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BUILD BIN report for CNORode on tokay2

This page was generated on 2019-10-16 12:27:02 -0400 (Wed, 16 Oct 2019).

Package 306/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORode 1.26.0
David Henriques
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CNORode
Branch: RELEASE_3_9
Last Commit: 17b68d9
Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNORode
Version: 1.26.0
Command: 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_1.26.0.tar.gz
StartedAt: 2019-10-16 08:56:24 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:57:40 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 76.4 seconds
RetCode: 0
Status:  OK  
PackageFile: CNORode_1.26.0.zip
PackageFileSize: 677.9 KiB

Command output

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###
### Running command:
###
###   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_1.26.0.tar.gz
###
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install for i386

* installing *source* package 'CNORode' ...
** using staged installation
** 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
** 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_1.26.0.zip
* DONE (CNORode)