CNORode 1.33.0
Enio Gjerga
| Snapshot Date: 2021-01-24 14:40:26 -0500 (Sun, 24 Jan 2021) |
| URL: https://git.bioconductor.org/packages/CNORode |
| Branch: master |
| Last Commit: faf1cdf |
| Last Changed Date: 2020-10-27 10:47:36 -0500 (Tue, 27 Oct 2020) |
| malbec2 | Linux (Ubuntu 20.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| riesling1 | Windows Server 2019 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/bioc/src/contrib/CNORode_1.33.0.tar.gz && rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNORode.buildbin-libdir CNORode_1.33.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CNORode_1.33.0.zip && rm CNORode_1.33.0.tar.gz CNORode_1.33.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'CNORode' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FG_transfer_function.c -o FG_transfer_function.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -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]
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:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodea_io.c -o cvodea_io.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -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]
if (count1 <= 2)
^~
cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
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]
realtype Deltap, rDeltap;
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_band.c -o cvodes_band.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bandpre.c -o cvodes_bandpre.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bbdpre.c -o cvodes_bbdpre.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_dense.c -o cvodes_dense.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_diag.c -o cvodes_diag.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_direct.c -o cvodes_direct.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_io.c -o cvodes_io.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spbcgs.c -o cvodes_spbcgs.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spgmr.c -o cvodes_spgmr.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spils.c -o cvodes_spils.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c decimal2binary.c -o decimal2binary.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findStates.c -o findStates.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fnvector_serial.c -o fnvector_serial.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumBits.c -o getNumBits.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumInputs.c -o getNumInputs.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getStateIndex.c -o getStateIndex.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_count_bits.c -o get_count_bits.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_input_index.c -o get_input_index.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_truth_tables_index.c -o get_truth_tables_index.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hill_function.c -o hill_function.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c linear_transfer_function.c -o linear_transfer_function.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill.c -o normHill.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill_mod.c -o normHill_mod.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nvector_serial.c -o nvector_serial.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printAdjMat.c -o printAdjMat.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printInterMat.c -o printInterMat.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printNminiTerms.c -o printNminiTerms.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printTruthTables.c -o printTruthTables.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rhsODE.c -o rhsODE.o
rhsODE.c:85: warning: "Ith" redefined
#define Ith(v,i) ( v[i] )
rhsODE.c:10: note: this is the location of the previous definition
#define Ith(v,i) ( NV_DATA_S(v)[i] )
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sim_logic_ode.c -o sim_logic_ode.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:169:11: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^~~~~~~
simulateODE.c:35:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
int i,j,neq,counter,flag;
^~~~~~~
simulateODE.c:255:4: warning: 'tout' may be used uninitialized in this function [-Wmaybe-uninitialized]
rhsODEF(tout,y0,ydot0, data);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_band.c -o sundials_band.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_dense.c -o sundials_dense.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_direct.c -o sundials_direct.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_iterative.c -o sundials_iterative.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_math.c -o sundials_math.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_nvector.c -o sundials_nvector.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_spbcgs.c -o sundials_spbcgs.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -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]
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:/rtools40/mingw32/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_sptfqmr.c -o sundials_sptfqmr.o
C:/rtools40/mingw32/bin/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:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.13-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.13-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
REDIRECT:topic CNORode -> CNORode-package.html [ SUCCESS ]
REDIRECT:file CNORode-package.html -> CNORode-package.html [ SUCCESS ]
finding level-2 HTML links ... done
cnodata html
REDIRECT:topic cnodata -> cnodata.html [ SUCCESS ]
cnolist html
REDIRECT:topic cnolist -> cnolist.html [ SUCCESS ]
cnolistCNORodeExample html
REDIRECT:topic cnolistCNORodeExample -> cnolistCNORodeExample.html [ SUCCESS ]
createLBodeContPars html
REDIRECT:topic createLBodeContPars -> createLBodeContPars.html [ SUCCESS ]
crossvalidateODE html
REDIRECT:topic crossvalidateODE -> crossvalidateODE.html [ SUCCESS ]
defaultParametersGA html
REDIRECT:topic defaultParametersGA -> defaultParametersGA.html [ SUCCESS ]
defaultParametersSSm html
REDIRECT:topic defaultParametersSSm -> defaultParametersSSm.html [ SUCCESS ]
getLBodeContObjFunction html
REDIRECT:topic getLBodeContObjFunction -> getLBodeContObjFunction.html [ SUCCESS ]
getLBodeDataSim html
REDIRECT:topic getLBodeDataSim -> getLBodeDataSim.html [ SUCCESS ]
