BioC 3.1: CHECK report for viper on petty

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 02:31:52 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:58:36 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 1603.7 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 Patched (2015-08-14 r69078)
* 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 ‘1.4.0’
* 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 ... [5s/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 ... [26m/26m] OK
Examples with CPU or elapsed time > 5s
                          user  system elapsed
shadow                 516.395 135.521 652.029
viperSignature-methods 208.296  57.833 266.139
msviperCombinatorial   112.787  18.178 131.372
bootstrapViper         114.645  12.929 127.617
msviperSynergy         100.895  18.042 118.961
msviper                 65.305  15.077  80.519
plot.msviper            50.180  12.209  62.617
ledge                   11.471   0.631  12.107
bootstrapmsviper         9.698   1.604  11.362
bootstrapTtest-methods   8.592   1.354   9.952
viperRPT                 8.368   1.106   9.475
ttestNull-methods        7.120   1.469   8.588
viper                    7.344   1.054   8.399
msviperAnnot             6.233   0.337   6.577
aracne2regulon           5.283   0.567   5.878
signatureDistance        4.926   0.342   5.267
msviperClass             3.646   0.167   7.266
* 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	0.278	0.017	0.295
aracne2regulon	5.283	0.567	5.878
bootstrapTtest-methods	8.592	1.354	9.952
bootstrapViper	114.645	12.929	127.617
bootstrapmsviper	9.698	1.604	11.362
distMode	1.699	0.060	1.763
fcvarna	1.733	0.051	1.785
filterCV-methods	1.911	0.082	1.995
frcv	1.636	0.050	1.691
frvarna	1.736	0.051	1.788
integrateSignatures	3.923	0.578	4.504
ledge	11.471	0.631	12.107
msviper	65.305	15.077	80.519
msviperAnnot	6.233	0.337	6.577
msviperClass	3.646	0.167	7.266
msviperCombinatorial	112.787	18.178	131.372
msviperSynergy	100.895	18.042	118.961
plot.msviper	50.180	12.209	62.617
pruneRegulon	1.404	0.038	1.442
rowTtest-methods	2.706	0.062	2.767
scaleGroups	1.431	0.046	1.477
shadow	516.395	135.521	652.029
signatureDistance	4.926	0.342	5.267
ttestNull-methods	7.120	1.469	8.588
viper	7.344	1.054	8.399
viperRPT	8.368	1.106	9.475
viperSignature-methods	208.296	57.833	266.139