Multiple platform build/check report for BioC 3.9 - CHECK report for CNORode on tokay2

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNORode.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNORode_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNORode.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNORode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORode' version '1.25.1'
* 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 'CNORode' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to 'MEIGOR' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'CellNOptR' 'genalg'
  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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

createLBodeContPars: no visible global function definition for 'runif'
getLBodeContObjFunction: no visible global function definition for
  'compatCNOlist'
getLBodeContObjFunction: no visible global function definition for
  'indexFinder'
getLBodeDataSim: no visible global function definition for
  'compatCNOlist'
getLBodeDataSim: no visible global function definition for
  'indexFinder'
getLBodeMINLPObjFunction: no visible global function definition for
  'compatCNOlist'
getLBodeMINLPObjFunction: no visible global function definition for
  'indexFinder'
getLBodeModelSim: no visible global function definition for
  'compatCNOlist'
getLBodeModelSim: no visible global function definition for
  'indexFinder'
minlpLBodeSSm: no visible global function definition for
  'compatCNOlist'
minlpLBodeSSm: no visible global function definition for 'essR'
minlpLBodeSSm: no visible global function definition for 'runif'
parEstimationLBode: no visible global function definition for
  'compatCNOlist'
parEstimationLBodeGA: no visible global function definition for
  'compatCNOlist'
parEstimationLBodeGA: no visible global function definition for
  'indexFinder'
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 'plot'
parEstimationLBodeGA : monitor_func: no visible global function
  definition for 'lines'
parEstimationLBodeGA: no visible global function definition for 'rbga'
parEstimationLBodeSSm: no visible global function definition for
  'compatCNOlist'
parEstimationLBodeSSm: no visible global function definition for
  'indexFinder'
parEstimationLBodeSSm: no visible global function definition for 'essR'
plotLBodeFitness: no visible global function definition for
  'compatCNOlist'
plotLBodeFitness: no visible global function definition for
  'indexFinder'
plotLBodeFitness: no visible global function definition for
  'plotOptimResults'
plotLBodeFitness: no visible global function definition for
  'plotOptimResultsPan'
plotLBodeFitness: no visible global function definition for 'CNOlist'
plotLBodeModelSim: no visible global function definition for
  'compatCNOlist'
plotLBodeModelSim: no visible global function definition for
  'indexFinder'
plotLBodeModelSim: no visible global function definition for
  'plotCNOlistLarge'
plotLBodeModelSim: no visible global function definition for 'CNOlist'
plotLBodeModelSim: no visible global function definition for
  'plotCNOlist'
simdata2cnolist: no visible global function definition for
  'compatCNOlist'
simdata2cnolist: no visible global function definition for 'CNOlist'
simulate: no visible global function definition for 'compatCNOlist'
simulate: no visible global function definition for 'indexFinder'
Undefined global functions or variables:
  CNOlist compatCNOlist essR indexFinder lines par plot plot.new
  plotCNOlist plotCNOlistLarge plotOptimResults plotOptimResultsPan
  rbga runif
Consider adding
  importFrom("graphics", "lines", "par", "plot", "plot.new")
  importFrom("stats", "runif")
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 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 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-3.9-bioc/R/library/CNORode/libs/i386/CNORode.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CNORode/libs/x64/CNORode.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  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. 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
parEstimationLBode   157.40   0.19  157.67
parEstimationLBodeGA  45.21   0.07   45.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
parEstimationLBode   34.03   0.14   34.17
parEstimationLBodeGA  7.19   0.03    7.22
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNORode.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CNORode_1.25.1.tar.gz && rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNORode.buildbin-libdir CNORode_1.25.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CNORode_1.25.1.zip && rm CNORode_1.25.1.tar.gz CNORode_1.25.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  322k  100  322k    0     0  5074k      0 --:--:-- --:--:-- --:--:-- 5657k

install for i386

* installing *source* package 'CNORode' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodea.c -o cvodea.o
cvodea.c: In function 'CVAhermiteStorePnt':
cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
   int is, retval;
           ^
cvodea.c: In function 'CVArhsQ':
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
   int flag, retval;
       ^
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2572:7: warning: 'ySd0' may be used uninitialized in this function [-Wmaybe-uninitialized]
       N_VLinearSum(ONE, YS[0][is], -delta, ySd0[is], YS[0][is]);
       ^
cvodea.c:2591:5: warning: 'yS0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]);
     ^
cvodea.c: In function 'CVodeB':
cvodea.c:1263:13: warning: 'flag' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int sign, flag;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodea_io.c -o cvodea_io.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes.c -o cvodes.o
cvodes.c: In function 'cvQuadSensRhs1InternalDQ':
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
   realtype Deltap, rDeltap;
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_band.c -o cvodes_band.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_bandpre.c -o cvodes_bandpre.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_bbdpre.c -o cvodes_bbdpre.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_dense.c -o cvodes_dense.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_diag.c -o cvodes_diag.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_direct.c -o cvodes_direct.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_io.c -o cvodes_io.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_spbcgs.c -o cvodes_spbcgs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_spgmr.c -o cvodes_spgmr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_spils.c -o cvodes_spils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c decimal2binary.c -o decimal2binary.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c findStates.c -o findStates.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c fnvector_serial.c -o fnvector_serial.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c getNumBits.c -o getNumBits.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c getNumInputs.c -o getNumInputs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c getStateIndex.c -o getStateIndex.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function 'getTruthTables':
getTruthTables.c:17:14: warning: unused variable 'n' [-Wunused-variable]
  int i,j,k,m,n,counter1,input,miniterm;
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c get_count_bits.c -o get_count_bits.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c get_input_index.c -o get_input_index.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c: In function 'get_support_truth_tables':
get_support_truth_tables.c:16:10: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k;
          ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c get_truth_tables_index.c -o get_truth_tables_index.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c hill_function.c -o hill_function.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c linear_transfer_function.c -o linear_transfer_function.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c normHill.c -o normHill.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c nvector_serial.c -o nvector_serial.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c printAdjMat.c -o printAdjMat.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c printInterMat.c -o printInterMat.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c printNminiTerms.c -o printNminiTerms.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c printTruthTables.c -o printTruthTables.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c rhsODE.c -o rhsODE.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sim_logic_ode.c -o sim_logic_ode.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:150:4: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
    flag = CVDense(cvode_mem, neq);
    ^
simulateODE.c:32:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
  int i,j,neq,counter,flag;
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_band.c -o sundials_band.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_dense.c -o sundials_dense.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_direct.c -o sundials_direct.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_iterative.c -o sundials_iterative.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_math.c -o sundials_math.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_nvector.c -o sundials_nvector.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_spbcgs.c -o sundials_spbcgs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c: In function 'SpgmrFree':
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;
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=generic -c sundials_sptfqmr.c -o sundials_sptfqmr.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CNORode.dll tmp.def 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 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNORode.buildbin-libdir/00LOCK-CNORode/00new/CNORode/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNORode'
    finding HTML links ... done
    CNORode-package                         html  
    finding level-2 HTML links ... done

