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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORode.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORode_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNORode.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 ‘CNORode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORode’ 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CNORode’ 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 ... WARNING
'::' or ':::' import not declared from: ‘MEIGOR’
'loadNamespace' or 'requireNamespace' call not declared from: ‘MEIGOR’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

createLBodeContPars: no visible global function definition for ‘runif’
crossvalidateODE: no visible global function definition for ‘error’
minlpLBodeSSm: no visible global function definition for ‘essR’
minlpLBodeSSm: no visible global function definition for ‘runif’
parEstimationLBodeGA: no visible global function definition for
  ‘plot.new’
parEstimationLBodeGA : monitor_func: no visible global function
  definition for ‘par’
parEstimationLBodeGA : monitor_func: no visible global function
  definition for ‘lines’
runCNORode: no visible global function definition for ‘pdf’
runCNORode: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off error essR lines par pdf plot.new runif
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot.new")
  importFrom("stats", "runif")
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:
  CNORode-package.Rd: CellNOptR
  defaultParametersGA.Rd: CellNOptR
  defaultParametersSSm.Rd: CellNOptR
  getLBodeContObjFunction.Rd: CellNOptR
  getLBodeDataSim.Rd: CellNOptR
  getLBodeMINLPObjFunction.Rd: CellNOptR
  getLBodeModelSim.Rd: CellNOptR
  getLBodeSimFunction.Rd: CellNOptR
  incidence2Adjacency.Rd: CellNOptR
  minlpLBodeSSm.Rd: CellNOptR
  parEstimationLBode.Rd: CellNOptR, rbga
  parEstimationLBodeGA.Rd: CellNOptR, rbga
  parEstimationLBodeSSm.Rd: CellNOptR
  plotLBodeFitness.Rd: CellNOptR
  plotLBodeModelSim.Rd: CellNOptR
  runCNORode.Rd: preprocessing
  simdata2cnolist.Rd: CellNOptR
  simulate.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 ... 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/CNORode/libs/CNORode.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___vsprintf_chk’, possibly from ‘vsprintf’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)

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 nor [v]sprintf. 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
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNORode.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNORode
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘CNORode’ ...
** 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   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c FG_transfer_function.c -o FG_transfer_function.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodea.c -o cvodea.o
cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
  int is, retval;
          ^
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
  int flag, retval;
      ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodea_io.c -o cvodea_io.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes.c -o cvodes.o
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
  realtype Deltap, rDeltap;
                   ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_band.c -o cvodes_band.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_bandpre.c -o cvodes_bandpre.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_dense.c -o cvodes_dense.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_diag.c -o cvodes_diag.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_direct.c -o cvodes_direct.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_io.c -o cvodes_io.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spgmr.c -o cvodes_spgmr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spils.c -o cvodes_spils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c decimal2binary.c -o decimal2binary.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c findStates.c -o findStates.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c fnvector_serial.c -o fnvector_serial.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getNumBits.c -o getNumBits.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getNumInputs.c -o getNumInputs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getStateIndex.c -o getStateIndex.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getTruthTables.c -o getTruthTables.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_count_bits.c -o get_count_bits.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_input_index.c -o get_input_index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_support_truth_tables.c -o get_support_truth_tables.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_truth_tables_index.c -o get_truth_tables_index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c hill_function.c -o hill_function.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c linear_transfer_function.c -o linear_transfer_function.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c normHill.c -o normHill.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c normHill_mod.c -o normHill_mod.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c nvector_serial.c -o nvector_serial.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printAdjMat.c -o printAdjMat.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printInterMat.c -o printInterMat.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printNminiTerms.c -o printNminiTerms.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printTruthTables.c -o printTruthTables.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c rhsODE.c -o rhsODE.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sim_logic_ode.c -o sim_logic_ode.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c simulateODE.c -o simulateODE.o
simulateODE.c:37:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
        int i,j,neq,counter,flag;
                    ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_band.c -o sundials_band.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_dense.c -o sundials_dense.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_direct.c -o sundials_direct.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_iterative.c -o sundials_iterative.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_math.c -o sundials_math.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_nvector.c -o sundials_nvector.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_spbcgs.c -o sundials_spbcgs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable]
  realtype **Hes, *givens, *yg;
                            ^
sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable]
  realtype **Hes, *givens, *yg;
                   ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
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 CNORode.so FG_transfer_function.o cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o normHill_mod.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.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-CNORode/00new/CNORode/libs
** R
** data
** 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 (CNORode)