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###
### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CNORode
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'CNORode' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FG_transfer_function.c -o FG_transfer_function.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
 2445 |   int is, retval;
      |           ^~~~~~
cvodea.c: In function 'CVArhsQ':
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
 2941 |   int flag, retval;
      |       ^~~~
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2569:7: warning: 'yS0' may be used uninitialized [-Wmaybe-uninitialized]
 2569 |       N_VLinearSum(ONE, yS1[is], -ONE, yS0[is], YS[0][is]);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cvodea.c:2507:13: note: 'yS0' was declared here
 2507 |   N_Vector *yS0, *ySd0, *yS1, *ySd1;
      |             ^~~
cvodea.c:2570:7: warning: 'ySd0' may be used uninitialized [-Wmaybe-uninitialized]
 2570 |       N_VLinearSum(ONE, ySd1[is],  ONE, ySd0[is], YS[1][is]);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cvodea.c:2507:19: note: 'ySd0' was declared here
 2507 |   N_Vector *yS0, *ySd0, *yS1, *ySd1;
      |                   ^~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodea_io.c -o cvodea_io.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes.c -o cvodes.o
cvodes.c: In function 'cvHin':
cvodes.c:4318:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4318 |       if (count1 <= 2)
      |       ^~
cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4320 |         if (retval == QRHSFUNC_RECVR) return(CV_REPTD_QRHSFUNC_ERR);
      |         ^~
cvodes.c: In function 'cvQuadSensRhs1InternalDQ':
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
 8834 |   realtype Deltap, rDeltap;
      |                    ^~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_band.c -o cvodes_band.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_bandpre.c -o cvodes_bandpre.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_dense.c -o cvodes_dense.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_diag.c -o cvodes_diag.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_direct.c -o cvodes_direct.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_io.c -o cvodes_io.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_spgmr.c -o cvodes_spgmr.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_spils.c -o cvodes_spils.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c decimal2binary.c -o decimal2binary.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findStates.c -o findStates.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fnvector_serial.c -o fnvector_serial.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getNumBits.c -o getNumBits.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getNumInputs.c -o getNumInputs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getStateIndex.c -o getStateIndex.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getTruthTables.c -o getTruthTables.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_count_bits.c -o get_count_bits.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_input_index.c -o get_input_index.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_support_truth_tables.c -o get_support_truth_tables.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_truth_tables_index.c -o get_truth_tables_index.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hill_function.c -o hill_function.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c linear_transfer_function.c -o linear_transfer_function.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c normHill.c -o normHill.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c normHill_mod.c -o normHill_mod.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nvector_serial.c -o nvector_serial.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c printAdjMat.c -o printAdjMat.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c printInterMat.c -o printInterMat.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c printNminiTerms.c -o printNminiTerms.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c printTruthTables.c -o printTruthTables.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rhsODE.c -o rhsODE.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sim_logic_ode.c -o sim_logic_ode.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:37:21: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
   37 |         int i,j,neq,counter,flag;
      |                     ^~~~~~~
simulateODE.c:250:5: warning: 'tout' may be used uninitialized [-Wmaybe-uninitialized]
  250 |     rhsODEF(tout,yf,ydotf, data);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
simulateODE.c:38:18: note: 'tout' was declared here
   38 |         realtype tout, ti, tf;
      |                  ^~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_band.c -o sundials_band.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_dense.c -o sundials_dense.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_direct.c -o sundials_direct.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_iterative.c -o sundials_iterative.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_math.c -o sundials_math.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_nvector.c -o sundials_nvector.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_spbcgs.c -o sundials_spbcgs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
  439 |   realtype **Hes, *givens, *yg;
      |                             ^~
sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable]
  439 |   realtype **Hes, *givens, *yg;
      |                    ^~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
gcc -shared -s -static-libgcc -o CNORode.dll tmp.def 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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-CNORode/00new/CNORode/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNORode)