BioC 3.4: CHECK report for lpNet on zin1

Package: lpNet

Version: 2.5.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings lpNet_2.5.0.tar.gz

StartedAt: 2016-09-20 08:41:04 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:41:39 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 35.7 seconds

RetCode: 0

Status:  OK

CheckDir: lpNet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings lpNet_2.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/lpNet.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lpNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lpNet’ version ‘2.5.0’
* 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 ‘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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/lpNet.Rcheck/00check.log’
for details.

* 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
* DONE (lpNet)

name	user	system	elapsed
CV	0.484	0.016	0.527
calcActivation	0.004	0.000	0.004
calcPrediction	0.004	0.000	0.003
calcRangeLambda	0.000	0.000	0.002
doILP	0.004	0.000	0.004
generateTimeSeriesNetStates	0.004	0.000	0.004
getAdja	0.004	0.000	0.005
getBaseline	0.008	0.000	0.005
getEdgeAnnot	0.000	0.000	0.001
getObsMat	0.004	0.000	0.004
getSampleAdja	0.004	0.000	0.002
summarizeRepl	0.020	0.000	0.027