BioC 3.2: CHECK report for viper on oaxaca

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 04:36:48 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:56:55 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 1207.2 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 (2015-08-14)
* 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 ‘1.5.2’
* 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 ... [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 ... [19m/19m] OK
Examples with CPU or elapsed time > 5s
                          user  system elapsed
shadow                 411.879 103.456 517.686
viperSignature-methods 129.881  27.520 157.399
msviperSynergy          86.496  13.897 100.953
bootstrapViper          79.087   8.198  95.603
msviperCombinatorial    73.911  11.237  85.196
plot.msviper            51.381  10.746  62.893
msviper                 46.639   8.847  55.511
bootstrapmsviper         7.050   1.064   8.156
ledge                    7.580   0.459   8.040
bootstrapTtest-methods   6.372   0.844   8.456
viperRPT                 5.135   0.623   5.758
ttestNull-methods        4.807   0.895   5.701
viper                    4.564   0.634   5.197
msviperAnnot             4.058   0.255  10.448
* 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	0.191	0.008	0.200
aracne2regulon	3.741	0.311	4.890
aracne2regulon4cnv	3.488	0.284	4.458
bootstrapTtest-methods	6.372	0.844	8.456
bootstrapViper	79.087	8.198	95.603
bootstrapmsviper	7.050	1.064	8.156
distMode	1.342	0.038	1.381
fcvarna	1.344	0.029	1.374
filterCV-methods	1.420	0.047	1.470
frcv	1.336	0.035	1.372
frvarna	1.359	0.024	1.383
integrateSignatures	2.981	0.430	3.417
ledge	7.580	0.459	8.040
msviper	46.639	8.847	55.511
msviperAnnot	4.058	0.255	10.448
msviperClass	2.876	0.139	3.017
msviperCombinatorial	73.911	11.237	85.196
msviperSynergy	86.496	13.897	100.953
plot.msviper	51.381	10.746	62.893
pruneRegulon	1.453	0.042	1.498
rowTtest-methods	2.784	0.060	2.852
scaleGroups	1.442	0.046	1.492
shadow	411.879	103.456	517.686
signatureDistance	3.093	0.167	3.261
ttestNull-methods	4.807	0.895	5.701
viper	4.564	0.634	5.197
viperRPT	5.135	0.623	5.758
viperSignature-methods	129.881	27.520	157.399