BioC 3.3: CHECK report for viper on linux2.bioconductor.org

Package: viper

Version: 1.7.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings viper_1.7.0.tar.gz

StartedAt: 2015-10-27 08:52:43 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:07:44 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 900.6 seconds

RetCode: 0

Status:  OK

CheckDir: viper.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings viper_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/viper.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.7.0’
* 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 ... [15m/15m] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
shadow                 327.543  0.820 328.842
viperSignature-methods 178.007  1.739 179.783
msviperSynergy          73.145  0.495  73.705
msviperCombinatorial    65.057  0.552  65.663
plot.msviper            54.229  0.204  54.464
bootstrapViper          53.538  0.192  53.775
msviper                 50.427  0.360  51.826
viperRPT                 7.368  0.020   7.388
viper                    6.661  0.064   6.725
ledge                    6.044  0.004   6.056
bootstrapmsviper         5.865  0.016   5.886
ttestNull-methods        5.144  0.028   5.173
* 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-3.3-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	0.129	0.004	0.133
aracne2regulon	2.628	0.040	2.672
aracne2regulon4cnv	2.692	0.020	2.712
bootstrapTtest-methods	4.915	0.019	4.940
bootstrapViper	53.538	0.192	53.775
bootstrapmsviper	5.865	0.016	5.886
distMode	1.101	0.012	1.114
fcvarna	1.105	0.000	1.105
filterCV-methods	1.142	0.000	1.143
frcv	1.086	0.000	1.087
frvarna	1.09	0.00	1.09
integrateSignatures	2.332	0.008	2.341
ledge	6.044	0.004	6.056
msviper	50.427	0.360	51.826
msviperAnnot	3.415	0.000	3.418
msviperClass	2.983	0.004	2.987
msviperCombinatorial	65.057	0.552	65.663
msviperSynergy	73.145	0.495	73.705
plot.msviper	54.229	0.204	54.464
pruneRegulon	1.124	0.012	1.137
rowTtest-methods	2.486	0.016	2.503
scaleGroups	1.616	0.012	1.624
shadow	327.543	0.820	328.842
signatureDistance	3.220	0.016	3.236
ttestNull-methods	5.144	0.028	5.173
viper	6.661	0.064	6.725
viperRPT	7.368	0.020	7.388
viperSignature-methods	178.007	1.739	179.783