BioC 3.3: CHECK report for viper on morelia

Package: viper

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings viper_1.7.0.tar.gz

StartedAt: 2015-10-22 12:22:04 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 12:41:28 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 1164.1 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/viper.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.7.0’
* 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 ... [2s/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 ... [19m/19m] OK
Examples with CPU or elapsed time > 5s
                          user  system elapsed
shadow                 368.303 107.391 478.838
viperSignature-methods 171.987  40.552 212.956
msviperSynergy          80.888  15.507  97.120
msviperCombinatorial    68.618  12.815  81.738
plot.msviper            52.563  12.623  65.585
bootstrapViper          55.051   5.865  61.017
msviper                 44.993  10.855  55.949
viper                    8.860   1.655  10.659
viperRPT                 8.165   1.492   9.664
bootstrapmsviper         6.261   1.166   7.456
ttestNull-methods        5.898   1.241   7.321
ledge                    6.208   0.410   6.637
bootstrapTtest-methods   4.475   0.545   5.033
* 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-3.3-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	0.123	0.006	0.129
aracne2regulon	2.444	0.234	2.736
aracne2regulon4cnv	2.302	0.271	2.588
bootstrapTtest-methods	4.475	0.545	5.033
bootstrapViper	55.051	5.865	61.017
bootstrapmsviper	6.261	1.166	7.456
distMode	1.069	0.028	1.099
fcvarna	1.076	0.022	1.098
filterCV-methods	1.179	0.039	1.220
frcv	1.092	0.022	1.115
frvarna	1.087	0.018	1.106
integrateSignatures	2.176	0.312	2.506
ledge	6.208	0.410	6.637
msviper	44.993	10.855	55.949
msviperAnnot	2.941	0.224	3.172
msviperClass	2.181	0.113	2.297
msviperCombinatorial	68.618	12.815	81.738
msviperSynergy	80.888	15.507	97.120
plot.msviper	52.563	12.623	65.585
pruneRegulon	1.216	0.033	1.251
rowTtest-methods	2.462	0.049	2.535
scaleGroups	1.245	0.030	1.276
shadow	368.303	107.391	478.838
signatureDistance	3.955	0.255	4.246
ttestNull-methods	5.898	1.241	7.321
viper	8.860	1.655	10.659
viperRPT	8.165	1.492	9.664
viperSignature-methods	171.987	40.552	212.956