getLBodeMINLPObjFunction html
REDIRECT:topic getLBodeMINLPObjFunction -> getLBodeMINLPObjFunction.html [ SUCCESS ]
getLBodeModelSim html
REDIRECT:topic getLBodeModelSim -> getLBodeModelSim.html [ SUCCESS ]
getLBodeSimFunction html
REDIRECT:topic getLBodeSimFunction -> getLBodeSimFunction.html [ SUCCESS ]
getStates html
REDIRECT:topic getStates -> getStates.html [ SUCCESS ]
incidence2Adjacency html
REDIRECT:topic incidence2Adjacency -> incidence2Adjacency.html [ SUCCESS ]
indices html
REDIRECT:topic indices -> indices.html [ SUCCESS ]
minlpLBodeSSm html
REDIRECT:topic minlpLBodeSSm -> minlpLBodeSSm.html [ SUCCESS ]
model html
REDIRECT:topic model -> model.html [ SUCCESS ]
parEstimationLBode html
REDIRECT:topic parEstimationLBode -> parEstimationLBode.html [ SUCCESS ]
parEstimationLBodeGA html
REDIRECT:topic parEstimationLBodeGA -> parEstimationLBodeGA.html [ SUCCESS ]
parEstimationLBodeSSm html
REDIRECT:topic parEstimationLBodeSSm -> parEstimationLBodeSSm.html [ SUCCESS ]
pknmodel html
REDIRECT:topic pknmodel -> pknmodel.html [ SUCCESS ]
plotLBodeFitness html
REDIRECT:topic plotLBodeFitness -> plotLBodeFitness.html [ SUCCESS ]
plotLBodeModelSim html
REDIRECT:topic plotLBodeModelSim -> plotLBodeModelSim.html [ SUCCESS ]
runCNORode html
REDIRECT:topic runCNORode -> runCNORode.html [ SUCCESS ]
simdata2cnolist html
REDIRECT:topic simdata2cnolist -> simdata2cnolist.html [ SUCCESS ]
simulate html
REDIRECT:topic simulate -> simulate.html [ SUCCESS ]
** 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:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FG_transfer_function.c -o FG_transfer_function.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -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]
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:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodea_io.c -o cvodea_io.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -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]
if (count1 <= 2)
^~
cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
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]
realtype Deltap, rDeltap;
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_band.c -o cvodes_band.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bandpre.c -o cvodes_bandpre.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_bbdpre.c -o cvodes_bbdpre.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_dense.c -o cvodes_dense.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_diag.c -o cvodes_diag.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_direct.c -o cvodes_direct.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_io.c -o cvodes_io.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spbcgs.c -o cvodes_spbcgs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spgmr.c -o cvodes_spgmr.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_spils.c -o cvodes_spils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c decimal2binary.c -o decimal2binary.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findStates.c -o findStates.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fnvector_serial.c -o fnvector_serial.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumBits.c -o getNumBits.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getNumInputs.c -o getNumInputs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getStateIndex.c -o getStateIndex.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_count_bits.c -o get_count_bits.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_input_index.c -o get_input_index.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get_truth_tables_index.c -o get_truth_tables_index.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hill_function.c -o hill_function.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c linear_transfer_function.c -o linear_transfer_function.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill.c -o normHill.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normHill_mod.c -o normHill_mod.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nvector_serial.c -o nvector_serial.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printAdjMat.c -o printAdjMat.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printInterMat.c -o printInterMat.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printNminiTerms.c -o printNminiTerms.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printTruthTables.c -o printTruthTables.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rhsODE.c -o rhsODE.o
rhsODE.c:85: warning: "Ith" redefined
#define Ith(v,i) ( v[i] )
rhsODE.c:10: note: this is the location of the previous definition
#define Ith(v,i) ( NV_DATA_S(v)[i] )
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sim_logic_ode.c -o sim_logic_ode.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:169:11: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^~~~~~~
simulateODE.c:35:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
int i,j,neq,counter,flag;
^~~~~~~
simulateODE.c:255:4: warning: 'tout' may be used uninitialized in this function [-Wmaybe-uninitialized]
rhsODEF(tout,y0,ydot0, data);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_band.c -o sundials_band.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_dense.c -o sundials_dense.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_direct.c -o sundials_direct.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_iterative.c -o sundials_iterative.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_math.c -o sundials_math.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_nvector.c -o sundials_nvector.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_spbcgs.c -o sundials_spbcgs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -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]
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:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sundials_sptfqmr.c -o sundials_sptfqmr.o
C:/rtools40/mingw64/bin/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:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.13-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.13-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNORode' as CNORode_1.33.0.zip
* DONE (CNORode)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'CNORode' successfully unpacked and MD5 sums checked