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BioC 3.5: CHECK report for CausalR on tokay2

This page was generated on 2017-08-16 13:24:37 -0400 (Wed, 16 Aug 2017).

Package 178/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CausalR 1.8.0
Glyn Bradley , Steven Barrett
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CausalR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CausalR
Version: 1.8.0
Command: rm -rf CausalR.buildbin-libdir CausalR.Rcheck && mkdir CausalR.buildbin-libdir CausalR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CausalR.buildbin-libdir CausalR_1.8.0.tar.gz >CausalR.Rcheck\00install.out 2>&1 && cp CausalR.Rcheck\00install.out CausalR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CausalR.buildbin-libdir --install="check:CausalR-install.out" --force-multiarch --no-vignettes --timings CausalR_1.8.0.tar.gz
StartedAt: 2017-08-15 22:31:40 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:34:04 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 143.5 seconds
RetCode: 0
Status:  OK  
CheckDir: CausalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CausalR.buildbin-libdir CausalR.Rcheck && mkdir CausalR.buildbin-libdir CausalR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CausalR.buildbin-libdir CausalR_1.8.0.tar.gz >CausalR.Rcheck\00install.out 2>&1 && cp CausalR.Rcheck\00install.out CausalR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CausalR.buildbin-libdir --install="check:CausalR-install.out" --force-multiarch --no-vignettes --timings CausalR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CausalR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CausalR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CausalR' 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 'CausalR' 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/CausalR.Rcheck/00check.log'
for details.


CausalR.Rcheck/00install.out:


install for i386

* installing *source* package 'CausalR' ...
** R
** 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 'CausalR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CausalR' as CausalR_1.8.0.zip
* DONE (CausalR)

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

nameusersystemelapsed
AnalysePredictionsList0.080.000.08
CalculateEnrichmentPValue000
CalculateSignificance0.280.000.28
CalculateSignificanceUsingCubicAlgorithm0.070.000.06
CalculateSignificanceUsingCubicAlgorithm1b0.040.000.05
CalculateSignificanceUsingQuarticAlgorithm0.050.000.05
CompareHypothesis0.000.000.08
CreateCCG0.090.000.09
CreateCG0.050.000.05
GetNodeName0.020.000.01
GetNumberOfPositiveAndNegativeEntries000
GetShortestPathsFromCCG0.010.000.02
MakePredictions0.100.000.09
MakePredictionsFromCCG0.010.000.02
MakePredictionsFromCG0.300.000.29
PlotGraphWithNodeNames0.080.010.10
RankTheHypotheses0.200.031.47
ReadExperimentalData0.060.000.06
ScoreHypothesis0.050.000.05
WriteAllExplainedNodesToSifFile0.280.002.68
WriteExplainedNodesToSifFile0.050.020.07
runSCANR0.530.022.78

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

nameusersystemelapsed
AnalysePredictionsList0.070.010.10
CalculateEnrichmentPValue0.020.000.01
CalculateSignificance0.340.000.34
CalculateSignificanceUsingCubicAlgorithm0.080.000.08
CalculateSignificanceUsingCubicAlgorithm1b0.080.000.08
CalculateSignificanceUsingQuarticAlgorithm0.090.000.09
CompareHypothesis0.030.000.05
CreateCCG0.130.000.12
CreateCG0.040.000.05
GetNodeName0.020.000.02
GetNumberOfPositiveAndNegativeEntries000
GetShortestPathsFromCCG0.020.000.07
MakePredictions0.150.000.16
MakePredictionsFromCCG0.020.000.02
MakePredictionsFromCG0.330.000.32
PlotGraphWithNodeNames0.140.000.18
RankTheHypotheses0.360.032.36
ReadExperimentalData0.060.000.06
ScoreHypothesis0.080.000.08
WriteAllExplainedNodesToSifFile0.390.002.99
WriteExplainedNodesToSifFile0.080.000.07
runSCANR0.780.034.02