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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORfuzzy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORfuzzy_1.49.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNORfuzzy.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORfuzzy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORfuzzy’ version ‘1.49.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘CNORfuzzy’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CNORfuzzy-package.Rd: CellNOptR
  CNORwrapFuzzy.Rd: makeCNOlist, readMIDAS, readSIF, CellNOptR
  simFuzzyT1.Rd: CellNOptR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'CNORwrapFuzzy.Rd':
  ‘verbose’
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
CNORwrapFuzzy 7.991  0.224   8.233
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNORfuzzy.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNORfuzzy
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘CNORfuzzy’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c simulatorT1.c -o simulatorT1.o
simulatorT1.c:320:28: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
            if((track_cond == nCond)) {
                ~~~~~~~~~~~^~~~~~~~
simulatorT1.c:320:28: note: remove extraneous parentheses around the comparison to silence this warning
            if((track_cond == nCond)) {
               ~           ^       ~
simulatorT1.c:320:28: note: use '=' to turn this equality comparison into an assignment
            if((track_cond == nCond)) {
                           ^~
                           =
1 warning generated.
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CNORfuzzy.so simulatorT1.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-CNORfuzzy/00new/CNORfuzzy/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNORfuzzy)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

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: rmarkdown
Loading required package: nloptr
[1] TRUE
> BiocGenerics:::testPackage("CNORfuzzy")
[1] "Begining Optimization"
[1] "Discrete GA Finished in: 9.389805 secs"
[1] "Calling interpretDiscreteGA"
[1] "Calling first Refinement"
[1] "...First Refinement Complete 0.1560731 secs"
[1] "Calling second Refinement"
[1] "...Second Refinement Complete 0.241183 secs"
[1] 0
[1] "Calling reduceFuzzy 1"
[1] "...done 0.007462978 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 1e-04
[1] "Calling reduceFuzzy 2"
[1] "...done 0.006350994 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 5e-04
[1] "Calling reduceFuzzy 3"
[1] "...done 0.00623107 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.001
[1] "Calling reduceFuzzy 4"
[1] "...done 0.006445169 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.003
[1] "Calling reduceFuzzy 5"
[1] "...done 0.00632 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.005
[1] "Calling reduceFuzzy 6"
[1] "...done 0.006356955 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] 0.01
[1] "Calling reduceFuzzy 7"
[1] "...done 0.00651288 secs"
[1] "Reduction did not change Model.  Copying previous refinement"
[1] "RedRef Finished.  Total time RedRef  0.04797578 secs"
[1] "Total Time:  9.857849 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 -- Wed Dec 11 20:09:49 2024 
*********************************************** 
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 
 11.356   0.354  11.729