BioC 3.2: CHECK report for viper on oaxaca

Package: viper

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings viper_1.6.1.tar.gz

StartedAt: 2016-04-23 05:12:20 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:18:07 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 347.3 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_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/viper.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.6.1’
* 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 ... [289s/305s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
viperSignature-methods 50.983  7.150  59.623
bootstrapViper         27.394  2.833  33.713
shadow                 23.337  3.527  26.900
msviperSynergy         16.409  2.291  19.753
msviperCombinatorial   15.553  2.085  19.880
viperRPT               15.716  1.895  17.622
viper                  14.402  1.861  16.274
msviper                13.609  2.084  17.747
plot.msviper           11.458  1.679  13.148
bootstrapmsviper        9.506  1.723  11.990
ttestNull-methods       8.974  1.095  10.080
ledge                   8.732  0.486  10.124
bootstrapTtest-methods  6.272  0.777   7.545
msviperAnnot            4.607  0.274   5.157
* 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	0.224	0.009	0.268
aracne2regulon	3.568	0.297	4.074
aracne2regulon4cnv	3.149	0.264	3.415
bootstrapTtest-methods	6.272	0.777	7.545
bootstrapViper	27.394	2.833	33.713
bootstrapmsviper	9.506	1.723	11.990
distMode	1.395	0.044	1.559
fcvarna	1.364	0.036	1.554
filterCV-methods	1.493	0.058	1.957
frcv	1.394	0.034	1.609
frvarna	1.400	0.036	1.752
integrateSignatures	2.988	0.472	3.916
ledge	8.732	0.486	10.124
msviper	13.609	2.084	17.747
msviperAnnot	4.607	0.274	5.157
msviperClass	3.315	0.155	3.899
msviperCombinatorial	15.553	2.085	19.880
msviperSynergy	16.409	2.291	19.753
plot.msviper	11.458	1.679	13.148
pruneRegulon	1.334	0.037	1.381
rowTtest-methods	2.625	0.065	2.693
scaleGroups	1.356	0.049	1.404
shadow	23.337	3.527	26.900
signatureDistance	3.989	0.221	4.212
ttestNull-methods	8.974	1.095	10.080
viper	14.402	1.861	16.274
viperRPT	15.716	1.895	17.622
viperSignature-methods	50.983	7.150	59.623