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BioC 3.1: CHECK report for DriverNet on moscato2

This page was generated on 2015-10-09 09:30:04 -0700 (Fri, 09 Oct 2015).

Package 273/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DriverNet 1.8.0
Jiarui Ding
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/DriverNet
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DriverNet
Version: 1.8.0
Command: rm -rf DriverNet.buildbin-libdir DriverNet.Rcheck && mkdir DriverNet.buildbin-libdir DriverNet.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DriverNet.buildbin-libdir DriverNet_1.8.0.tar.gz >DriverNet.Rcheck\00install.out 2>&1 && cp DriverNet.Rcheck\00install.out DriverNet-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=DriverNet.buildbin-libdir --install="check:DriverNet-install.out" --force-multiarch --no-vignettes --timings DriverNet_1.8.0.tar.gz
StartedAt: 2015-10-09 01:21:00 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:23:19 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 138.9 seconds
RetCode: 0
Status:  OK  
CheckDir: DriverNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DriverNet.buildbin-libdir DriverNet.Rcheck && mkdir DriverNet.buildbin-libdir DriverNet.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DriverNet.buildbin-libdir DriverNet_1.8.0.tar.gz >DriverNet.Rcheck\00install.out 2>&1 && cp DriverNet.Rcheck\00install.out DriverNet-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=DriverNet.buildbin-libdir --install="check:DriverNet-install.out" --force-multiarch --no-vignettes --timings DriverNet_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/DriverNet.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DriverNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DriverNet' version '1.8.0'
* 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 whether package 'DriverNet' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [47s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DriverNet-package       23.48   0.19   23.67
computeDrivers          15.30   0.11   15.41
computeRandomizedResult  6.46   0.02    6.48
** running examples for arch 'x64' ... [64s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DriverNet-package       30.39   0.19   30.57
computeDrivers          22.26   0.29   22.54
computeRandomizedResult  9.38   0.03    9.42
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/DriverNet.Rcheck/00check.log'
for details.


DriverNet.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'DriverNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DriverNet' as DriverNet_1.8.0.zip
* DONE (DriverNet)

DriverNet.Rcheck/examples_i386/DriverNet-Ex.timings:

nameusersystemelapsed
DriverNet-package23.48 0.1923.67
DriverNetResult-class0.010.020.03
actualEvents0.060.010.08
computeDrivers15.30 0.1115.41
computeRandomizedResult6.460.026.48
drivers0.020.060.08
getPatientOutlierMatrix0.190.030.22
preprocessMatrices0.170.030.20
resultSummary0.230.030.26
sampleDriversList0.020.020.03
sampleGeneNames0.010.010.04
sampleInfluenceGraph0.160.020.17
samplePatientExpressionMatrix0.110.000.11
samplePatientMutationMatrix0.010.000.01
samplePatientOutlierMatrix0.000.010.02
sampleRandomDriversResult0.000.020.01
totalEvents0.030.000.03

DriverNet.Rcheck/examples_x64/DriverNet-Ex.timings:

nameusersystemelapsed
DriverNet-package30.39 0.1930.57
DriverNetResult-class0.010.010.03
actualEvents0.030.030.07
computeDrivers22.26 0.2922.54
computeRandomizedResult9.380.039.42
drivers0.020.040.06
getPatientOutlierMatrix0.200.020.22
preprocessMatrices0.170.010.19
resultSummary0.200.070.27
sampleDriversList0.020.010.03
sampleGeneNames0.030.000.03
sampleInfluenceGraph0.110.020.12
samplePatientExpressionMatrix0.080.010.10
samplePatientMutationMatrix0.000.020.01
samplePatientOutlierMatrix0.010.000.02
sampleRandomDriversResult000
totalEvents0.000.030.03