446	0.037	1.484
filterCV-methods	1.566	0.064	1.630
frcv	1.441	0.035	1.477
frvarna	1.430	0.036	1.467
integrateSignatures	3.170	0.499	3.669
ledge	8.965	0.629	9.595
msviper	86.161	19.428	105.594
msviperAnnot	4.858	0.269	5.130
msviperClass	3.188	0.153	3.348
msviperCombinatorial	122.581	22.211	144.881
msviperSynergy	132.319	24.388	156.878
plot.msviper	83.821	19.906	104.546
pruneRegulon	1.436	0.038	1.476
rowTtest-methods	2.844	0.063	2.908
scaleGroups	1.495	0.046	1.542
shadow	570.796	146.137	716.959
signatureDistance	4.657	0.344	5.001
ttestNull-methods	6.993	1.510	8.503
viper	12.280	2.242	14.522
viperRPT	13.343	2.311	15.654
viperSignature-methods	278.469	56.003	334.485