* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘BoolNet’ ...
** package ‘BoolNet’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/Rtmp2Q4izl/R.INSTALLcc0957c3e7207/BoolNet/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c attractor_info.c -o attractor_info.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c attractor_search_interface.c -o attractor_search_interface.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common.c -o common.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c picosat.c -o picosat.o
picosat.c: In function ‘relemhead’:
picosat.c:3263:15: warning: variable ‘fmt’ set but not used [-Wunused-but-set-variable]
3263 | const char *fmt;
| ^~~
picosat.c: In function ‘fanalyze’:
picosat.c:3776:10: warning: unused variable ‘start’ [-Wunused-variable]
3776 | double start = picosat_time_stamp ();
| ^~~~~
picosat.c: In function ‘picosat_mus_assumptions’:
picosat.c:7377:24: warning: unused variable ‘norig’ [-Wunused-variable]
7377 | int i, j, ilit, len, norig = ps->alshead - ps->als, nwork, * work, res;
| ^~~~~
picosat.c: In function ‘picosat_stats’:
picosat.c:7991:12: warning: variable ‘redlits’ set but not used [-Wunused-but-set-variable]
7991 | unsigned redlits;
| ^~~~~~~
picosat.c: At top level:
picosat.c:6967:21: warning: ‘enumstr’ defined but not used [-Wunused-function]
6967 | static const char * enumstr (int i) {
| ^~~~~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c probabilistic_boolean_network.c -o probabilistic_boolean_network.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c reconstruct_network.c -o reconstruct_network.o
reconstruct_network.c: In function ‘reconstructNetwork_R’:
reconstruct_network.c:1069:11: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
1069 | else
| ^~~~
reconstruct_network.c:1074:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
1074 | SETCADR(entrySXP,funcSXP);
| ^~~~~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sat_search.c -o sat_search.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c statespace_search.c -o statespace_search.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c symbolic_network.c -o symbolic_network.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c symbolic_simulator.c -o symbolic_simulator.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o BoolNet.so attractor_info.o attractor_search_interface.o common.o init.o picosat.o probabilistic_boolean_network.o reconstruct_network.o sat_search.o statespace_search.o symbolic_network.o symbolic_simulator.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp2Q4izl/R.INSTALLcc0957c3e7207/BoolNet/src'
make[1]: Entering directory '/tmp/Rtmp2Q4izl/R.INSTALLcc0957c3e7207/BoolNet/src'
make[1]: Leaving directory '/tmp/Rtmp2Q4izl/R.INSTALLcc0957c3e7207/BoolNet/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-BoolNet/00new/BoolNet/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘BoolNet’
finding HTML links ... done
attractorsToLaTeX html
binarizeTimeSeries html
cellcycle html
chooseNetwork html
examplePBN html
fixGenes html
generateRandomNKNetwork html
generateState html
generateTimeSeries html
generationFunctions html
getAttractorSequence html
getAttractors html
getBasinOfAttraction html
getPathToAttractor html
getStateSummary html
getTransitionProbabilities html
getTransitionTable html
igf html
loadBioTapestry html
loadNetwork html
loadSBML html
markovSimulation html
perturbNetwork html
perturbTrajectories html
plotAttractors html
plotNetworkWiring html
plotPBNTransitions html
plotSequence html
plotStateGraph html
print.AttractorInfo html
print.BooleanNetwork html
print.MarkovSimulation html
print.ProbabilisticBooleanNetwork html
print.SymbolicSimulation html
print.TransitionTable html
reconstructNetwork html
saveNetwork html
sequenceToLaTeX html
simplifyNetwork html
simulateSymbolicModel html
stateTransition html
symbolicToTruthTable html
testNetworkProperties html
toPajek html
toSBML html
truthTableToSymbolic html
yeastTimeSeries html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BoolNet)