rjags/0000755000175100001440000000000012643237515011406 5ustar hornikusersrjags/configure.ac0000644000175100001440000001532112643166746013705 0ustar hornikusersAC_INIT([rjags], [4]) if test -z "${R_HOME}"; then AC_MSG_ERROR("R_HOME is not defined") fi CC=`"${R_HOME}/bin/R" CMD config CC` CXX=`"${R_HOME}/bin/R" CMD config CXX` CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS` CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS` CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS` # Try using pkg-config to set compiler flags PKG_CONFIG_OK="FALSE" AC_PATH_PROG([PKG_CONFIG], [pkg-config], [], [$PATH:/usr/local/bin]) if test [ -n "${PKG_CONFIG}" ] ; then if `${PKG_CONFIG} --exists jags`; then if `${PKG_CONFIG} --exists --atleast-version=${PACKAGE_VERSION}.0.0 jags` && `${PKG_CONFIG} --exists --max-version=${PACKAGE_VERSION}.99.99 jags`; then JAGS_LIBS=`${PKG_CONFIG} --libs jags` JAGS_CFLAGS=`${PKG_CONFIG} --cflags jags` JAGS_LIBDIR=`${PKG_CONFIG} --variable libdir jags` if test [ -z "${JAGS_LIBS}" -a -z "${JAGS_CFLAGS}" ] ; then AC_MSG_WARN([Cannot get information about jags ${PACKAGE_VERSION} from pkg-config]) else AC_MSG_NOTICE([Setting compile and link flags according to pkg-config]) AC_MSG_NOTICE([Compile flags are $JAGS_CFLAGS]) AC_MSG_NOTICE([Link flags are $JAGS_LIBS]) PKG_CONFIG_OK="TRUE" fi else jags_installed_version=`${PKG_CONFIG} --modversion jags` AC_MSG_ERROR([pkg-config found JAGS ${jags_installed_version} but rjags requires JAGS ${PACKAGE_VERSION}.x.y]) fi else AC_MSG_WARN([pkg-config file for jags ${PACKAGE_VERSION} unavailable]) AC_MSG_WARN([Consider adding the directory containing `jags.pc`]) AC_MSG_WARN([to the PKG_CONFIG_PATH environment variable]) fi fi ########################## Begin legacy configuration ##################### if test "${PKG_CONFIG_OK}" != TRUE; then AC_MSG_NOTICE([Attempting legacy configuration of rjags]) # Set JAGS_PREFIX # # For installations in a non-standard location, set the prefix for # JAGS manually, using either option --with-jags-prefix or environment # variable JAGS_PREFIX. Otherwise we get the prefix from the jags # executable. AC_ARG_WITH([jags-prefix], AC_HELP_STRING([--with-jags-prefix=PREFIX_PATH], [Prefix used when JAGS was installed]), [jags_prefix_path=$withval], [jags_prefix_path=""]) if test [ -n "$jags_prefix_path" ] ; then JAGS_PREFIX=${jags_prefix_path} else if test [ -z "${JAGS_PREFIX}" ] ; then AC_PATH_PROG(jags_bin_path, [jags]) if test -n "$jags_bin_path"; then jags_bin_path=`AS_DIRNAME(["$jags_bin_path"])` JAGS_PREFIX=`AS_DIRNAME(["$jags_bin_path"])` else AC_MSG_ERROR("automatic detection of JAGS failed. Please use pkg-config to locate the JAGS library. See the INSTALL file for details.") fi fi fi # Set include path with option --with-jags-includedir or environment # variable JAGS_INCLUDEDIR. By default, this is determined from # JAGS_PREFIX. AC_ARG_WITH([jags-includedir], AC_HELP_STRING([--with-jags-includedir=INCLUDE_PATH], [the value of includedir used when JAGS was installed]), [jags_include_path=$withval], [jags_include_path=""]) if test [ -n "$jags_include_path" ] ; then JAGS_INCLUDEDIR=${jags_include_path} else if test [ -z "${JAGS_INCLUDEDIR}" ] ; then JAGS_INCLUDEDIR=${JAGS_PREFIX}/include fi fi JAGS_PKGINCLUDEDIR=${JAGS_INCLUDEDIR}/JAGS AC_LANG_PUSH(C++) OCPPFLAGS=${CPPFLAGS} CPPFLAGS=-I${JAGS_PKGINCLUDEDIR} AC_CHECK_HEADER(Console.h, [], [AC_MSG_ERROR("cannot find header file ${JAGS_PKGINCLUDEDIR}/Console.h. Please use pkg-config to locate the JAGS library. See the INSTALL file for details.")]) CPPFLAGS=${OCPPFLAGS} AC_LANG_POP() # There is no consensus on where 64- versus 32-bit libraries should be # installed. We take a hint from R, assuming that if R is installed # in, say, /usr/LIBnn/R then we can find the jags library in # ${JAGS_PREFIX}/LIBnn. # # This is a reasonable assumption if both JAGS and R have been # properly packaged, but may not be true if either has been manually # installed. The user can set the environment variable LIBnn to # override this. if test -z "${LIBnn}"; then LIBnn=`"${R_HOME}/bin/R" CMD config LIBnn` fi # Set optional library path with option --with-jags-libdir or # environment variable JAGS_LIBDIR. By default this is determined by # JAGS_PREFIX and LIBnn. AC_ARG_WITH([jags-libdir], AC_HELP_STRING([--with-jags-libdir=LIB_PATH], [the value of libdir used when JAGS was installed]), [jags_lib_path=$withval]) if test [ -n "$jags_lib_path" ] ; then JAGS_LIBDIR=$jags_lib_path else if test [ -z "${JAGS_LIBDIR}" ] ; then JAGS_LIBDIR=${JAGS_PREFIX}/${LIBnn} fi fi JAGS_CFLAGS="-I${JAGS_PKGINCLUDEDIR}" JAGS_LIBS="-L${JAGS_LIBDIR} -ljags" AC_MSG_NOTICE([Compile flags are $JAGS_CFLAGS]) AC_MSG_NOTICE([Link flags are $JAGS_LIBS]) fi ####################### END legacy configuration ########################## # Support for private installations of JAGS. If the jags library is not # on the linker path then it helps to hard-code the location of JAGS into # the DSO for rjags. Suggested by Doug Bates, April 2011. AC_ARG_ENABLE([rpath], AC_HELP_STRING([--enable-rpath], [Hard link the location of the JAGS library])) if test [ "x$enable_rpath" = "xyes"]; then JAGS_RPATH="-Wl,-rpath ${JAGS_LIBDIR}" fi # Sanity checks. OLDFLAGS=${LDFLAGS} OCFLAGS=${CFLAGS} AC_LANG_PUSH(C) CFLAGS=${JAGS_CFLAGS} # Can we link to the library? LDFLAGS="-L${JAGS_LIBDIR}" AC_CHECK_LIB(jags, jags_version, [], [AC_MSG_ERROR("cannot link to JAGS library in ${JAGS_LIBDIR}.")]) AC_LANG_POP(C) CFLAGS=${OCFLAGS} # Does the library have the correct major version number? AC_LANG_PUSH(C++) OCXXFLAGS=${CXXFLAGS} CXXFLAGS=${JAGS_CFLAGS} LDFLAGS="${JAGS_LIBS} ${JAGS_RPATH}" AC_MSG_CHECKING([version of JAGS library]) # Need to run this trivial test program first to detect runtime linkage problems AC_RUN_IFELSE( [AC_LANG_SOURCE([ #include int main() { return 0; }])], [], [AC_MSG_RESULT([link error]) AC_MSG_ERROR([Runtime link error: See the INSTALL file for help])]) # Now we can test AC_RUN_IFELSE( [AC_LANG_SOURCE([ #include int main() { return JAGS_MAJOR == ${PACKAGE_VERSION} ? 0 : 1; }])], [AC_MSG_RESULT([OK])], [AC_MSG_RESULT([wrong version]) AC_MSG_ERROR([rjags requires JAGS version ${PACKAGE_VERSION}.x.y])]) AC_LANG_POP() LDFLAGS=${OLDFLAGS} CXXFLAGS=${OCXXFLAGS} # Set location of modules JAGS_MODDIR=${JAGS_LIBDIR}/JAGS/modules-${PACKAGE_VERSION} AC_SUBST(JAGS_LIBS) AC_SUBST(JAGS_CFLAGS) AC_SUBST(JAGS_MODDIR) AC_SUBST(JAGS_RPATH) AC_OUTPUT(src/Makevars) AC_OUTPUT(R/unix/zzz.R) rjags/src/0000755000175100001440000000000012611461563012172 5ustar hornikusersrjags/src/jags.cc0000644000175100001440000004335712643210763013440 0ustar hornikusers/* * R package rjags file src/jags.cc * Copyright (C) 2006-2013 Martyn Plummer * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * version 2 as published by the Free Software Foundation. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * A copy of the GNU General Public License is available at * http://www.r-project.org/Licenses/ */ #include #include #include #include #include #include #include #include #include #include #include using std::string; using std::map; using std::pair; using std::vector; using std::copy; using jags::SArray; using jags::Console; using jags::SimpleRange; using jags::DUMP_DATA; using jags::DUMP_PARAMETERS; using jags::FactoryType; using jags::SAMPLER_FACTORY; using jags::MONITOR_FACTORY; using jags::RNG_FACTORY; using jags::RNG; /* Workaround length being remapped to Rf_length by the preprocessor */ static unsigned int sarray_len(SArray const &s) { return s.length(); } #include #include #include #include std::ostringstream jags_out; //Output stream std::ostringstream jags_err; //Error stream static SEXP JAGS_console_tag; //Run-time type checking for external pointer static bool quiet=false; //Suppress information messages static void checkConsole (SEXP s) { if (TYPEOF(s) != EXTPTRSXP || R_ExternalPtrTag(s) != JAGS_console_tag) { error("bad JAGS console pointer"); } } static int intArg(SEXP arg) { if (!isNumeric(arg)) { error("Invalid integer parameter"); } SEXP intarg; PROTECT(intarg = AS_INTEGER(arg)); int i = INTEGER(intarg)[0]; UNPROTECT(1); //intarg return i; } static char const *stringArg(SEXP arg, unsigned int i = 0) { if (!isString(arg)) { error("Invalid string parameter"); } return R_CHAR(STRING_ELT(arg,i)); } static bool boolArg(SEXP arg) { if (!isLogical(arg)) { error("Invalid logical parameter"); } return LOGICAL_POINTER(arg)[0]; } static Console * ptrArg(SEXP ptr) { checkConsole(ptr); Console *console = static_cast(R_ExternalPtrAddr(ptr)); if (console == NULL) error("JAGS model must be recompiled"); return console; } static void printMessages(bool status) { /* Print any messages from JAGS and clear the stream buffer */ if(!jags_out.str().empty()) { if (!quiet) Rprintf("%s\n", jags_out.str().c_str()); jags_out.str(""); } string msg; if (!jags_err.str().empty()) { msg = jags_err.str(); jags_err.str(""); } if (status == true) { if (!msg.empty()) { warning("%s\n", msg.c_str()); } } else { //Something bad happened if (!msg.empty()) { error("%s\n", msg.c_str()); } else { error("Internal