BioC 3.1: CHECK report for viper on zin2

Package: viper

Version: 1.4.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings viper_1.4.0.tar.gz

StartedAt: 2015-10-09 06:16:04 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:31:02 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 897.8 seconds

RetCode: 0

Status:  OK

CheckDir: viper.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings viper_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.4.0’
* 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 ... [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 ... [14m/14m] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
shadow                 375.587  0.301 384.650
viperSignature-methods 160.494  0.863 161.398
bootstrapViper          64.487  0.100  64.550
msviperSynergy          62.173  0.368  62.639
msviperCombinatorial    56.352  0.376  56.796
msviper                 39.143  0.107  39.333
plot.msviper            38.179  0.140  38.356
ledge                    5.979  0.008   5.995
ttestNull-methods        5.820  0.064   5.880
viperRPT                 5.586  0.016   5.598
bootstrapTtest-methods   5.460  0.036   5.495
bootstrapmsviper         5.452  0.020   5.479
viper                    5.140  0.008   5.157
* 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-3.1-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	0.158	0.009	0.166
aracne2regulon	3.121	0.032	3.181
bootstrapTtest-methods	5.460	0.036	5.495
bootstrapViper	64.487	0.100	64.550
bootstrapmsviper	5.452	0.020	5.479
distMode	1.170	0.004	1.173
fcvarna	1.150	0.004	1.154
filterCV-methods	1.216	0.000	1.214
frcv	1.143	0.004	1.147
frvarna	1.142	0.008	1.149
integrateSignatures	2.563	0.016	2.582
ledge	5.979	0.008	5.995
msviper	39.143	0.107	39.333
msviperAnnot	3.665	0.012	3.679
msviperClass	2.503	0.016	2.522
msviperCombinatorial	56.352	0.376	56.796
msviperSynergy	62.173	0.368	62.639
plot.msviper	38.179	0.140	38.356
pruneRegulon	1.360	0.008	1.369
rowTtest-methods	2.665	0.008	2.676
scaleGroups	1.380	0.008	1.388
shadow	375.587	0.301	384.650
signatureDistance	3.460	0.016	3.473
ttestNull-methods	5.820	0.064	5.880
viper	5.140	0.008	5.157
viperRPT	5.586	0.016	5.598
viperSignature-methods	160.494	0.863	161.398