BioC 3.2: CHECK report for viper on zin1

Package: viper

Version: 1.6.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings viper_1.6.1.tar.gz

StartedAt: 2016-04-23 06:26:48 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 06:30:40 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 232.0 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_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/viper.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.6.1’
* 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 ... [200s/202s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
viperSignature-methods 37.515  0.072  38.236
bootstrapViper         22.536  0.112  22.676
shadow                 18.467  0.040  18.534
msviperSynergy         12.301  0.020  13.287
msviperCombinatorial   11.482  0.016  11.562
viperRPT               10.277  0.016  10.314
msviper                10.024  0.020  10.075
plot.msviper            9.538  0.012   9.699
viper                   9.386  0.004   9.424
bootstrapmsviper        7.312  0.011   7.332
ledge                   6.507  0.008   6.534
ttestNull-methods       6.209  0.024   6.231
bootstrapTtest-methods  5.587  0.036   5.618
* 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	0.179	0.000	0.178
aracne2regulon	3.215	0.036	3.301
aracne2regulon4cnv	3.144	0.020	3.170
bootstrapTtest-methods	5.587	0.036	5.618
bootstrapViper	22.536	0.112	22.676
bootstrapmsviper	7.312	0.011	7.332
distMode	1.190	0.008	1.201
fcvarna	1.191	0.000	1.193
filterCV-methods	1.322	0.008	1.347
frcv	1.304	0.000	1.304
frvarna	1.203	0.000	1.204
integrateSignatures	2.759	0.004	2.769
ledge	6.507	0.008	6.534
msviper	10.024	0.020	10.075
msviperAnnot	4.006	0.020	4.029
msviperClass	2.722	0.008	2.724
msviperCombinatorial	11.482	0.016	11.562
msviperSynergy	12.301	0.020	13.287
plot.msviper	9.538	0.012	9.699
pruneRegulon	1.327	0.008	1.333
rowTtest-methods	2.423	0.008	2.429
scaleGroups	1.287	0.004	1.287
shadow	18.467	0.040	18.534
signatureDistance	3.939	0.012	3.954
ttestNull-methods	6.209	0.024	6.231
viper	9.386	0.004	9.424
viperRPT	10.277	0.016	10.314
viperSignature-methods	37.515	0.072	38.236