error in JAGS library"); } } } static void setSArrayValue(SArray &sarray, SEXP e) { vector v(length(e)); copy(NUMERIC_POINTER(e), NUMERIC_POINTER(e) + length(e), v.begin()); //Replace R missing values with JAGS missing values for (vector::iterator p = v.begin(); p != v.end(); ++p) { if (ISNA(*p)) { *p = JAGS_NA; } } sarray.setValue(v); } /* Write data from an R list into a JAGS data table */ static void writeDataTable(SEXP data, map &table) { SEXP names = getAttrib(data, R_NamesSymbol); if (!isNewList(data)) { error("data must be a list"); } if (length(names) != length(data)) { error("data must be a named list"); } for (int i = 0; i < length(data); ++i) { SEXP e = AS_NUMERIC(VECTOR_ELT(data, i)); if (length(e) > 0) { string ename = CHAR(STRING_ELT(names, i)); SEXP dim = getAttrib(VECTOR_ELT(data, i), R_DimSymbol); if (dim == R_NilValue) { // Scalar or vector entry. SArray sarray(vector(1, length(e))); setSArrayValue(sarray, e); table.insert(pair(ename, sarray)); } else { // Array entry int ndim = length(dim); vector idim(ndim); for (int j = 0; j < ndim; ++j) { idim[j] = INTEGER(dim)[j]; } SArray sarray(idim); setSArrayValue(sarray, e); table.insert(pair(ename, sarray)); } } } } static SimpleRange makeRange(SEXP lower, SEXP upper) { if (lower == R_NilValue || upper == R_NilValue) { return SimpleRange(); } if (length(lower) != length(upper)) { error("length mismatch between lower and upper limits"); } int n = length(lower); SEXP il, iu; PROTECT(il = AS_INTEGER(lower)); PROTECT(iu = AS_INTEGER(upper)); vector lvec(n), uvec(n); copy(INTEGER(il), INTEGER(il) + n, lvec.begin()); copy(INTEGER(iu), INTEGER(iu) + n, uvec.begin()); UNPROTECT(2); //il, iu SimpleRange r; try { r = SimpleRange(lvec, uvec); } catch (std::logic_error except) { error("Invalid range"); } return r; } /* Read data from a JAGS data table into an R list */ static SEXP readDataTable(map const &table) { int N = table.size(); SEXP data; PROTECT(data = allocVector(VECSXP, N)); int i; map::const_iterator p; for (i = 0, p = table.begin(); p != table.end(); ++p, ++i) { int len = sarray_len(p->second); //Allocate new numeric vector SEXP e; PROTECT(e = allocVector(REALSXP, len)); //Copy values vector const &value = p->second.value(); for (int j = 0; j < len; ++j) { if (value[j] == JAGS_NA) { NUMERIC_POINTER(e)[j] = NA_REAL; } else { NUMERIC_POINTER(e)[j] = value[j]; } } if (p->second.ndim(false) > 1) { //Set dim attribute vector const &idim = p->second.dim(false); unsigned int ndim = idim.size(); SEXP dim; PROTECT(dim = allocVector(INTSXP, ndim)); for (unsigned int k = 0; k < ndim; ++k) { INTEGER(dim)[k] = idim[k]; } //Set names of the dimensions vector const &names = p->second.dimNames(); if (!names.empty()) { SEXP dimnames; PROTECT(dimnames = allocVector(STRSXP, ndim)); for (unsigned int k = 0; k < ndim; ++k) { SET_STRING_ELT(dimnames, k, mkChar(names[k].c_str())); } setAttrib(dim, R_NamesSymbol, dimnames); UNPROTECT(1); //dimnames } SET_DIM(e, dim); UNPROTECT(1); //dim //Set S dimnames bool set_s_dimnames = false; for (unsigned int k = 0; k < ndim; ++k) { if (!p->second.getSDimNames(k).empty()) { set_s_dimnames = true; break; } } if (set_s_dimnames) { SEXP sdimnames; PROTECT(sdimnames = allocVector(VECSXP, ndim)); for (unsigned int k = 0; k < ndim; ++k) { vector const &names_k = p->second.getSDimNames(k); if (names_k.empty()) { SET_VECTOR_ELT(sdimnames, k, R_NilValue); } else { SEXP snames_k; PROTECT(snames_k = allocVector(STRSXP, names_k.size())); for (unsigned int l = 0; l < names_k.size(); ++l) { SET_STRING_ELT(sdimnames, l, mkChar(names_k[l].c_str())); } UNPROTECT(1); //snames_k } } setAttrib(e, R_DimNamesSymbol, sdimnames); UNPROTECT(1); //sdimnames } } else if (!p->second.getSDimNames(0).empty()) { //Set names attribute SEXP snames; vector const &names = p->second.getSDimNames(0); PROTECT(snames = allocVector(STRSXP, names.size())); for (unsigned int l = 0; l < names.size(); ++l) { SET_STRING_ELT(snames, l, mkChar(names[l].c_str())); } setAttrib(e, R_NamesSymbol, snames); UNPROTECT(1); //snames } SET_ELEMENT(data, i, e); UNPROTECT(1); //e } //Set names SEXP names; PROTECT(names = allocVector(STRSXP, table.size())); for (i = 0, p = table.begin() ; p != table.end(); ++p, ++i) { SET_STRING_ELT(names, i, mkChar(p->first.c_str())); } setAttrib(data, R_NamesSymbol, names); UNPROTECT(2); //names, data return data; } static FactoryType asFactoryType(SEXP type) { string ft = stringArg(type); FactoryType ans = SAMPLER_FACTORY; if (ft == "sampler") { ans = SAMPLER_FACTORY; } else if (ft == "rng") { ans = RNG_FACTORY; } else if (ft == "monitor") { ans = MONITOR_FACTORY; } else { error("Invalid factory type"); } return ans; } extern "C" { void quietMessages(SEXP s) { quiet = boolArg(s); } void R_init_rjags(DllInfo *info) { JAGS_console_tag = install("JAGS_CONSOLE_TAG"); } void R_unload_rjags(DllInfo *info) { //FIXME: Need to zero console pointers vector loaded_modules = Console::listModules(); for (vector::reverse_iterator p = loaded_modules.rbegin(); p != loaded_modules.rend(); ++p) { Console::unloadModule(*p); } } SEXP clear_console(SEXP s) { /* Finalizer for console pointers. Frees the external memory and zeroes the pointer when the R object is deleted */ checkConsole(s); Console *console = static_cast(R_ExternalPtrAddr(s)); if (console != NULL) { delete console; R_ClearExternalPtr(s); } return R_NilValue; } SEXP make_console() { void *p = static_cast(new Console(jags_out, jags_err)); SEXP ptr = R_MakeExternalPtr(p, JAGS_console_tag, R_NilValue); R_RegisterCFinalizer(ptr, (R_CFinalizer_t) clear_console); return ptr; } SEXP check_model(SEXP ptr, SEXP name) { /* Name should be a name of a file containing the model */ string sname = R_ExpandFileName(stringArg(name)); FILE *file = fopen(sname.c_str(), "r"); if (!file) { jags_err << "Failed to open file " << sname << "\n"; return R_NilValue; } else { bool status = ptrArg(ptr)->checkModel(file); printMessages(status); fclose(file); return R_NilValue; } } SEXP compile(SEXP ptr, SEXP data, SEXP nchain, SEXP gendata) { if (!isNumeric(nchain)) { error("nchain must be numeric"); } if (!isVector(data)) { error("invalid data"); } map table; writeDataTable(data, table); bool status = ptrArg(ptr)->compile(table, intArg(nchain), boolArg(gendata)); printMessages(status); return R_NilValue; } SEXP set_parameters(SEXP ptr, SEXP data, SEXP nchain) { map data_table; writeDataTable(data, data_table); bool status = ptrArg(ptr)->setParameters(data_table, intArg(nchain)); printMessages(status); return R_NilValue; } SEXP set_rng_name(SEXP ptr, SEXP name, SEXP chain) { bool status = ptrArg(ptr)->setRNGname(stringArg(name), intArg(chain)); printMessages(status); return R_NilValue; } SEXP initialize(SEXP ptr) { bool status = ptrArg(ptr)->initialize(); printMessages(status); return R_NilValue; } SEXP check_adaptation(SEXP ptr) { Console *console = ptrArg(ptr); bool status = true; console->checkAdaptation(status); return ScalarLogical(status); } SEXP is_adapting(SEXP ptr) { Console *console = ptrArg(ptr); return ScalarLogical(console->isAdapting()); } SEXP adapt_off(SEXP ptr) { Console *console = ptrArg(ptr); console->adaptOff(); return R_NilValue; } SEXP update(SEXP ptr, SEXP rniter) { int niter = intArg(rniter); Console *console = ptrArg(ptr); if (!console->update(niter)) { Rprintf("\n"); printMessages(false); } return R_NilValue; } SEXP set_monitors(SEXP ptr, SEXP names, SEXP lower, SEXP upper, SEXP thin, SEXP type) { if (!isString(names)) { error("names must be a character vector"); } int n = length(names); if (length(lower) != n || length(upper) != n) { error("length of names must match length of lower and upper"); } SEXP status; //Was attempt to set monitor successful? PROTECT(status = allocVector(LGLSXP, n)); for (int i = 0; i < n; ++i) { SimpleRange range = makeRange(VECTOR_ELT(lower, i), VECTOR_ELT(upper, i)); bool ok = ptrArg(ptr)->setMonitor(stringArg(names,i), range, intArg(thin), stringArg(type)); printMessages(true); LOGICAL_POINTER(status)[i] = ok; } UNPROTECT(1); //status return status; } SEXP clear_monitor(SEXP ptr, SEXP name, SEXP lower, SEXP upper, SEXP type) { SimpleRange range = makeRange(lower, upper); bool status = ptrArg(ptr)->clearMonitor(stringArg(name), range, stringArg(type)); printMessages(status); return R_NilValue; } SEXP get_monitored_values(SEXP ptr, SEXP type) { map data_table; bool status = ptrArg(ptr)->dumpMonitors(data_table, stringArg(type), false); printMessages(status); return readDataTable(data_table); } //FIXME: lazy cut-and-paste here SEXP get_monitored_values_flat(SEXP ptr, SEXP type) { map data_table; bool status = ptrArg(ptr)->dumpMonitors(data_table, stringArg(type), true); printMessages(status); return readDataTable(data_table); } SEXP get_data(SEXP ptr) { map data_table; string rngname; //Not actually needed bool status = ptrArg(ptr)->dumpState(data_table, rngname, DUMP_DATA, 1); printMessages(status); return readDataTable(data_table); } SEXP get_state(SEXP ptr) { Console *console = ptrArg(ptr); unsigned int nchain = console->nchain(); if (nchain == 0) { return R_NilValue; } //ans is the list