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BioC 3.0: CHECK report for DriverNet on zin1

This page was generated on 2015-04-10 09:40:25 -0700 (Fri, 10 Apr 2015).

Package 253/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DriverNet 1.6.0
Jiarui Ding
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DriverNet
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: DriverNet
Version: 1.6.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DriverNet_1.6.0.tar.gz
StartedAt: 2015-04-09 23:26:08 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:27:12 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 63.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DriverNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DriverNet_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/DriverNet.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DriverNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DriverNet’ 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 ‘DriverNet’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DriverNet-package       24.169  0.056  24.371
computeDrivers          16.093  0.056  16.185
computeRandomizedResult  8.121  0.012   8.184
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/DriverNet.Rcheck/00check.log’
for details.

DriverNet.Rcheck/00install.out:

* installing *source* package ‘DriverNet’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DriverNet)

DriverNet.Rcheck/DriverNet-Ex.timings:

nameusersystemelapsed
DriverNet-package24.169 0.05624.371
DriverNetResult-class0.0120.0040.017
actualEvents0.0520.0240.076
computeDrivers16.093 0.05616.185
computeRandomizedResult8.1210.0128.184
drivers0.0720.0120.087
getPatientOutlierMatrix0.2120.0000.213
preprocessMatrices0.1760.0080.182
resultSummary0.1880.0160.205
sampleDriversList0.0120.0080.021
sampleGeneNames0.0240.0000.026
sampleInfluenceGraph0.1440.0000.145
samplePatientExpressionMatrix0.0920.0000.091
samplePatientMutationMatrix0.0120.0000.012
samplePatientOutlierMatrix0.0120.0000.013
sampleRandomDriversResult0.0000.0000.002
totalEvents0.0200.0000.022