    cnolistCNORodeExample                   html  
    createLBodeContPars                     html  
    defaultParametersGA                     html  
    defaultParametersSSm                    html  
    getLBodeContObjFunction                 html  
    getLBodeDataSim                         html  
    getLBodeMINLPObjFunction                html  
    getLBodeModelSim                        html  
    getLBodeSimFunction                     html  
    getStates                               html  
    incidence2Adjacency                     html  
    indices                                 html  
    minlpLBodeSSm                           html  
    model                                   html  
    parEstimationLBode                      html  
    parEstimationLBodeGA                    html  
    parEstimationLBodeSSm                   html  
    plotLBodeFitness                        html  
    plotLBodeModelSim                       html  
    simdata2cnolist                         html  
    simulate                                html  
** building package indices
** installing vignettes
   'CNORode-vignette.Rnw' using 'UTF-8' 
** 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

install for x64

* installing *source* package 'CNORode' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodea.c -o cvodea.o
cvodea.c: In function 'CVAhermiteStorePnt':
cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
   int is, retval;
           ^
cvodea.c: In function 'CVArhsQ':
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
   int flag, retval;
       ^
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2572:7: warning: 'ySd0' may be used uninitialized in this function [-Wmaybe-uninitialized]
       N_VLinearSum(ONE, YS[0][is], -delta, ySd0[is], YS[0][is]);
       ^
cvodea.c:2591:5: warning: 'yS0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]);
     ^
cvodea.c: In function 'CVodeB':
cvodea.c:1263:13: warning: 'flag' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int sign, flag;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodea_io.c -o cvodea_io.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes.c -o cvodes.o
cvodes.c: In function 'cvQuadSensRhs1InternalDQ':
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
   realtype Deltap, rDeltap;
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_band.c -o cvodes_band.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_bandpre.c -o cvodes_bandpre.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_bbdpre.c -o cvodes_bbdpre.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_dense.c -o cvodes_dense.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_diag.c -o cvodes_diag.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_direct.c -o cvodes_direct.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_io.c -o cvodes_io.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_spbcgs.c -o cvodes_spbcgs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_spgmr.c -o cvodes_spgmr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_spils.c -o cvodes_spils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c decimal2binary.c -o decimal2binary.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c findStates.c -o findStates.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c fnvector_serial.c -o fnvector_serial.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c getNumBits.c -o getNumBits.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c getNumInputs.c -o getNumInputs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c getStateIndex.c -o getStateIndex.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function 'getTruthTables':
getTruthTables.c:17:14: warning: unused variable 'n' [-Wunused-variable]
  int i,j,k,m,n,counter1,input,miniterm;
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c get_count_bits.c -o get_count_bits.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c get_input_index.c -o get_input_index.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c: In function 'get_support_truth_tables':
get_support_truth_tables.c:16:10: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k;
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c get_truth_tables_index.c -o get_truth_tables_index.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c hill_function.c -o hill_function.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c linear_transfer_function.c -o linear_transfer_function.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c normHill.c -o normHill.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c nvector_serial.c -o nvector_serial.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c printAdjMat.c -o printAdjMat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c printInterMat.c -o printInterMat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c printNminiTerms.c -o printNminiTerms.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c printTruthTables.c -o printTruthTables.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c rhsODE.c -o rhsODE.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sim_logic_ode.c -o sim_logic_ode.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:150:4: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
    flag = CVDense(cvode_mem, neq);
    ^
simulateODE.c:32:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
  int i,j,neq,counter,flag;
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_band.c -o sundials_band.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_dense.c -o sundials_dense.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_direct.c -o sundials_direct.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_iterative.c -o sundials_iterative.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_math.c -o sundials_math.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_nvector.c -o sundials_nvector.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_spbcgs.c -o sundials_spbcgs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c: In function 'SpgmrFree':
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;
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=generic -c sundials_sptfqmr.c -o sundials_sptfqmr.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CNORode.dll tmp.def 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 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNORode' as CNORode_1.25.1.zip
* DONE (CNORode)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CNORode' successfully unpacked and MD5 sums checked

CHECK report for CNORode on tokay2

Summary

Command output

Installation output

Tests output

Example timings