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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-cran-boolnet-2.1.5/inst/doc/BoolNet_package_vignette.Snw.Rnw-181-
r-cran-boolnet-2.1.5/inst/doc/BoolNet_package_vignette.Snw.Rnw:182:The cell cycle network is a classical Boolean network, where each transition function only depends on the previous state of the network. E.g., \verb+CycB, ! Cdc20 & ! Cdh1+ can be written formally as $CycB(t) = \neg Cdc20(t-1) \wedge \neg Cdh1(t-1)$. As already discussed before, \texttt{BoolNet} also incorporates several temporal extensions. For example, a transition function can also depend on the states of genes at earlier time points:
r-cran-boolnet-2.1.5/inst/doc/BoolNet_package_vignette.Snw.Rnw-183-\begin{verbatim}
##############################################
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-440-{
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:441: if (NULL == R_ExternalPtrAddr(network))
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-442- return;
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-443- //Rprintf("finalizing\n");
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:444: SymbolicBooleanNetwork * _network = R_ExternalPtrAddr(network);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-445-
##############################################
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-558-{
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:559: SymbolicBooleanNetwork * _network = R_ExternalPtrAddr(network);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-560-
##############################################
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-806-{
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:807: SymbolicBooleanNetwork * _network = R_ExternalPtrAddr(network);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-808-
##############################################
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-886- }
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:887: SETCADDR(retSXP, attractorListSXP);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-888- PutRNGstate();
##############################################
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-905-{
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:906: SymbolicBooleanNetwork * _network = R_ExternalPtrAddr(network);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-907-
##############################################
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-1154- }
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:1155: SETCADDR(retSXP, attractorListSXP);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-1156-
##############################################
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-1354- SETCADR(graphSXP, nextStatesSXP);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:1355: SETCADDR(graphSXP, attractorAssignmentSXP);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-1356- SETCADR(retSXP, graphSXP);
##############################################
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-1383-{
r-cran-boolnet-2.1.5/src/symbolic_simulator.c:1384: void * p = R_ExternalPtrAddr(ptr);
r-cran-boolnet-2.1.5/src/symbolic_simulator.c-1385-
##############################################
r-cran-boolnet-2.1.5/src/attractor_search_interface.c-199- memcpy(array, res->stepsToAttractor, res->tableSize * sizeof(int));
r-cran-boolnet-2.1.5/src/attractor_search_interface.c:200: SETCADDR(stateInfoSXP, stepSXP);
r-cran-boolnet-2.1.5/src/attractor_search_interface.c-201- UNPROTECT(1); //stepSXP 1
##############################################
r-cran-boolnet-2.1.5/src/attractor_search_interface.c-310- }
r-cran-boolnet-2.1.5/src/attractor_search_interface.c:311: SETCADDR(attractorSXP, attrInitialStateSXP);
r-cran-boolnet-2.1.5/src/attractor_search_interface.c-312- SETCADDDR(attractorSXP, attrNextStateSXP);
##############################################
r-cran-boolnet-2.1.5/src/probabilistic_boolean_network.c-632-
r-cran-boolnet-2.1.5/src/probabilistic_boolean_network.c:633: SETCADDR(resSXP,initialStateSXP);
r-cran-boolnet-2.1.5/src/probabilistic_boolean_network.c-634- SETCADDDR(resSXP,nextStateSXP);
##############################################
r-cran-boolnet-2.1.5/src/symbolic_network.c-577-{
r-cran-boolnet-2.1.5/src/symbolic_network.c:578: SymbolicBooleanNetwork * _network = R_ExternalPtrAddr(network);
r-cran-boolnet-2.1.5/src/symbolic_network.c-579-
##############################################
r-cran-boolnet-2.1.5/src/reconstruct_network.c-1079- *array = errors[gene];
r-cran-boolnet-2.1.5/src/reconstruct_network.c:1080: SETCADDR(entrySXP,errorSXP);
r-cran-boolnet-2.1.5/src/reconstruct_network.c-1081- UNPROTECT(1);
##############################################
r-cran-boolnet-2.1.5/R/loadNetwork.R-66- {
r-cran-boolnet-2.1.5/R/loadNetwork.R:67: if (regexec("^[a-zA-Z_][a-zA-Z0-9_]*$", target)[[1]] == -1)
r-cran-boolnet-2.1.5/R/loadNetwork.R-68- stop(paste("Invalid gene name:",target))
##############################################
r-cran-boolnet-2.1.5/vignettes/BoolNet_package_vignette.Snw.Rnw-181-
r-cran-boolnet-2.1.5/vignettes/BoolNet_package_vignette.Snw.Rnw:182:The cell cycle network is a classical Boolean network, where each transition function only depends on the previous state of the network. E.g., \verb+CycB, ! Cdc20 & ! Cdh1+ can be written formally as $CycB(t) = \neg Cdc20(t-1) \wedge \neg Cdh1(t-1)$. As already discussed before, \texttt{BoolNet} also incorporates several temporal extensions. For example, a transition function can also depend on the states of genes at earlier time points:
r-cran-boolnet-2.1.5/vignettes/BoolNet_package_vignette.Snw.Rnw-183-\begin{verbatim}
##############################################
r-cran-boolnet-2.1.5/debian/tests/run-unit-test-2-oname=BoolNet
r-cran-boolnet-2.1.5/debian/tests/run-unit-test:3:pkg=r-cran-`echo $oname | tr '[A-Z]' '[a-z]'`
r-cran-boolnet-2.1.5/debian/tests/run-unit-test-4-
r-cran-boolnet-2.1.5/debian/tests/run-unit-test-5-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
r-cran-boolnet-2.1.5/debian/tests/run-unit-test:6: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
r-cran-boolnet-2.1.5/debian/tests/run-unit-test-7- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
##############################################
r-cran-boolnet-2.1.5/debian/tests/run-unit-test-12-for rnw in `ls *.[rRS]nw` ; do
r-cran-boolnet-2.1.5/debian/tests/run-unit-test:13:rfile=`echo $rnw | sed 's/\.[rR]nw/.R/'`
r-cran-boolnet-2.1.5/debian/tests/run-unit-test-14-R --no-save <<EOT