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BioC 3.6: CHECK report for lpNet on tokay1

This page was generated on 2017-08-16 13:31:11 -0400 (Wed, 16 Aug 2017).

Package 740/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lpNet 2.9.0
Lars Kaderali
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lpNet
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: lpNet
Version: 2.9.0
Command: rm -rf lpNet.buildbin-libdir lpNet.Rcheck && mkdir lpNet.buildbin-libdir lpNet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lpNet.buildbin-libdir lpNet_2.9.0.tar.gz >lpNet.Rcheck\00install.out 2>&1 && cp lpNet.Rcheck\00install.out lpNet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=lpNet.buildbin-libdir --install="check:lpNet-install.out" --force-multiarch --no-vignettes --timings lpNet_2.9.0.tar.gz
StartedAt: 2017-08-16 00:32:04 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:33:24 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 80.0 seconds
RetCode: 0
Status:  OK  
CheckDir: lpNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf lpNet.buildbin-libdir lpNet.Rcheck && mkdir lpNet.buildbin-libdir lpNet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lpNet.buildbin-libdir lpNet_2.9.0.tar.gz >lpNet.Rcheck\00install.out 2>&1 && cp lpNet.Rcheck\00install.out lpNet-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=lpNet.buildbin-libdir --install="check:lpNet-install.out" --force-multiarch --no-vignettes --timings lpNet_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/lpNet.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 'lpNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lpNet' version '2.9.0'
* 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 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 ... NOTE
.calcRangeLambda_steadyState: no visible global function definition for
  'var'
.calcRangeLambda_timeSeries: no visible global function definition for
  'var'
.calculatePredictionValue_Kfold_ts: no visible global function
  definition for 'rnorm'
.calculatePredictionValue_LOOCV_ss: no visible global function
  definition for 'rnorm'
.calculatePredictionValue_LOOCV_ts: no visible global function
  definition for 'rnorm'
.set_per_gene_exp_time_values: no visible global function definition
  for 'rnorm'
.set_per_gene_exp_values: no visible global function definition for
  'rnorm'
.set_per_gene_time_values: no visible global function definition for
  'rnorm'
.set_per_gene_values: no visible global function definition for 'rnorm'
.set_single_values: no visible global function definition for 'rnorm'
getSampleAdja: no visible binding for global variable 'median'
getSampleAdjaMAD: no visible binding for global variable 'median'
getSampleAdjaMAD: no visible binding for global variable 'mad'
summarizeRepl: no visible binding for global variable 'median'
Undefined global functions or variables:
  mad median rnorm var
Consider adding
  importFrom("stats", "mad", "median", "rnorm", "var")
to your NAMESPACE file.
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runitCalcActivation.R'
  Running 'runitCalcPredictionKfoldCV.R'
  Running 'runitCalcPredictionKfoldCV_timeSeries.R'
  Running 'runitCalcPredictionLOOCV.R'
  Running 'runitCalcPredictionLOOCV_timeSeries.R'
  Running 'runitCalcRangeLambda.R'
  Running 'runitDoILP.R'
  Running 'runitDoILP_timeSeries.R'
  Running 'runitGenerateTimeSeriesNetStates.R'
  Running 'runitGetAdja.R'
  Running 'runitGetBaseline.R'
  Running 'runitGetEdgeAnnot.R'
  Running 'runitGetObsMat.R'
  Running 'runitGetSampleAdja.R'
  Running 'runitGetSampleAdjaMAD.R'
  Running 'runitKfoldCV.R'
  Running 'runitKfoldCV_timeSeries.R'
  Running 'runitLOOCV.R'
  Running 'runitLOOCV_timeSeries.R'
 OK
** running tests for arch 'x64' ...
  Running 'runitCalcActivation.R'
  Running 'runitCalcPredictionKfoldCV.R'
  Running 'runitCalcPredictionKfoldCV_timeSeries.R'
  Running 'runitCalcPredictionLOOCV.R'
  Running 'runitCalcPredictionLOOCV_timeSeries.R'
  Running 'runitCalcRangeLambda.R'
  Running 'runitDoILP.R'
  Running 'runitDoILP_timeSeries.R'
  Running 'runitGenerateTimeSeriesNetStates.R'
  Running 'runitGetAdja.R'
  Running 'runitGetBaseline.R'
  Running 'runitGetEdgeAnnot.R'
  Running 'runitGetObsMat.R'
  Running 'runitGetSampleAdja.R'
  Running 'runitGetSampleAdjaMAD.R'
  Running 'runitKfoldCV.R'
  Running 'runitKfoldCV_timeSeries.R'
  Running 'runitLOOCV.R'
  Running 'runitLOOCV_timeSeries.R'
 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/lpNet.Rcheck/00check.log'
for details.


lpNet.Rcheck/00install.out:


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_2.9.0.zip
* DONE (lpNet)

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

nameusersystemelapsed
CV0.830.112.93
calcActivation000
calcPrediction000
calcRangeLambda000
doILP0.020.000.01
generateTimeSeriesNetStates0.060.000.07
getAdja0.020.000.01
getBaseline000
getEdgeAnnot000
getObsMat000
getSampleAdja000
summarizeRepl0.060.000.14

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

nameusersystemelapsed
CV1.000.062.26
calcActivation000
calcPrediction000
calcRangeLambda000
doILP0.020.000.01
generateTimeSeriesNetStates0.060.000.07
getAdja0.020.000.01
getBaseline000
getEdgeAnnot000
getObsMat000
getSampleAdja0.010.000.02
summarizeRepl0.020.000.01