that contains the state for each chain SEXP ans; PROTECT(ans = allocVector(VECSXP, nchain)); for (unsigned int n = 0; n < nchain; ++n) { string srng; map param_table; console->dumpState(param_table, srng, DUMP_PARAMETERS, n+1); //Read the parameter values into an R list SEXP params; PROTECT(params = readDataTable(param_table)); int nparam = length(params); SEXP names = getAttrib(params, R_NamesSymbol); //Now we have to make a copy of the list with an extra element SEXP staten, namesn; PROTECT(staten = allocVector(VECSXP, nparam + 1)); PROTECT(namesn = allocVector(STRSXP, nparam + 1)); for (int j = 0; j < nparam; ++j) { SET_ELEMENT(staten, j, VECTOR_ELT(params, j)); SET_STRING_ELT(namesn, j, STRING_ELT(names, j)); } //Assign .RNG.name as the last element SEXP rngname; PROTECT(rngname = mkString(srng.c_str())); SET_ELEMENT(staten, nparam, rngname); SET_STRING_ELT(namesn, nparam, mkChar(".RNG.name")); setAttrib(staten, R_NamesSymbol, namesn); //And we're done with this chain SET_ELEMENT(ans, n, staten); UNPROTECT(4); //rngname, namesn, staten, params } UNPROTECT(1); //ans return ans; } SEXP get_variable_names(SEXP ptr) { Console *console = ptrArg(ptr); vector const &namevec = console->variableNames(); SEXP varnames; PROTECT(varnames = allocVector(STRSXP,namevec.size())); for (unsigned int i = 0; i < namevec.size(); ++i) { SET_STRING_ELT(varnames, i, mkChar(namevec[i].c_str())); } UNPROTECT(1); //varnames return varnames; } SEXP get_samplers(SEXP ptr) { Console *console = ptrArg(ptr); vector > samplers; bool status = console->dumpSamplers(samplers); printMessages(status); unsigned int n = samplers.size(); SEXP node_list, sampler_names; PROTECT(node_list = allocVector(VECSXP, n)); PROTECT(sampler_names = allocVector(STRSXP, n)); for (unsigned int i = 0; i < n; ++i) { int nnode = samplers[i].size() - 1; SEXP e; PROTECT(e=allocVector(STRSXP, nnode)); for (int j = 0; j < nnode; ++j) { SET_STRING_ELT(e, j, mkChar(samplers[i][j+1].c_str())); } SET_ELEMENT(node_list, i, e); SET_STRING_ELT(sampler_names, i, mkChar(samplers[i][0].c_str())); UNPROTECT(1); //e } setAttrib(node_list, R_NamesSymbol, sampler_names); UNPROTECT(2); //node_list, sampler_names return node_list; } SEXP get_factories(SEXP type) { FactoryType ft = asFactoryType(type); vector > factories = Console::listFactories(ft); unsigned int n = factories.size(); SEXP fac_list; PROTECT(fac_list = allocVector(VECSXP, 2)); SEXP names, status; PROTECT(names = allocVector(STRSXP, n)); PROTECT(status = allocVector(LGLSXP, n)); for (unsigned int i = 0; i < n; ++i) { SET_STRING_ELT(names, i, mkChar(factories[i].first.c_str())); LOGICAL_POINTER(status)[i] = factories[i].second; } SET_ELEMENT(fac_list, 0, names); SET_ELEMENT(fac_list, 1, status); UNPROTECT(2); //names, status SEXP fac_names; PROTECT(fac_names = allocVector(STRSXP,2)); SET_STRING_ELT(fac_names, 0, mkChar("factory")); SET_STRING_ELT(fac_names, 1, mkChar("status")); setAttrib(fac_list, R_NamesSymbol, fac_names); UNPROTECT(1); //fac_names UNPROTECT(1); //fac_list return fac_list; } SEXP set_factory_active(SEXP name, SEXP type, SEXP status) { Console::setFactoryActive(stringArg(name), asFactoryType(type), boolArg(status)); return R_NilValue; } SEXP get_iter(SEXP ptr) { return ScalarInteger(ptrArg(ptr)->iter()); } SEXP get_nchain(SEXP ptr) { return ScalarInteger(ptrArg(ptr)->nchain()); } SEXP load_module(SEXP name) { return ScalarLogical(Console::loadModule(stringArg(name))); } SEXP unload_module(SEXP name) { return ScalarLogical(Console::unloadModule(stringArg(name))); } SEXP get_modules() { vector modules = Console::listModules(); unsigned int n = modules.size(); SEXP mod_list; PROTECT(mod_list = allocVector(STRSXP, n)); for (unsigned int i = 0; i < n; ++i) { SET_STRING_ELT(mod_list, i, mkChar(modules[i].c_str())); } UNPROTECT(1); //mod_list return mod_list; } SEXP get_version() { return mkString(jags_version()); } } rjags/src/parallel.cc0000644000175100001440000000630412643210763014277 0ustar hornikusers/* * R package rjags file src/parallel.cc * Copyright (C) 2011-2013 Martyn Plummer * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * version 2 as published by the Free Software Foundation. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * A copy of the GNU General Public License is available at * http://www.r-project.org/Licenses/ */ /* Utility function to get parallel seeds for execution in parallel * * Makes extensive use of JAGS internals and is potentially unsafe on Windows * if an exception is thrown. */ #include #include #include #include #include #include #include using std::string; using std::pair; using std::vector; using std::list; using jags::RNG; using jags::RNGFactory; using jags::Model; #include #include #include //Cut and pasted from jags.cc static int intArg(SEXP arg) { if (!isNumeric(arg)) { error("Invalid integer parameter"); } SEXP intarg; PROTECT(intarg = AS_INTEGER(arg)); int i = INTEGER(intarg)[0]; UNPROTECT(1); //intarg return i; } static char const *stringArg(SEXP arg, unsigned int i = 0) { if (!isString(arg)) { error("Invalid string parameter"); } return R_CHAR(STRING_ELT(arg,i)); } extern "C" { SEXP parallel_seeds(SEXP fac, SEXP n) { unsigned int nchain = intArg(n); string factory = stringArg(fac); vector rngvec; list > const &flist = Model::rngFactories(); for (list >::const_iterator p = flist.begin(); p != flist.end(); ++p) { if (p->first->name() == factory) { if (p->second) { rngvec = p->first->makeRNGs(nchain); break; } else { string msg = string("RNG factory not active: ") + factory; error(msg.c_str()); } } } if (rngvec.empty()) { string msg = string("RNG factory not found: ") + factory; error(msg.c_str()); } SEXP rng_list; PROTECT(rng_list = allocVector(VECSXP, rngvec.size())); SEXP elt_names; PROTECT(elt_names = allocVector(STRSXP, 2)); SET_STRING_ELT(elt_names, 0, mkChar(".RNG.name")); SET_STRING_ELT(elt_names, 1, mkChar(".RNG.state")); for (unsigned int i = 0; i < rngvec.size(); ++i) { SEXP rngname; PROTECT(rngname = mkString(rngvec[i]->name().c_str())); SEXP rngstate; vector istate; rngvec[i]->getState(istate); PROTECT(rngstate = allocVector(INTSXP, istate.size())); for (unsigned int j = 0; j < istate.size(); ++j) { INTEGER(rngstate)[j] = istate[j]; } SEXP rng_i; PROTECT(rng_i = allocVector(VECSXP, 2)); SET_ELEMENT(rng_i, 0, rngname); SET_ELEMENT(rng_i, 1, rngstate); UNPROTECT(2); //istate, rngstate setAttrib(rng_i, R_NamesSymbol, elt_names); SET_ELEMENT(rng_list, i, rng_i); UNPROTECT(1); //rng_i; } UNPROTECT(2); //elt_names, rng_list return rng_list; } } rjags/src/Makevars.in0000644000175100001440000000007612643210763014275 0ustar hornikusersPKG_CPPFLAGS=@JAGS_CFLAGS@ PKG_LIBS=@JAGS_LIBS@ @JAGS_RPATH@ rjags/src/Makevars.win0000644000175100001440000000013012643210763014453 0ustar hornikusersPKG_CPPFLAGS=-I"$(JAGS_ROOT)/include" PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-4 rjags/NAMESPACE0000644000175100001440000000155512612424177012631 0ustar hornikusersif(.Platform$OS.type == "windows") { importFrom(utils, readRegistry, winProgressBar, setWinProgressBar, packageVersion, file_test) } importFrom(utils, txtProgressBar, setTxtProgressBar) importFrom(stats, variable.names, sd, update) importFrom(coda, as.mcmc.list, as.mcmc, mcmc.list, mcmc, spectrum0, "varnames<-") export ( jags.model, jags.samples, coda.samples, load.module, unload.module, list.modules, dic.samples, diffdic, adapt, list.samplers, list.factories, set.factory, read.data, read.jagsdata, read.bugsdata, parallel.seeds ) S3method(print, jags) S3method(coef, jags) S3method(update, jags) S3method(variable.names, jags) S3method(print, mcarray) S3method(summary, mcarray) S3method(print, summary.mcarray) S3method(as.mcmc.list, mcarray) S3method("-", dic) S3method(print, dic) S3method(print, diffdic) rjags/INSTALL0000644000175100001440000001716512643206534012446 0ustar hornikusersInstallation instructions for the rjags package ----------------------------------------------- The rjags package is an interface to the JAGS library. In order to build a binary package, or install from source, you must have a matching installation of the JAGS library. Contents: 1 Windows 2 Unix/Linux: pkg-config 3 Unix/Linux: runtime linkage 4 Unix/Linux: legacy configuration 1 Windows --------- If you are compiling the rjags package from source on Windows then you must supply the location of JAGS using the make variable JAGS_ROOT, defining it in the file HOME/.R/Makevars.win, e.g. JAGS_ROOT=c:/Progra~1/JAGS/JAGS-4.0.0 where HOME is the default starting directory for an R session launched from the start menu (typically your Documents folder). If you are installing the Windows binary rjags package, then R will consult the Windows registry to find the location of JAGS. Alternatively, you can specify the location of JAGS by setting the environment variable JAGS_HOME. 2 Unix/Linux: pkg-config ------------------------ If you have pkg-config installed then the configure script will use it to detect the JAGS library and set the compiler and linker flags for rjags. You can test this capability in a unix shell by typing pkg-config --modversion jags If this does not detect your JAGS installation then it means that the file 'jags.pc' is not on the search path of pkg-config. In this case you should add it by setting the environment variable PKG_CONFIG_PATH. For example if the full path to 'jags.pc' is '/usr/local/lib64/pkgconfig/jags.pc', then set export PKG_CONFIG_PATH=/usr/local/lib64/pkgconfig before installing rjags. Recall that most Linux distributions divide software into `user' and `developer' versions, so if you are using a pre-built JAGS binary package for your Linux distribution then remember to install the developer version before attempting to install the rjags package. 