##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNORfuzzy.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CNORfuzzy_1.37.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CNORfuzzy.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNORfuzzy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORfuzzy' version '1.37.0'
* 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 'CNORfuzzy' 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'CellNOptR' 'nloptr'
  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
.getk: no visible global function definition for 'approx'
.std: no visible global function definition for 'var'
CNORwrapFuzzy: no visible global function definition for 'checkSignals'
CNORwrapFuzzy: no visible global function definition for
  'preprocessing'
CNORwrapFuzzy: no visible global function definition for 'getFit'
CNORwrapFuzzy: no visible global function definition for 'indexFinder'
cSimulator: no visible global function definition for 'indexFinder'
compileMultiRes: no visible global function definition for 'par'
compileMultiRes: no visible global function definition for 'axis'
compileMultiRes: no visible global function definition for 'mtext'
compileMultiRes: no visible global function definition for 'legend'
computeScoreFuzzy: no visible global function definition for
  'indexFinder'
computeScoreFuzzy: no visible global function definition for 'getFit'
gaDiscreteT1: no visible global function definition for 'indexFinder'
gaDiscreteT1: no visible global function definition for 'runif'
getEC50: no visible global function definition for 'nloptr'
getMeanFuzzy: no visible global function definition for 'indexFinder'
getMeanModel: no visible global function definition for 'indexFinder'
getNetworkInfoFuzzy: no visible global function definition for
  'indexFinder'
getNetworkInfoFuzzy: no visible global function definition for
  'findNONC'
getRefinedModel: no visible global function definition for
  'indexFinder'
getRefinedModel : objFunParams: no visible global function definition
  for 'getFit'
getRefinedModel: no visible global function definition for 'nloptr'
plotMeanFuzzyFit: no visible global function definition for
  'indexFinder'
plotMeanFuzzyFit: no visible global function definition for
  'plotOptimResultsPan'
prep4simFuzzy: no visible global function definition for 'prep4sim'
prep4simFuzzy: no visible global function definition for 'indexFinder'
rSimFuzzyT1: no visible global function definition for 'indexFinder'
rSimulator: no visible global function definition for 'indexFinder'
reduceFuzzy: no visible global function definition for 'indexFinder'
reduceFuzzy: no visible global function definition for 'getFit'
shift: no visible global function definition for 'tail'
shift: no visible global function definition for 'head'
simulate: no visible global function definition for 'indexFinder'
writeNetworkW: no visible global function definition for 'writeDot'
writeNetworkW: no visible global function definition for 'write.table'
Undefined global functions or variables:
  approx axis checkSignals findNONC getFit head indexFinder legend
  mtext nloptr par plotOptimResultsPan prep4sim preprocessing runif
  tail var write.table writeDot
Consider adding
  importFrom("graphics", "axis", "legend", "mtext", "par")
  importFrom("stats", "approx", "runif", "var")
  importFrom("utils", "head", "tail", "write.table")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/CNORfuzzy/libs/x64/CNORfuzzy.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
CNORwrapFuzzy 12.05   0.42   12.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/CNORfuzzy.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CNORfuzzy
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CNORfuzzy' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c simulatorT1.c -o simulatorT1.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CNORfuzzy.dll tmp.def simulatorT1.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CNORfuzzy/00new/CNORfuzzy/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNORfuzzy'
    finding HTML links ... done
    CNORfuzzy-package                       html  
    finding level-2 HTML links ... done

    CNORwrapFuzzy                           html  
    compileMultiRes                         html  
    computeScoreFuzzy                       html  
    defaultParametersFuzzy                  html  
    gaDiscreteT1                            html  
    getRefinedModel                         html  
    interpretDiscreteGA                     html  
    plotMeanFuzzyFit                        html  
    prep4simFuzzy                           html  
    reduceFuzzy                             html  
    simFuzzyT1                              html  
    writeFuzzyNetwork                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNORfuzzy)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'cmapR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'maskBAD' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("CNORfuzzy") || stop("unable to load CNORfuzzy")
Loading required package: CNORfuzzy
Loading required package: CellNOptR
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: hash
hash-2.2.6.1 provided by Decision Patterns

Loading required package: RCurl
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: ggplot2
Loading required package: nloptr
[1] TRUE
> BiocGenerics:::testPackage("CNORfuzzy")
[1] "Begining Optimization"
[1] "Discrete GA Finished in: 11.79494 secs"
[1] "Calling interpretDiscreteGA"
[1] "Calling first Refinement"
[1] "...First Refinement Complete 0.1406031 secs"
[1] "Calling second Refinement"
[1] "...Second Refinement Complete 0.09373403 secs"
[1] 0
[1] "Calling reduceFuzzy 1"
[1] "...done 0 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 1e-04
[1] "Calling reduceFuzzy 2"
[1] "...done 0.0156219 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 5e-04
[1] "Calling reduceFuzzy 3"
[1] "...done 0 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.001
[1] "Calling reduceFuzzy 4"
[1] "...done 0.01562309 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.003
[1] "Calling reduceFuzzy 5"
[1] "...done 0 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.005
[1] "Calling reduceFuzzy 6"
[1] "...done 0.0156219 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.01
[1] "Calling reduceFuzzy 7"
[1] "...done 0 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] "RedRef Finished.  Total time RedRef  0.04686689 secs"
[1] "Total Time:  12.10738 secs"
[1] "The following species are measured: Akt, Hsp27, NFkB, Erk, p90RSK, Jnk, cJun"
[1] "The following species are stimulated: EGF, TNFa"
[1] "The following species are inhibited: Raf, PI3K"
[1] "The following species are not observable and/or not controllable: "
[1] "The following species are measured: Akt, Hsp27, NFkB, Erk, p90RSK, Jnk, cJun"
[1] "The following species are stimulated: EGF, TNFa"
[1] "The following species are inhibited: Raf, PI3K"
[1] 0.1316292


RUNIT TEST PROTOCOL -- Thu Mar 17 18:46:55 2022 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CNORfuzzy RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  13.34    0.64   13.96