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BioC 3.1: CHECK report for viper on zin2

This page was generated on 2015-10-09 09:26:01 -0700 (Fri, 09 Oct 2015).

Package 1009/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
viper 1.4.0
Mariano J Alvarez
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/viper
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


viper.Rcheck/00install.out:

* 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)

viper.Rcheck/viper-Ex.timings:

nameusersystemelapsed
approxk2d0.1580.0090.166
aracne2regulon3.1210.0323.181
bootstrapTtest-methods5.4600.0365.495
bootstrapViper64.487 0.10064.550
bootstrapmsviper5.4520.0205.479
distMode1.1700.0041.173
fcvarna1.1500.0041.154
filterCV-methods1.2160.0001.214
frcv1.1430.0041.147
frvarna1.1420.0081.149
integrateSignatures2.5630.0162.582
ledge5.9790.0085.995
msviper39.143 0.10739.333
msviperAnnot3.6650.0123.679
msviperClass2.5030.0162.522
msviperCombinatorial56.352 0.37656.796
msviperSynergy62.173 0.36862.639
plot.msviper38.179 0.14038.356
pruneRegulon1.3600.0081.369
rowTtest-methods2.6650.0082.676
scaleGroups1.3800.0081.388
shadow375.587 0.301384.650
signatureDistance3.4600.0163.473
ttestNull-methods5.8200.0645.880
viper5.1400.0085.157
viperRPT5.5860.0165.598
viperSignature-methods160.494 0.863161.398