3 Unix/Linux: runtime linkage ----------------------------- Although pkg-config helps to find the right flags for linking to the JAGS library at compile time, it does not help at runtime. In order to detect potential problems with runtime linkage, the configure script of the rjags package will compile and run a test program that links to the JAGS library. If this fails with the message "runtime link error" then you may take the following actions to fix the problem: If you have administrative privileges (sudo or root access): 1) Add the directory containing the JAGS library to the linker path, typically by editing the file /etc/ld.so.conf. 2) If the directory is already on the linker path then you may need to run /sbin/ldconfig as root to update the linker cache. If you do not have administrative privileges: 3) Set the environment variable LD_RUN_PATH to the directory containing the JAGS library before installing rjags, or 4) Use the --enable-rpath option when installing rjags, i.e. from the unix shell: R CMD INSTALL --configure-args='--enable-rpath' rjags or, within R > install.packages("rjags", configure.args="--enable-rpath") You may also consider: 5) Set the environment variable LD_LIBRARY_PATH to the directory containing the JAGS library. Unlike options 3) and 4) if you use LD_LIBRARY_PATH then it must be set every time you load the rjags package, not just at compile time. Thus it is best to set this in the file .bash_profile (or the equivalent file if you using another shell). 4 Unix/Linux: legacy configuration ---------------------------------- Legacy configuration is used whenever pkg-config is not installed or otherwise fails to detect the JAGS library. Legacy configuration is deprecated and will be removed in a future version. If you experience problems with installing rjags then it is strongly recommended that you try to get pkg-config working rather than use the options below. The configure script will try to guess the location of the JAGS library. It does this by querying the R and jags executables, so both of these need to be on your PATH for automatic detection to work properly. If you have installed JAGS in a non-standard place then you may need to supply hints to the configure script. This can be done by passing configure arguments or setting environment variables (see below). The options/environment variables correspond to options that were used when JAGS was installed. They are shown in the table below: JAGS configure rjags configure Environmnent default option option variable -------------- --------------- ------------ ------- --prefix --with-jags-prefix JAGS_PREFIX /usr/local --libdir --with-jags-libdir JAGS_LIBDIR ${prefix}/${LIBnn} --includedir --with-jags-includedir JAGS_INCLUDEDIR ${prefix}/include By default LIBnn is the value returned by `R CMD config LIBnn`. This can be overridden by setting the environment variable LIBnn. 4.1 Setting the prefix ---------------------- By default, all JAGS files are installed in subdirectories of /usr/local. This is the prefix of the installation, and it can be changed to any value by supplying the --prefix argument when installing JAGS. - The jags script goes in ${prefix}/bin - The jags executable launched by the script goes in ${prefix}/libexec - The libraries go in ${prefix}/lib - The modules go in ${prefix}/lib/JAGS - The headers go in ${prefix}/include/JAGS Suppose that when you installed JAGS, you used the configure argument '--prefix=/opt' to install JAGS in the directory /opt instead of the default /usr/local. If /opt/bin is on your PATH then the configure script should still automatically detect JAGS for you. Otherwise, you need to supply the configure argument '--with-jags-prefix=/opt' when installing rjags. Alternatively you can set the environment variable JAGS_PREFIX before building rjags: export JAGS_PREFIX=/opt 4.2 Setting the library directory --------------------------------- Suppose you are on a 64-bit system and installed the JAGS library in /usr/local/lib64 instead of the default /usr/local/lib. If R_HOME is /usr/lib64/R then the configure script should automatically look in the right place for the JAGS library. Otherwise, you need to supply the configure argument '--with-jags-libdir=/usr/local/lib64' when installing rjags. Alternatively you can set the environment variable JAGS_LIBDIR before building rjags: export JAGS_LIBDIR=/usr/local/lib64 If the library directory is in the right prefix, but just has a different name (e.g. ${prefix}/lib64 or ${prefix}/lib32 instead of the default ${prefix}/lib), then you can just set the environment variable LIBnn. export LIBnn=lib64 4.3 Setting the include directory --------------------------------- It is unlikely that you will need to set the include directory, as there is no good reason for changing the default. Nevertheless, this option is included for completeness. By default, the header files go into ${prefix}/include, in a sub-directory JAGS. If you have put this subdirectory somewhere other than ${prefix}/include by supplying the --includedir option to configure when you built JAGS, then the corresponding option for rjags is --with-jags-includedir. Alternatively, you may set the environment variable JAGS_INCLUDEDIR. 4.4 Passing configure arguments ------------------------------- Configure options for rjags are passed via the --configure-args argument to R CMD INSTALL: R CMD INSTALL --configure-args='--with-jags...' or, if you are using the install.packages() function from an R session, using the configure.args argument: install.packages("rjags", configure.args="--with-jags...") If configure arguments are set, they always override the corresponding environment variables. rjags/data/0000755000175100001440000000000012611461563012314 5ustar hornikusersrjags/data/LINE.RData0000644000175100001440000000335212611461563013763 0ustar hornikusersrDTr^)-iN@MڴPa|59hgScs+H"ض>݃SV_Y!HQdnZJ镱o`vHv;OKKN胍 )J/=BGh/> ʇ$}3'G rݦ5EvhWJl 'ꝝfbG3VYN =qo"llRY}\fZ{|Iz<զB"INsB@ô`G#7|@8**X&nx^.OpfKtܶ+u{0pYb9$S6vYe7fwxOXH\]Cn{"N@c߇ϰDS7Kh ;!ط{r_rnC0Fy4CB_%DP5䖣]b405a?ièHXMJLtFjjK1DMfG+1:8焯 k 4X'y~/$i \TI/r(IȤCg&lVñ0HIFB/=\闻_Hk TT tͅ[qaB0{my gK"nQmZo{W?UB֏?PG-^}%!%"N;m׬6 h5 cZ^؆&wq06nU1tQVKv'V^vRҲ|I%х]DDs{v+J>?T0󳳗\ PGٚ!CTNFd"X+` SaAfgU7\ (m)  fHqJ23 #`KMss0:j?l/F_ofކ.EҪ8B^kKfN7oVUoӓ?GX 0) { cat("\nMarginalizing over:", paste(paste(names(x$drop.dims), "(", x$drop.dims,")" , sep=""), collapse=","),"\n") } } make.coda.names <- function(basename, dim) { if (all(dim == 1)) { return(basename) } else { ll <- lapply(as.list(dim), function(n) seq(from=1, to=n)) elements <- expand.grid(ll) elt.names <- apply(elements, 1, paste, collapse=",") elt.names <- paste0(basename, "[", elt.names, "]") return(elt.names) } } as.mcmc.list.mcarray <- function(x, ...) { if (is.null(dim(x)) || is.null(names(dim(x)))) { NextMethod() } xdim <- dim(x) ndim <- length(xdim) dn <- names(xdim) which.iter <- which(dn=="iteration") if (length(which.iter) != 1) { stop("Bad iteration dimension in mcarray") } which.chain <- which(dn=="chain") if (length(which.chain) > 1) { stop("Bad chain dimension in mcarray") } niter <- xdim[which.iter] if (length(which.chain) == 0) { perm <- c((1:ndim)[-which.iter], which.iter) y <- matrix(aperm(x, perm), nrow=niter, byrow=TRUE) ans <- mcmc.list(mcmc(y)) } else { nchain <- xdim[which.chain] ans <- vector("list",nchain) len <- prod(xdim[-which.chain]) perm <- c((1:ndim)[-c(which.iter,which.chain)], which.iter, which.chain) y <- aperm(x,perm) for (i in 1:nchain) { ans[[i]] <- mcmc(matrix(y[1:len + (i-1)*len], nrow=niter, byrow=TRUE)) } ans <- mcmc.list(ans) } bugs.name <- attr(x, "varname", exact=TRUE) if (!is.null(bugs.name)) { elt.names <- make.coda.names(bugs.name, xdim[-c(which.iter, which.chain)]) ### Work around bug in coda::varnames<- for (i in 1:nchain) { colnames(ans[[i]]) <-elt.names } } return(ans) } rjags/R/jags.R0000644000175100001440000004733012611462372012661 0ustar hornikusers# R package rjags file R/jags.R # Copyright (C) 2006-2013 Martyn Plummer # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License version # 2 as published by the Free Software Foundation. