BioC 3.3: CHECK report for lpNet on windows2.bioconductor.org

Package: lpNet

Version: 2.3.0

Command: rm -rf lpNet.buildbin-libdir lpNet.Rcheck && mkdir lpNet.buildbin-libdir lpNet.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lpNet.buildbin-libdir lpNet_2.3.0.tar.gz >lpNet.Rcheck\00install.out 2>&1 && cp lpNet.Rcheck\00install.out lpNet-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=lpNet.buildbin-libdir --install="check:lpNet-install.out" --force-multiarch --no-vignettes --timings lpNet_2.3.0.tar.gz

StartedAt: 2015-10-27 03:39:02 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:39:54 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 51.2 seconds

RetCode: 0

Status:  OK

CheckDir: lpNet.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf lpNet.buildbin-libdir lpNet.Rcheck && mkdir lpNet.buildbin-libdir lpNet.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lpNet.buildbin-libdir lpNet_2.3.0.tar.gz >lpNet.Rcheck\00install.out 2>&1 && cp lpNet.Rcheck\00install.out lpNet-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=lpNet.buildbin-libdir --install="check:lpNet-install.out" --force-multiarch --no-vignettes --timings lpNet_2.3.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/lpNet.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lpNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lpNet' version '2.3.0'
* 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 'lpNet' 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runitCalcActivation.R' [0s]
  Running 'runitCalcPredictionKfoldCV.R' [0s]
  Running 'runitCalcPredictionKfoldCV_timeSeries.R' [0s]
  Running 'runitCalcPredictionLOOCV.R' [0s]
  Running 'runitCalcPredictionLOOCV_timeSeries.R' [0s]
  Running 'runitCalcRangeLambda.R' [0s]
  Running 'runitDoILP.R' [0s]
  Running 'runitDoILP_timeSeries.R' [0s]
  Running 'runitGenerateTimeSeriesNetStates.R' [0s]
  Running 'runitGetAdja.R' [0s]
  Running 'runitGetBaseline.R' [0s]
  Running 'runitGetEdgeAnnot.R' [0s]
  Running 'runitGetObsMat.R' [0s]
  Running 'runitGetSampleAdja.R' [0s]
  Running 'runitGetSampleAdjaMAD.R' [0s]
  Running 'runitKfoldCV.R' [0s]
  Running 'runitKfoldCV_timeSeries.R' [0s]
  Running 'runitLOOCV.R' [0s]
  Running 'runitLOOCV_timeSeries.R' [0s]
 [3s] OK
** running tests for arch 'x64' ...
  Running 'runitCalcActivation.R' [0s]
  Running 'runitCalcPredictionKfoldCV.R' [0s]
  Running 'runitCalcPredictionKfoldCV_timeSeries.R' [0s]
  Running 'runitCalcPredictionLOOCV.R' [0s]
  Running 'runitCalcPredictionLOOCV_timeSeries.R' [0s]
  Running 'runitCalcRangeLambda.R' [0s]
  Running 'runitDoILP.R' [0s]
  Running 'runitDoILP_timeSeries.R' [0s]
  Running 'runitGenerateTimeSeriesNetStates.R' [0s]
  Running 'runitGetAdja.R' [0s]
  Running 'runitGetBaseline.R' [0s]
  Running 'runitGetEdgeAnnot.R' [0s]
  Running 'runitGetObsMat.R' [0s]
  Running 'runitGetSampleAdja.R' [0s]
  Running 'runitGetSampleAdjaMAD.R' [0s]
  Running 'runitKfoldCV.R' [0s]
  Running 'runitKfoldCV_timeSeries.R' [0s]
  Running 'runitLOOCV.R' [0s]
  Running 'runitLOOCV_timeSeries.R' [0s]
 [3s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'KEGGgraph'
* 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:/biocbld/bbs-3.3-bioc/meat/lpNet.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'lpNet' ...
** 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 'lpNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lpNet' as lpNet_2.3.0.zip
* DONE (lpNet)

name	user	system	elapsed
CV	0.51	0.06	0.58
calcActivation	0	0	0
calcPrediction	0.02	0.00	0.01
calcRangeLambda	0	0	0
doILP	0	0	0
generateTimeSeriesNetStates	0.02	0.00	0.02
getAdja	0	0	0
getBaseline	0	0	0
getEdgeAnnot	0	0	0
getObsMat	0.01	0.00	0.02
getSampleAdja	0	0	0
summarizeRepl	0.02	0.00	0.01

name	user	system	elapsed
CV	0.52	0.11	0.63
calcActivation	0	0	0
calcPrediction	0	0	0
calcRangeLambda	0	0	0
doILP	0	0	0
generateTimeSeriesNetStates	0	0	0
getAdja	0.02	0.00	0.02
getBaseline	0	0	0
getEdgeAnnot	0	0	0
getObsMat	0.01	0.00	0.02
getSampleAdja	0	0	0
summarizeRepl	0.02	0.00	0.01