BioC 3.2: CHECK report for viper on zin1

Package: viper

Version: 1.5.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings viper_1.5.2.tar.gz

StartedAt: 2015-08-24 04:39:37 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:55:09 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 931.7 seconds

RetCode: 0

Status:  OK

CheckDir: viper.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings viper_1.5.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/viper.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [2s/2s] 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 ... [15m/15m] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
shadow                 387.783  0.259 396.350
viperSignature-methods 167.171  1.042 169.499
bootstrapViper          67.327  0.112  69.777
msviperSynergy          61.599  0.307  62.099
msviperCombinatorial    56.668  0.180  56.939
msviper                 39.228  0.108  39.432
plot.msviper            37.873  0.084  38.056
ttestNull-methods        6.544  0.036   6.839
viperRPT                 6.505  0.008   6.551
bootstrapTtest-methods   6.366  0.004   6.375
ledge                    6.164  0.004   6.173
bootstrapmsviper         5.689  0.020   5.724
viper                    5.576  0.016   5.623
* 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
  ‘/home/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	0.173	0.005	0.180
aracne2regulon	3.527	0.044	3.671
aracne2regulon4cnv	3.197	0.015	3.253
bootstrapTtest-methods	6.366	0.004	6.375
bootstrapViper	67.327	0.112	69.777
bootstrapmsviper	5.689	0.020	5.724
distMode	1.198	0.000	1.197
fcvarna	1.281	0.004	1.285
filterCV-methods	1.245	0.004	1.258
frcv	1.172	0.000	1.174
frvarna	1.173	0.004	1.177
integrateSignatures	2.688	0.012	2.702
ledge	6.164	0.004	6.173
msviper	39.228	0.108	39.432
msviperAnnot	3.576	0.012	3.607
msviperClass	2.415	0.012	2.444
msviperCombinatorial	56.668	0.180	56.939
msviperSynergy	61.599	0.307	62.099
plot.msviper	37.873	0.084	38.056
pruneRegulon	1.235	0.008	1.244
rowTtest-methods	2.436	0.012	2.452
scaleGroups	1.329	0.012	1.339
shadow	387.783	0.259	396.350
signatureDistance	3.878	0.024	4.020
ttestNull-methods	6.544	0.036	6.839
viper	5.576	0.016	5.623
viperRPT	6.505	0.008	6.551
viperSignature-methods	167.171	1.042	169.499