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # A copy of the GNU General Public License is available at # http://www.r-project.org/Licenses/ # .quiet.messages <- function(quiet) { .Call("quietMessages", quiet, PACKAGE="rjags") } print.jags <- function(x, ...) { cat("JAGS model:\n\n") model <- x$model() for (i in 1:length(model)) { cat(model[i],"\n",sep="") } data <- x$data() full <- !sapply(lapply(data, is.na), any) if (any(full)) { cat("Fully observed variables:\n", names(data)[full], "\n") } part <- !full & !sapply(lapply(data, is.na), all) if (any(part)) { cat("Partially observed variables:\n", names(data)[part], "\n") } } jags.model <- function(file, data=NULL, inits, n.chains = 1, n.adapt=1000, quiet=FALSE) { if (missing(file)) { stop("Model file name missing") } if (is.character(file)) { modfile <- file ## Check file exists and can be opened in text mode con <- try(file(modfile, "rt")) if (inherits(con, "try-error")) { stop(paste("Cannot open model file \"", modfile, "\"", sep="")) } close(con) ## Need this for print method and for recompile function model.code <- readLines(file, warn=FALSE) } else if (inherits(file, "connection")) { modfile <- tempfile() ## JAGS library requires a physical file, so we need to copy ## the contents of the connection to a temporary file model.code <- readLines(file, warn=FALSE) writeLines(model.code, modfile) } else { stop("'file' must be a character string or connection") } if (quiet) { .quiet.messages(TRUE) on.exit(.quiet.messages(FALSE), add=TRUE) } p <- .Call("make_console", PACKAGE="rjags") .Call("check_model", p, modfile, PACKAGE="rjags") if (!is.character(file)) { unlink(modfile) #Remove temporary copy } varnames <- .Call("get_variable_names", p, PACKAGE="rjags") if (missing(data) || is.null(data)) { data <- list() } else if (is.environment(data)) { ##Get a list of numeric objects from the supplied environment data <- mget(varnames, envir=data, mode="numeric", ifnotfound=list(NULL)) ##Strip null entries data <- data[!sapply(data, is.null)] } else if (is.list(data)) { v <- names(data) if (is.null(v) && length(v) != 0) { stop("data must be a named list") } if (any(nchar(v)==0)) { stop("unnamed variables in data list") } if (any(duplicated(v))) { stop("Duplicated names in data list: ", paste(v[duplicated(v)], collapse=" ")) } relevant.variables <- v %in% varnames data <- data[relevant.variables] unused.variables <- setdiff(v, varnames) for (i in seq(along=unused.variables)) { warning("Unused variable \"", unused.variables[i], "\" in data") } ### Check for data frames df <- which(as.logical(sapply(data, is.data.frame))) for (i in seq(along=df)) { if (all(sapply(data[[df[i]]], is.numeric))) { #Turn numeric data frames into matrices data[[df[i]]] <- as.matrix(data[[df[i]]]) } else { stop("Data frame with non-numeric elements provided as data: ", names(data)[df[i]]) } } } else { stop("data must be a list or environment") } .Call("compile", p, data, as.integer(n.chains), TRUE, PACKAGE="rjags") ### Setting initial values if (!missing(inits) && !is.null(inits)) { checkParameters <- function(inits) { if(!is.list(inits)) { return("inits parameter must be a list") } inames <- names(inits) if (is.null(inames) || any(nchar(inames) == 0)) { return("No variable names supplied for the initial values") } dupinames <- duplicated(inames) if (any(dupinames)) { return(paste("Duplicated initial values for variable(s): ", paste0(unique(inames[dupinames]), collapse = ", ") ) ) } if (any(inames==".RNG.name")) { rngname <- inits[[".RNG.name"]] if (!is.character(rngname) || length(rngname) != 1) { return("Incorrect .RNG.name value") } inits[[".RNG.name"]] <- NULL } ## Strip null initial values, but give a warning null.inits <- sapply(inits, is.null) if (any(null.inits)) { warning(paste("NULL initial value supplied for variable(s) ", paste(inames[null.inits], collapse=", "), sep="")) inits <- inits[!null.inits] } num_vals <- sapply(inits, is.numeric) if (any(!num_vals)) { return(paste("Non-numeric initial values supplied for variable(s) ", paste(inames[!num_vals], collapse=", "), sep="")) } return ("ok") } setParameters <- function(inits, chain) { if (!is.null(inits[[".RNG.name"]])) { .Call("set_rng_name", p, inits[[".RNG.name"]], as.integer(chain), PACKAGE="rjags") inits[[".RNG.name"]] <- NULL } .Call("set_parameters", p, inits, as.integer(chain), PACKAGE="rjags") } init.values <- vector("list", n.chains) if (is.function(inits)) { if (any(names(formals(inits)) == "chain")) { for (i in 1:n.chains) { init.values[[i]] <- inits(chain=i) } } else { for (i in 1:n.chains) { init.values[[i]] <- inits() } } } else if (is.list(inits)) { if ( !is.null(names(inits)) ) { ## Replicate initial values for all chains for (i in 1:n.chains) { init.values[[i]] <- inits } } else { if (length(inits) != n.chains) { stop("Length mismatch between inits and n.chains") } init.values <- inits } } for (i in 1:n.chains) { msg <- checkParameters(init.values[[i]]) if (!identical(msg, "ok")) { stop("Invalid parameters for chain ", i, ":\n", msg); } setParameters(init.values[[i]], i) unused.inits <- setdiff(names(init.values[[i]]), varnames) unused.inits <- setdiff(unused.inits, c(".RNG.seed", ".RNG.state", ".RNG.name")) for (j in seq(along=unused.inits)) { warning("Unused initial value for \"", unused.inits[j], "\" in chain ", i) } } } .Call("initialize", p, PACKAGE="rjags") model.state <- .Call("get_state", p, PACKAGE="rjags") model.data <- .Call("get_data", p, PACKAGE="rjags") model <- list("ptr" = function() {p}, "data" = function() {model.data}, "model" = function() {model.code}, "state" = function(internal=FALSE) { if(!internal) { for(i in 1:n.chains) { model.state[[i]][[".RNG.state"]] <- NULL model.state[[i]][[".RNG.name"]] <- NULL } } return(model.state) }, "nchain" = function() { .Call("get_nchain", p, PACKAGE="rjags") }, "iter" = function() { .Call("get_iter", p, PACKAGE="rjags") }, "sync" = function() { model.state <<- .Call("get_state", p, PACKAGE="rjags") }, "recompile" = function() { ## Clear the console .Call("clear_console", p, PACKAGE="rjags") p <<- .Call("make_console", PACKAGE="rjags") ## Write the model to a temporary file so we can re-read it mf <- tempfile() writeLines(model.code, mf) .Call("check_model", p, mf, PACKAGE="rjags") unlink(mf) ## Re-compile .Call("compile", p, data, n.chains, FALSE, PACKAGE="rjags") ## Re-initialize if (!is.null(model.state)) { if (length(model.state) != n.chains) { stop("Incorrect number of chains in saved state") } for (i in 1:n.chains) { statei <- model.state[[i]] rng <- statei[[".RNG.name"]] if (!is.null(rng)) { .Call("set_rng_name", p, rng, i, PACKAGE="rjags") statei[[".RNG.name"]] <- NULL } .Call("set_parameters", p, statei, i, PACKAGE="rjags") } .Call("initialize", p, PACKAGE="rjags") ## Redo adaptation adapting <- .Call("is_adapting", p, PACKAGE="rjags") if(n.adapt > 0 && adapting) { cat("Adapting\n") .Call("update", p, n.adapt, PACKAGE="rjags") if (!.Call("check_adaptation", p, PACKAGE="rjags")) { warning("Adaptation incomplete"); } } model.state <<- .Call("get_state", p, PACKAGE="rjags") } invisible(NULL) }) class(model) <- "jags" if (n.adapt > 0) { pb <- if(quiet) NULL else getOption("jags.pb") ok <- adapt(model, n.adapt, end.adaptation=FALSE, progress.bar=pb) if (ok) { .Call("adapt_off", p, PACKAGE="rjags") } else { warning("Adaptation incomplete") } } return(model) } parse.varname <- function(varname) { ## Try to parse string of form "a" or "a[n,p:q,r]" where "a" is a ## variable name and n,p,q,r are integers v <- try(parse(text=varname, n=1), silent=TRUE) if (!is.expression(v) || length(v) != 1) return(NULL) v <- v[[1]] if (is.name(v)) { ##Full node array requested return(list(name=deparse(v))) } else if (is.call(v) && identical(deparse(v[[1]]), "[") && length(v) > 2) { ##Subset requested ndim <- length(v) - 2 lower <- upper <- numeric(ndim) if (any(nchar(sapply(v, deparse)) == 0)) { ##We have to catch empty indices here or they will cause trouble ##below return(NULL) } for (i in 1:ndim) { index <- v[[i+2]] if (is.numeric(index)) { ##Single index lower[i] <- upper[i] <- index } else if (is.call(index) && length(index) == 3 && identical(deparse(index[[1]]), ":") && is.numeric(index[[2]]) && is.numeric(index[[3]])) { ##Index range lower[i] <- index[[2]] upper[i] <- index[[3]] } else return(NULL) } if (any(upper < lower)) return (NULL) return(list(name = deparse(v[[2]]), lower=lower, upper=upper)) } return(NULL) } parse.varnames <- function(varnames) { names <- character(length(varnames)) lower <- upper <- vector("list", length(varnames)) for (i in seq(along=varnames)) { y <- parse.varname(varnames[i]) if (is.null(y)) { stop(paste("Invalid variable subset", varnames[i])) } names[i] <- y$name if (!is.null(y$lower)) { lower[[i]] <- y$lower } if (!is.null(y$upper)) { upper[[i]] <- y$upper } } return(list(names=names, lower=lower, upper=upper)) } jags.samples <- function(model, variable.names, n.iter, thin=1, type="trace", ...) { if (class(model) != "jags") stop("Invalid JAGS model") if (!is.character(variable.names) || length(variable.names) == 0) stop("variable.names must be a character vector") if (!is.numeric(n.iter) || length(n.iter) != 1 || n.iter <= 0) stop("n.iter must be a positive integer") if (!is.character(type)) stop("type must be a character vector") pn <- parse.varnames(variable.names) status <- .Call("set_monitors", model$ptr(), pn$names, pn$lower, pn$upper, as.integer(thin), type, PACKAGE="rjags") if (!any(status)) stop("No valid monitors set") update.jags(model, n.iter, ...) ans <- .Call("get_monitored_values", model$ptr(), type, PACKAGE="rjags") for (i in seq(along=ans)) { class(ans[[i]]) <- "mcarray" attr(ans[[i]], "varname") <- names(ans)[i] } for (i in seq(along=variable.names)) { if (status[i]) { .Call("clear_monitor", model$ptr(), pn$names[i], pn$lower[[i]], pn$upper[[i]], type, PACKAGE="rjags") } } return(ans) } list.samplers <- function(object) { if (!inherits(object, "jags")) { stop("not a jags model object") } .Call("get_samplers", object$ptr(), PACKAGE="rjags") } list.factories <- function(type) { type = match.arg(type, c("sampler","monitor","rng")) as.data.frame(.Call("get_factories", type, PACKAGE="rjags")) } set.factory <- function(name, type, state) { if (!is.character(name) || length(name) != 1) stop("invalid name") if (!is.character(type) || length(type) != 1) stop("invalid name") if (length(state) != 1) stop("invalid state") type <- match.arg(type, c("sampler","rng","monitor")) .Call("set_factory_active", name, type, as.logical(state), PACKAGE="rjags") } coda.names <- function(basename, dim) { ## Utility function used to get the names of the individual elements ## of a node array if (prod(dim) == 1) return(basename) ##Default lower and upper limits ndim <- length(dim) lower <- rep(1, ndim) upper <- dim ##If the node name is a subset, we try to parse it to get the ##names of its elements. For example, if basename is "A[2:3]" ##we want to return names "A[2]", "A[3]" not "A[2:3][1]", "A[2:3][2]". pn <- parse.varname(basename) if (!is.null(pn) && !is.null(pn$lower) && !is.null(pn$upper)) { if (length(pn$lower) == length(pn$upper)) { dim2 <- pn$upper - pn$lower + 1 if (isTRUE(all.equal(dim[dim!=1], dim2[dim2!=1], check.attributes=FALSE))) { basename <- pn$name lower <- pn$lower upper <- pn$upper ndim <- length(dim2) } } } indices <- as.character(lower[1]:upper[1]) if (ndim > 1) { for (i in 2:ndim) { indices <- outer(indices, lower[i]:upper[i], FUN=paste, sep=",") } } paste(basename,"[",as.vector(indices),"]",sep="") } nchain <- function(model) { if (!inherits(model, "jags")) stop("Invalid JAGS model object in nchain") .Call("get_nchain", model$ptr(), PACKAGE="rjags") } coda.samples <- function(model, variable.names=NULL, n.iter, thin=1, na.rm = TRUE, ...) { start <- model$iter() + thin out <- jags.samples(model, variable.names, n.iter, thin, type="trace", ...) ans <- vector("list", nchain(model)) for (ch in 1:nchain(model)) { ans.ch <- vector("list", length(out)) vnames.ch <- NULL for (i in seq(along=out)) { varname <- names(out)[[i]] d <- dim(out[[i]]) if (length(d) < 3) { stop("Invalid dimensions for sampled output") } vardim <- d[1:(length(d)-2)] nvar <- prod(vardim) niter <- d[length(d) - 1] nchain <- d[length(d)] values <- as.vector(out[[i]]) var.i <- matrix(NA, nrow=niter, ncol=nvar) for (j in 1:nvar) { var.i[,j] <- values[j + (0:(niter-1))*nvar + (ch-1)*niter*nvar] } vnames.ch <- c(vnames.ch, coda.names(varname, vardim)) ans.ch[[i]] <- var.i } ans.ch <- do.call("cbind", ans.ch) colnames(ans.ch) <- vnames.ch ans[[ch]] <- mcmc(ans.ch, start=start, thin=thin) } if (isTRUE(na.rm)) { ## Drop variables that are missing for all iterations in at least ## one chain all.missing <- sapply(ans, function(x) {apply(is.na(x), 2, any)}) drop.vars <- if (is.matrix(all.missing)) { apply(all.missing, 1, any) } else { any(all.missing) } ans <- lapply(ans, function(x) return(x[, !drop.vars, drop=FALSE])) } mcmc.list(ans) } load.module <- function(name, path, quiet=FALSE) { if (name %in% list.modules()) { ## This is a stop-gap measure as JAGS 2.1.0 does allow you ## to load the same module twice. This should be fixed in ## later versions. return(invisible()) #Module already loaded } if (missing(path)) { path = getOption("jags.moddir") if (is.null(path)) { stop("option jags.moddir is not set") } } if (!is.character(path) || length(path) != 1) stop("invalid path") if (!is.character(name) || length(name) != 1) stop("invalid name") file <- file.path(path, paste(name, .Platform$dynlib.ext, sep="")) if (!file.exists(file)) { stop("File not found: ", file) } if (!isDLLLoaded(file)) { ## We must avoid calling dyn.load twice on the same DLL This ## may result in the DLL being unloaded and then reloaded, ## which will invalidate pointers to the distributions, ## functions and factories in the module. dyn.load(file) } ok <- .Call("load_module", name, PACKAGE="rjags") if (!ok) { stop(paste("module", name, "not found\n")) } else if (!quiet) { message("module ", name, " loaded") } invisible() } unload.module <- function(name, quiet=FALSE) { if (!is.character(name) || length(name) != 1) stop("invalid name") ok <- .Call("unload_module", name, PACKAGE="rjags") if (!ok) { warning(paste("module", name, "not loaded")) } else if (!quiet) { cat("Module", name, "unloaded\n", sep=" ") } invisible() } list.modules <- function() { .Call("get_modules", PACKAGE="rjags"); } isDLLLoaded <- function(file) { dll.list <- getLoadedDLLs() for (i in seq(along=dll.list)) { if (dll.list[[i]]["path"][1] == file) return(TRUE) } return(FALSE) } parallel.seeds <- function(factory, nchain) { .Call("parallel_seeds", factory, nchain, PACKAGE="rjags") } rjags/R/jags.object.R0000644000175100001440000000605112611461731014117 0ustar hornikusers# R package rjags file R/jags.object.R # Copyright (C) 2007-2011 Martyn Plummer # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License version # 2 as published by the Free Software Foundation. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # A copy of the GNU General Public License is available at # http://www.r-project.org/Licenses/ # update.jags <- function(object, n.iter = 1, by, progress.bar, ...) { if (!is.numeric(n.iter) || n.iter < 1) { stop("Invalid n.iter") } adapting <- .Call("is_adapting", object$ptr(), PACKAGE="rjags") on.exit(object$sync()) if (missing(progress.bar)) { progress.bar <- getOption("jags.pb") } if (!is.null(progress.bar)) { match.arg(progress.bar, c("text","gui","none")) if (progress.bar=="none") progress.bar <- NULL } do.pb <- interactive() && !is.null(progress.bar) && n.iter >= 100 if (do.pb) { start.iter <- object$iter() end.iter <- start.iter + n.iter pb <- switch(progress.bar, "text" = txtProgressBar(start.iter, end.iter, initial = start.iter, style=3, width=50, char=ifelse(adapting,"+","*")), "gui" = updatePB(start.iter, end.iter, adapting)) } ## Set refresh frequency for progress bar if (missing(by) || by <= 0) { ##In JAGS 3.x.y there is a memory reallocation bug when ##monitoring that slows down updates. Drop refresh ##frequency to avoid triggering memory reallocations. ##by <- min(ceiling(n.iter/50), 100) by <- ceiling(n.iter/50) } else { by <- ceiling(by) } ## Do updates n <- n.iter while (n > 0) { .Call("update", object$ptr(), min(n,by), PACKAGE="rjags") if (do.pb) { switch(progress.bar, "text" = setTxtProgressBar(pb, object$iter()), "gui" = setPB(pb, object$iter())) } n <- n - by } if (do.pb) { close(pb) } invisible(NULL) } adapt <- function(object, n.iter, end.adaptation = FALSE, ...) { if(.Call("is_adapting", object$ptr(), PACKAGE="rjags")) { if(n.iter > 0) update.jags(object, n.iter, ...) ok <- .Call("check_adaptation", object$ptr(), PACKAGE="rjags") if (end.adaptation) { .Call("adapt_off", object$ptr(), PACKAGE="rjags") } return(ok) } else { return(TRUE) } } coef.jags <- function(object, chain = 1, ...) { if (!is.numeric(chain) || chain < 1 || chain > object$nchain()) { stop("Invalid chain") } object$state(internal=FALSE)[[chain]] } variable.names.jags <- function(object, ...) { .Call("get_variable_names", object$ptr(), PACKAGE="rjags") } rjags/R/dic.R0000644000175100001440000000642512611461563012475 0ustar hornikusers# R package rjags file R/dic.R # Copyright (C) 2009-2013 Martyn Plummer # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License version # 2 as published by the Free Software Foundation. