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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellNOptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CellNOptR_1.38.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CellNOptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CellNOptR' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'RBGL', 'graph', 'hash', 'RCurl', 'Rgraphviz', 'XML', 'ggplot2'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'CellNOptR' can be installed ... WARNING
Found the following significant warnings:
  simulatorT1.c:502:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.Rcheck/00install.out' for details.
* 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
* 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 dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  'foreach' 'plyr'
'loadNamespace' or 'requireNamespace' call not declared from: 'plyr'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
build_sif_table_from_rule : rename_gates: no visible global function
  definition for 'mutate_if'
build_sif_table_from_rule : rename_gates: no visible global function
  definition for 'mutate'
build_sif_table_from_rule : rename_gates: no visible binding for global
  variable 'node_in'
build_sif_table_from_rule : rename_gates: no visible binding for global
  variable 'node_out'
build_sif_table_from_rule : simplify_gates: no visible global function
  definition for 'filter'
build_sif_table_from_rule : simplify_gates: no visible global function
  definition for 'mutate'
build_sif_table_from_rule : simplify_gates: no visible binding for
  global variable 'node_in'
build_sif_table_from_rule : simplify_gates: no visible binding for
  global variable 'node_out'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'setNames'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'mutate_if'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'filter'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'mutate'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'num_or'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'node_out'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'new_node_out'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'unnest'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'node_in'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'new_node_in'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'distinct'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'group_by'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'summarise'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'select'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'or_members'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'ungroup'
build_sif_table_from_rule : write_sif: no visible global function
  definition for 'mutate'
build_sif_table_from_rule : write_sif: no visible binding for global
  variable 'node_in'
build_sif_table_from_rule : write_sif: no visible binding for global
  variable 'node_out'
build_sif_table_from_rule : write_sif: no visible binding for global
  variable 'sign1'
build_sif_table_from_rule : write_sif: no visible binding for global
  variable 'sign2'
crossvalidateBoolean: no visible global function definition for 'error'
crossvalidateBoolean: no visible global function definition for
  '%dopar%'
readBND: no visible global function definition for 'read_file'
readBNET: no visible global function definition for 'rowwise'
readBNET: no visible global function definition for 'mutate'
readBNET: no visible binding for global variable 'factors'
readBNET: no visible binding for global variable 'i_and_gates'
readBNET: no visible global function definition for 'do'
readBNET: no visible binding for global variable '.'
readBNET: no visible global function definition for 'unnest'
readBNET: no visible global function definition for 'ungroup'
Undefined global functions or variables:
  %dopar% . distinct do error factors filter group_by i_and_gates
  mutate mutate_if new_node_in new_node_out node_in node_out num_or
  or_members read_file rowwise select setNames sign1 sign2 summarise
  ungroup unnest
Consider adding
  importFrom("stats", "filter", "setNames")
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:
  'cnodata' 'pknmodel'
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 ... WARNING
Codoc mismatches from documentation object 'normaliseCNOlist':
normaliseCNOlist
  Code: function(CNOlist, EC50Data = 0.5, HillCoef = 2, EC50Noise = 0,
                 detection = 0, saturation = Inf, changeTh = 0,
                 norm2TorCtrl = NULL, mode = "time", options =
                 list(rescale_negative = TRUE), verbose = FALSE)
  Docs: function(CNOlist, EC50Data = 0.5, HillCoef = 2, EC50Noise = 0,
                 detection = 0, saturation = Inf, changeTh = 0,
                 norm2TorCtrl = NULL, mode = "time", options =
                 list(rescale_negative = T), verbose = FALSE)
  Mismatches in argument default values:
    Name: 'options' Code: list(rescale_negative = TRUE) Docs: list(rescale_negative = T)

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'createAndRunILP':
  createAndRunILP <- function(model = model, 
                              midas = midas, 
                              cnolist = cnolist, 
                              accountForModelSize = accountForModelSize, 
                              sizeFac = sizeFac, 
                              source_path = source_path, 
                              mipGap = mipGap, 
                              relGap = relGap, 
                              timelimit = timelimit,
                              cplexPath = cplexPath, 
                              method = method, 
                              numSolutions = numSolutions, 
                              limitPop = limitPop, 
                              poolIntensity = poolIntensity, 
                              poolReplace = poolReplace)
Bad \usage lines found in documentation object 'createILPBitstringAll':
  createILPBitstringAll<- function(cplexSolutionFileName,
                                   y_vector,
                                   binary_variables)
Bad \usage lines found in documentation object 'create_binaries':
  create_binaries <- function(model, 
                              midas, 
                              numberOfExperiments, 
                              y_vector)
Bad \usage lines found in documentation object 'crossvalidateBoolean':
  crossvalidateBoolean = function(CNOlist,model,nfolds=10,foldid=NULL, 
                                  type=c('datapoint','experiment','observable'),timeIndex = 2,parallel=FALSE, ...)
