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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lpNet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings lpNet_2.38.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/lpNet.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'lpNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lpNet' version '2.38.0'
* 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 code 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'KEGGgraph'
  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 ... 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 ... WARNING
Undocumented data sets:
  'dat.normalized' 'dat.unnormalized'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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 ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/lpNet.Rcheck/00check.log'
for details.