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BioC 3.2: CHECK report for DriverNet on zin1

This page was generated on 2015-08-24 10:49:01 -0700 (Mon, 24 Aug 2015).

Package 282/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DriverNet 1.9.0
Jiarui Ding
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DriverNet
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DriverNet
Version: 1.9.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DriverNet_1.9.0.tar.gz
StartedAt: 2015-08-23 23:26:39 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 23:27:38 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 59.8 seconds
RetCode: 0
Status:  OK 
CheckDir: DriverNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DriverNet_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/DriverNet.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 ‘DriverNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DriverNet’ version ‘1.9.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DriverNet-package       23.591  0.092  23.673
computeDrivers          15.204  0.048  15.266
computeRandomizedResult  7.725  0.004   7.726
* 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/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-package23.591 0.09223.673
DriverNetResult-class0.0140.0040.017
actualEvents0.0410.0320.073
computeDrivers15.204 0.04815.266
computeRandomizedResult7.7250.0047.726
drivers0.0380.0280.066
getPatientOutlierMatrix0.180.000.18
preprocessMatrices0.1630.0000.163
resultSummary0.1740.0120.186
sampleDriversList0.0110.0040.015
sampleGeneNames0.0220.0000.022
sampleInfluenceGraph0.1110.0080.120
samplePatientExpressionMatrix0.0780.0000.078
samplePatientMutationMatrix0.0100.0000.011
samplePatientOutlierMatrix0.0140.0000.013
sampleRandomDriversResult0.0020.0000.001
totalEvents0.0130.0040.017