BioC 3.2: CHECK report for viper on linux1.bioconductor.org

Package: viper

Version: 1.6.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings viper_1.6.0.tar.gz

StartedAt: 2015-10-27 09:00:50 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:18:43 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 1073.7 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_1.6.0.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 ‘1.6.0’
* 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/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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17m/17m] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
shadow                 409.445  1.139 411.429
viperSignature-methods 188.319  1.652 190.025
msviperSynergy          90.315  0.635  91.047
msviperCombinatorial    79.342  0.284  79.690
plot.msviper            65.716  0.220  65.999
msviper                 65.260  0.192  66.771
bootstrapViper          62.154  0.196  62.438
viperRPT                 8.598  0.000   8.600
bootstrapmsviper         8.498  0.012   8.521
viper                    7.832  0.040   7.873
ledge                    7.091  0.008   7.100
bootstrapTtest-methods   6.354  0.032   6.399
ttestNull-methods        5.221  0.024   5.246
* 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	0.133	0.008	0.140
aracne2regulon	3.313	0.040	3.361
aracne2regulon4cnv	2.761	0.020	2.782
bootstrapTtest-methods	6.354	0.032	6.399
bootstrapViper	62.154	0.196	62.438
bootstrapmsviper	8.498	0.012	8.521
distMode	1.447	0.008	1.459
fcvarna	1.439	0.000	1.439
filterCV-methods	1.583	0.004	1.586
frcv	1.222	0.004	1.226
frvarna	1.080	0.012	1.092
integrateSignatures	3.039	0.000	3.039
ledge	7.091	0.008	7.100
msviper	65.260	0.192	66.771
msviperAnnot	4.026	0.012	4.037
msviperClass	2.611	0.004	2.617
msviperCombinatorial	79.342	0.284	79.690
msviperSynergy	90.315	0.635	91.047
plot.msviper	65.716	0.220	65.999
pruneRegulon	1.364	0.004	1.368
rowTtest-methods	2.869	0.016	2.889
scaleGroups	1.466	0.012	1.478
shadow	409.445	1.139	411.429
signatureDistance	3.346	0.000	3.346
ttestNull-methods	5.221	0.024	5.246
viper	7.832	0.040	7.873
viperRPT	8.598	0.000	8.600
viperSignature-methods	188.319	1.652	190.025