Bad \usage lines found in documentation object 'ilpBinaryT1':
  ilpBinaryT1 <- function(cnolist, 
                          model, 
                          sizeFac = 0.0001, 
                          mipGap = 0, 
                          relGap = 0, 
                          timelimit = 3600, 
                          cplexPath, 
                          method = "quadratic",
                          numSolutions = 100, 
                          limitPop = 500, 
                          poolIntensity = 4, 
                          poolReplace = 2)
Bad \usage lines found in documentation object 'ilpBinaryT2':
  ilpBinaryT2 <- function(cnolist, 
                          model, 
                          sizeFac = 0.0001, 
                          mipGap = 0, 
                          relGap = 0, 
                          timelimit = 3600, 
                          cplexPath, 
                          method = "quadratic",
                          numSolutions = 100, 
                          limitPop = 500, 
                          poolIntensity = 4, 
                          poolReplace = 2)
Bad \usage lines found in documentation object 'ilpBinaryTN':
  ilpBinaryTN <- function(cnolist, 
                          model, 
                          sizeFac = 0.0001, 
                          mipGap = 0, 
                          relGap = 0, 
                          timelimit = 3600, 
                          cplexPath, 
                          method = "quadratic",
                          numSolutions = 100, 
                          limitPop = 500, 
                          poolIntensity = 0, 
                          poolReplace = 2,
                          timeIndices = c(1, 2))
Bad \usage lines found in documentation object 'invokeCPLEX':
  invokeCPLEX <- function(inputFileName, 
                          outputFileName, 
                          mipGap=mipGap, 
                          relGap = relGap, 
                          timelimit=timelimit, 
                          cplexPath = cplexPath, 
                          numSolutions = numSolutions, 
                          limitPop = limitPop, 
                          poolIntensity = poolIntensity, 
                          poolReplace = poolReplace)
Bad \usage lines found in documentation object 'writeFile':
  writeFile <- function(objectiveFunction,
                        constraints,
                        bounds,
                        binaries,
                        cplexPath)
Bad \usage lines found in documentation object 'writeObjectiveFunction':
  writeObjectiveFunction <- function(model, 
                                     midasExperimentPart, 
                                     y_vector=y_vector,
                                     accountForModelSize = TRUE, 
                                     sizeFac = .000001, 
                                     meansOfMeasurements_at_t0, 
                                     method = "quadratic" )
Bad \usage lines found in documentation object 'write_bounds':
  write_bounds <- function(model,
                           midasTreatmentPart,
                           y_vector,
                           binary_variables)
Bad \usage lines found in documentation object 'write_constraints':
  write_constraints <- function(model,
                                midasExperimentPart,
                                midasTreatmentPart,
                                reaction_sets,
                                y_vector, 
                                midas, 
                                binary_variables)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CellNOptR/libs/i386/CellNOptR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CellNOptR/libs/x64/CellNOptR.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
crossvalidateBoolean 4.66   0.86    5.51
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_gaBinaryT1.R'
  Running 'test_gaBinaryT2.R'
  Running 'test_gaBinaryT3.R'
  Running 'test_import_rules.R'
  Running 'test_manySteadyStates.R'
  Running 'test_priorBitString.R'
  Running 'test_simulateTN.R'
 OK
** running tests for arch 'x64' ...
  Running 'test_gaBinaryT1.R'
  Running 'test_gaBinaryT2.R'
  Running 'test_gaBinaryT3.R'
  Running 'test_import_rules.R'
  Running 'test_manySteadyStates.R'
  Running 'test_priorBitString.R'
  Running 'test_simulateTN.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: 5 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/CellNOptR.Rcheck/00check.log'
for details.