BioC 3.1: CHECK report for viper on morelia

Package: viper

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings viper_1.4.0.tar.gz

StartedAt: 2015-10-09 07:10:49 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 07:29:31 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 1121.7 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.4.0’
* 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/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 ... [18m/18m] OK
Examples with CPU or elapsed time > 5s
                          user  system elapsed
shadow                 386.279 119.344 505.968
viperSignature-methods 140.176  42.250 182.423
msviperSynergy          71.342  14.707  86.115
msviperCombinatorial    62.325  12.437  74.855
bootstrapViper          58.446   8.544  67.002
plot.msviper            43.493  10.802  54.410
msviper                 37.302   9.141  46.449
ledge                    6.380   0.453   6.833
viperRPT                 5.754   0.864   6.619
bootstrapmsviper         5.447   0.891   6.339
ttestNull-methods        4.842   1.155   6.017
viper                    4.762   0.822   5.584
bootstrapTtest-methods   4.626   0.900   8.872
* 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-3.1-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	0.145	0.008	0.152
aracne2regulon	2.823	0.346	3.236
bootstrapTtest-methods	4.626	0.900	8.872
bootstrapViper	58.446	8.544	67.002
bootstrapmsviper	5.447	0.891	6.339
distMode	1.153	0.042	1.197
fcvarna	1.054	0.020	1.074
filterCV-methods	1.268	0.064	1.332
frcv	1.246	0.025	1.271
frvarna	1.286	0.166	1.452
integrateSignatures	2.421	0.322	2.743
ledge	6.380	0.453	6.833
msviper	37.302	9.141	46.449
msviperAnnot	3.403	0.351	3.758
msviperClass	2.191	0.263	2.456
msviperCombinatorial	62.325	12.437	74.855
msviperSynergy	71.342	14.707	86.115
plot.msviper	43.493	10.802	54.410
pruneRegulon	1.343	0.047	1.391
rowTtest-methods	2.504	0.145	2.650
scaleGroups	1.300	0.126	1.427
shadow	386.279	119.344	505.968
signatureDistance	3.457	0.477	3.935
ttestNull-methods	4.842	1.155	6.017
viper	4.762	0.822	5.584
viperRPT	5.754	0.864	6.619
viperSignature-methods	140.176	42.250	182.423