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # A copy of the GNU General Public License is available at # http://www.r-project.org/Licenses/ # "dic.samples" <- function(model, n.iter, thin=1, type="pD", ...) { if (nchain(model) == 1) { stop("2 or more parallel chains required") } if (!inherits(model, "jags")) stop("Invalid JAGS model") if (!is.numeric(n.iter) || length(n.iter) != 1 || n.iter <= 0) stop("n.iter must be a positive integer") load.module("dic", quiet=TRUE) limits <- vector("list",2) pdtype <- match.arg(type, c("pD","popt")) status <- .Call("set_monitors", model$ptr(), c("deviance",pdtype), limits, limits, as.integer(thin), "mean", PACKAGE="rjags") if (!any(status)) { stop("Failed to set monitors") } update(model, n.iter = as.integer(n.iter), ...) dev <- .Call("get_monitored_values_flat", model$ptr(), "mean", PACKAGE="rjags") for (i in seq(along=dev)) { class(dev[[i]]) <- "mcarray" } if (status[1]) { .Call("clear_monitor", model$ptr(), "deviance", NULL, NULL, "mean", PACKAGE="rjags") } if (status[2]) { .Call("clear_monitor", model$ptr(), pdtype, NULL, NULL, "mean", PACKAGE="rjags") } ans <- list("deviance" = dev$deviance, "penalty" = dev[[type]], "type" = type) class(ans) <- "dic" return(ans) } "print.dic" <- function(x, digits= max(3, getOption("digits") - 3), ...) { deviance <- sum(x$deviance) cat("Mean deviance: ", format(deviance, digits=digits), "\n") psum <- sum(x[[2]]) cat(names(x)[[2]], format(mean(psum), digits=digits), "\n") cat("Penalized deviance:", format(deviance + psum, digits=digits), "\n") invisible(x) } "-.dic" <- function(e1, e2) { diffdic(e1, e2) } "diffdic" <- function(dic1,dic2) { if (!identical(dic1$type, dic2$type)) { stop("incompatible dic object: different penalty types") } n1 <- names(dic1$deviance) n2 <- names(dic2$deviance) if (!identical(n1, n2)) { ### Try matching names in lexicographic order if(!identical(sort(n1), sort(n2))) { stop("incompatible dic objects: variable names differ") } ### Reset names to order of the first argument ord1 <- order(n1) ord2 <- order(n2) dic2$deviance[ord1] <- dic2$deviance[ord2] dic2$penalty[ord1] <- dic2$penalty[ord2] } delta <- sapply(dic1$deviance, mean) + sapply(dic1$penalty, mean) - sapply(dic2$deviance, mean) - sapply(dic2$penalty, mean) class(delta) <- "diffdic" return(delta) } "print.diffdic" <- function(x, ...) { cat("Difference: ", sum(x), "\n", sep="") cat("Sample standard error: ", sqrt(length(x)) * sd(x), "\n", sep="") invisible(x) } rjags/R/windows/0000755000175100001440000000000012611464432013274 5ustar hornikusersrjags/R/windows/progress.bar.R0000644000175100001440000000167212611461563016036 0ustar hornikusers# R package rjags file R/windows/progress.bar.R # Copyright (C) 2009 Martyn Plummer # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License version # 2 as published by the Free Software Foundation. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # A copy of the GNU General Public License is available at # http://www.r-project.org/Licenses/ # updatePB <- function(start.iter, end.iter, adapting) { winProgressBar(title=ifelse(adapting, "Adapting","Updating"), label="Iteration 0", min = start.iter, max=end.iter, initial=start.iter) } setPB <- function(pb, iter) { setWinProgressBar(pb, iter, label=paste("Iteration",iter)) } rjags/R/windows/zzz.R0000644000175100001440000001130512611464432014254 0ustar hornikusers.check.jags.home <- function(jags.home, major) { ## Check that folder jags.home actually exists and contains the DLL ## in the appropriate sub-folder. ## Registry entries created by the JAGS instsaller may be invalid ## if the user removes JAGS by manually deleting files rather than ## using the uninstaller. So this function is used to check that ## the installation still exists. if (is.null(jags.home)) return(FALSE) if (!is.vector(jags.home, mode="character") || length(jags.home) != 1) { return(FALSE) } if (!file_test("-d", jags.home)) return(FALSE) bindir <- file.path(jags.home, .Platform$r_arch, "bin") jags.dll <- file.path(bindir, paste("libjags-", major, .Platform$dynlib.ext, sep="")) return(file.exists(jags.dll)) } .findJAGS <- function(hive, major) { ## Returns the registry key corresponding to the latest release of ## JAGS-major.x.y, or NULL if no release is found regkey <- try(readRegistry("SOFTWARE\\JAGS", hive = hive, maxdepth = 2, view="32-bit"), silent = TRUE) if (inherits(regkey, "try-error")) { return(NULL) } keynames <- names(regkey) keynames <- keynames[grep(paste0("^JAGS-", major, "\\."), keynames)] if (length(keynames) == 0) { return(NULL) } else { keynames <- rev(keynames) #Search in reverse order of release number regkey <- regkey[keynames] for (i in seq(along=keynames)) { if(.check.jags.home(regkey[[i]][["InstallDir"]], major)) { return(regkey[i]) } } return(NULL) } } .noJAGS <- function(major) { paste("Failed to locate any version of JAGS version ", major, "\n\n", "The rjags package is just an interface to the JAGS library\n", "Make sure you have installed JAGS-", major, ".x.y.exe (for any x >=0, y>=0) from\n", "http://www.sourceforge.net/projects/mcmc-jags/files\n", sep="") } .onLoad <- function(lib, pkg) { ### First task is to get installation directory of JAGS ## Major version of JAGS library should match major version ## of the rjags package jags.major <- packageVersion(pkg, lib)$major ## Try environment variable first jags.home <- Sys.getenv("JAGS_HOME") if (nchar(jags.home) > 0) { if (!.check.jags.home(jags.home, jags.major)) { stop("The environment variable JAGS_HOME is set to\n", jags.home, "\nbut no JAGS installation can be found there\n") } } else { ## Search the registry. We need to look for both machine-wide and ## user-specific installations key1 <- .findJAGS("HLM", jags.major) key2 <- .findJAGS("HCU", jags.major) if (is.null(key1)) { if (is.null(key2)) { stop(.noJAGS(jags.major)) } else { latest <- key2 } } else if (is.null(key2) || names(key2) < names(key1)) { latest <- key1 } else { latest <- key2 } jags.home <- latest[[1]][["InstallDir"]] } ### Add the JAGS bin to the windows PATH, if not already present path <- Sys.getenv("PATH") split.path <- strsplit(path, .Platform$path.sep)$PATH bindir <- file.path(jags.home, .Platform$r_arch, "bin") if (!any(split.path == bindir)) { path <- paste(bindir, path, sep=.Platform$path.sep) if (!Sys.setenv("PATH"=path)) { stop("Failed to add the rjags bin directory to the PATH:\n", bindir) } } ### Load the rjags dll library.dynam("rjags", pkg, lib) ### Set the module directory, if the option jags.moddir is not already set if (is.null(getOption("jags.moddir"))) { options("jags.moddir" = file.path(jags.home, .Platform$r_arch, "modules")) } ### Check that the module directory actually exists moddir <- getOption("jags.moddir") if (!file.exists(moddir)) { stop(moddir, " not found\n\n", "rjags is looking for the JAGS modules in\n", moddir, "\nbut this folder does not exist\n") } load.module("basemod", quiet=TRUE) load.module("bugs", quiet=TRUE) ### Set progress bar type if (is.null(getOption("jags.pb"))) { options("jags.pb"="text") } } .onAttach <- function(lib, pkg) { packageStartupMessage("Linked to JAGS ", .Call("get_version", PACKAGE="rjags")) packageStartupMessage("Loaded modules: ", paste(list.modules(), collapse=",")) } .onUnload <- function(libpath) { library.dynam.unload("rjags", libpath) } rjags/R/unix/0000755000175100001440000000000012611461563012567 5ustar hornikusersrjags/R/unix/zzz.R.in0000644000175100001440000000140212611461563014151 0ustar hornikusers.onLoad <- function(lib, pkg) { ## Load the rjags wrapper. library.dynam("rjags", pkg, lib, local=FALSE) ## Set the module directory if (is.null(getOption("jags.moddir"))) { options("jags.moddir" = "@JAGS_MODDIR@") } load.module("basemod", quiet=TRUE) load.module("bugs", quiet=TRUE) ## Set progress bar type if (is.null(getOption("jags.pb"))) { options("jags.pb"="text") } } .onAttach <- function(lib, pkg) { packageStartupMessage("Linked to JAGS ", .Call("get_version", PACKAGE="rjags")) packageStartupMessage("Loaded modules: ", paste(list.modules(), collapse=",")) } .onUnload <- function(libpath) { library.dynam.unload("rjags", libpath) } rjags/R/unix/progress.bar.R0000644000175100001440000000172012611461563015321 0ustar hornikusers# R package rjags file R/unix/progress.bar.R # Copyright (C) 2009-2013 Martyn Plummer # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License version # 2 as published by the Free Software Foundation. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # A copy of the GNU General Public License is available at # http://www.r-project.org/Licenses/ # updatePB <- function(start.iter, end.iter, adapting) { tcltk::tkProgressBar(title=ifelse(adapting, "Adapting","Updating"), label="Iteration 0", min = start.iter, max=end.iter, initial=start.iter) } setPB <- function(pb, iter) { tcltk::setTkProgressBar(pb, iter, label=paste("Iteration",iter)) } rjags/R/read.data.R0000644000175100001440000000231012611461563013546 0ustar hornikusers# R package rjags file R/read.data.R # Copyright (C) 2009-2011 Martyn Plummer # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License version # 2 as published by the Free Software Foundation. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # A copy of the GNU General Public License is available at # http://www.r-project.org/Licenses/ # read.data <- function(file, format=c("jags","bugs")) { .Deprecated("read.jagsdata", package="rjags") format <- match.arg(format) switch(format, "jags"=read.jagsdata(file), "bugs"=read.bugsdata(file)) } read.jagsdata <- function(file) { e <- new.env() eval(parse(file), e) return(as.list(e)) } read.bugsdata <- function(file) { bugs.dat <- dget(file) for (n in names(bugs.dat)) { if (!is.null(dim(bugs.dat[[n]]))) { dim(bugs.dat[[n]]) <- rev(dim(bugs.dat[[n]])) bugs.dat[[n]] <- aperm(bugs.dat[[n]]) } } return(bugs.dat) } rjags/MD50000644000175100001440000000345412643237515011724 0ustar hornikusers7d48b2b938c70c62666dcfe3ba67475e *DESCRIPTION e256cb2da52e175d0cc40289ff92e9c7 *INSTALL de66cc2266d358254b2aab3ae485b96d *NAMESPACE 5fcd1fe183901e91067edf32f69da754 *R/dic.R 1c36106e8fdb63425fcac41d604ce2d9 *R/jags.R 1ed51e4f1e0e39360c280ecdadfe0284 *R/jags.object.R fb121e03013181040bb43241fc7fde5e *R/mcarray.R 77c07ef7017558fbf12288dd45a742b0 *R/read.data.R a4bb7181ba06fab0cdd88b07ef471b8b *R/unix/progress.bar.R 68045d38e4ecad47ce33d8b1cf2e17a0 *R/unix/zzz.R.in 921d90c18a3aac1ff6ce243e187a0fae *R/windows/progress.bar.R dcd59bf5f902704c278ff26d1b79ddb1 *R/windows/zzz.R 857c748215feff397d05cdaf65e7f6c2 *cleanup 87989973e91e5c5eeed4ac234b92979c *configure 70aeb53e32969f93a8b9c20737a4ea32 *configure.ac d41d8cd98f00b204e9800998ecf8427e *configure.win baf8a3492838ff4e0aa0b67b38bdd297 *data/LINE.RData e295c53351091ac56d81803c2e087938 *man/adapt.Rd 25612ace3e2d1be654a4bc6ea7c1e156 *man/coda.samples.Rd 1ec1a6359ba06d662060b4c95b40245d *man/control.Rd 255e93fb2e1fca973dca8b037dc4973d *man/dic.samples.Rd 2273377e0a579d66418c13b52bc3b870 *man/diffdic.Rd 5e0b4a154ed2f8087a8e5836ff8476c9 *man/jags.model.Rd acc639648f722ef4a740a87a6e97d3c6 *man/jags.module.Rd 1452d48e130bbd652b8dacb166647091 *man/jags.object.Rd 5c427dd5774bb2cf5c3e9511d3cea57d *man/jags.samples.Rd 0e6f792e3882b9c359ce6addec9b6031 *man/line.Rd 221b944e4a73614658a0344f5b663619 *man/mcarray.object.Rd e1d4581b80556b14c34f61b804629b93 *man/parallel.Rd fc82322b1e9e147f33cfb2b214975009 *man/read.jagsdata.Rd 9d9b4c1924d2af1664ff825fa5418941 *man/rjags-deprecated.Rd 2957a9323cff4aa7e32d53ae95341e41 *man/rjags-package.Rd 696040753b8b498dbb9a68b0436b8e9c *man/update.Rd 9e833b0dd9f06c7464486c908b71eda5 *src/Makevars.in aa71142021fe413b879ad36bf926e399 *src/Makevars.win 3d575416eae24c280fc2a83f40c505b8 *src/jags.cc 934cc6b1e926cfce7dc12e0c597b91f6 *src/parallel.cc rjags/DESCRIPTION0000644000175100001440000000135012643237515013113 0ustar hornikusersPackage: rjags Version: 4-5 Date: 2016-01-06 Title: Bayesian Graphical Models using MCMC Authors@R: c(person("Martyn", "Plummer", role=c("aut","cre"), email="plummerm@iarc.fr"), person("Alexey", "Stukalov", role="ctb"), person("Matt", "Denwood", role="ctb")) Depends: R (>= 2.14.0), coda (>= 0.13) SystemRequirements: JAGS 4.x.y URL: http://mcmc-jags.sourceforge.net Suggests: tcltk Description: Interface to the JAGS MCMC library. License: GPL (== 2) NeedsCompilation: yes Packaged: 2016-01-06 13:09:07 UTC; martyn Author: Martyn Plummer [aut, cre], Alexey Stukalov [ctb], Matt Denwood [ctb] Maintainer: Martyn Plummer Repository: CRAN Date/Publication: 2016-01-06 17:22:37 rjags/configure0000755000175100001440000054403112643167031013317 0ustar hornikusers#! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.69 for rjags 4. # # # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc. # # # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. ## -------------------- ## ## M4sh Initialization. ## ## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else case `(set -o) 2>/dev/null` in #( *posix*) : set -o posix ;; #( *) : ;; esac fi as_nl=' ' export as_nl # Printing a long string crashes Solaris 7 /usr/bin/printf. as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo # Prefer a ksh shell builtin over an external printf program on Solaris, # but without wasting forks for bash or zsh. if test -z "$BASH_VERSION$ZSH_VERSION" \ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='print -r --' as_echo_n='print -rn --' elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' as_echo_n='/usr/ucb/echo -n' else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; case $arg in #( *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; esac; expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" ' export as_echo_n_body as_echo_n='sh -c $as_echo_n_body as_echo' fi export as_echo_body as_echo='sh -c $as_echo_body as_echo' fi # The user is always right. if test "${PATH_SEPARATOR+set}" != set; then PATH_SEPARATOR=: (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || PATH_SEPARATOR=';' } fi # IFS # We need space, tab and new line, in precisely that order. Quoting is # there to prevent editors from complaining about space-tab. # (If _AS_PATH_WALK were called with IFS unset, it would disable word # splitting by setting IFS to empty value.) IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. as_myself= case $0 in #(( *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break done IFS=$as_save_IFS ;; esac # We did not find ourselves, most probably we were run as `sh COMMAND' # in which case we are not to be found in the path. if test "x$as_myself" = x; then as_myself=$0 fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 exit 1 fi # Unset variables that we do not need and which cause bugs (e.g. in # pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" # suppresses any "Segmentation fault" message there. '((' could # trigger a bug in pdksh 5.2.14. for as_var in BASH_ENV ENV MAIL MAILPATH do eval test x\${$as_var+set} = xset \ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : done PS1='$ ' PS2='> ' PS4='+ ' # NLS nuisances. LC_ALL=C export LC_ALL LANGUAGE=C export LANGUAGE # CDPATH. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH # Use a proper internal environment variable to ensure we don't fall # into an infinite loop, continuously re-executing ourselves. if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then _as_can_reexec=no; export _as_can_reexec; # We cannot yet assume a decent shell, so we have to provide a # neutralization value for shells without unset; and this also # works around shells that cannot unset nonexistent variables. # Preserve -v and -x to the replacement shell. BASH_ENV=/dev/null ENV=/dev/null (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV case $- in # (((( *v*x* | *x*v* ) as_opts=-vx ;; *v* ) as_opts=-v ;; *x* ) as_opts=-x ;; * ) as_opts= ;; esac exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"} # Admittedly, this is quite paranoid, since all the known shells bail # out after a failed `exec'. $as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2 as_fn_exit 255 fi # We don't want this to propagate to other subprocesses. { _as_can_reexec=; unset _as_can_reexec;} if test "x$CONFIG_SHELL" = x; then as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which # is contrary to our usage. Disable this feature. alias -g '\${1+\"\$@\"}'='\"\$@\"' setopt NO_GLOB_SUBST else case \`(set -o) 2>/dev/null\` in #( *posix*) : set -o posix ;; #( *) : ;; esac fi " as_required="as_fn_return () { (exit \$1); } as_fn_success () { as_fn_return 0; } as_fn_failure () { as_fn_return 1; } as_fn_ret_success () { return 0; } as_fn_ret_failure () { return 1; } exitcode=0 as_fn_success || { exitcode=1; echo as_fn_success failed.; } as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; } as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; } as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then : else exitcode=1; echo positional parameters were not saved. fi test x\$exitcode = x0 || exit 1 test -x / || exit 1" as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" && test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1 test \$(( 1 + 1 )) = 2 || exit 1" if (eval "$as_required") 2>/dev/null; then : as_have_required=yes else as_have_required=no fi if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR as_found=false for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. as_found=: case $as_dir in #( /*) for as_base in sh bash ksh sh5; do # Try only shells that exist, to save several forks. as_shell=$as_dir/$as_base if { test -f "$as_shell" || test -f "$as_shell.exe"; } && { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : CONFIG_SHELL=$as_shell as_have_required=yes if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : break 2 fi fi done;; esac as_found=false done $as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : CONFIG_SHELL=$SHELL as_have_required=yes fi; } IFS=$as_save_IFS if test "x$CONFIG_SHELL" != x; then : export CONFIG_SHELL # We cannot yet assume a decent shell, so we have to provide a # neutralization value for shells without unset; and this also # works around shells that cannot unset nonexistent variables. # Preserve -v and -x to the replacement shell. BASH_ENV=/dev/null ENV=/dev/null (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV case $- in # (((( *v*x* | *x*v* ) as_opts=-vx ;; *v* ) as_opts=-v ;; *x* ) as_opts=-x ;; * ) as_opts= ;; esac exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"} # Admittedly, this is quite paranoid, since all the known shells bail # out after a failed `exec'. $as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2 exit 255 fi if test x$as_have_required = xno; then : $as_echo "$0: This script requires a shell more modern than all" $as_echo "$0: the shells that I found on your system." if test x${ZSH_VERSION+set} = xset ; then $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" $as_echo "$0: be upgraded to zsh 4.3.4 or later." else $as_echo "$0: Please tell bug-autoconf@gnu.org about your system, $0: including any error possibly output before this $0: message. Then install a modern shell, or manually run $0: the script under such a shell if you do have one." fi exit 1 fi fi fi SHELL=${CONFIG_SHELL-/bin/sh} export SHELL # Unset more variables known to interfere with behavior of common tools. CLICOLOR_FORCE= GREP_OPTIONS= unset CLICOLOR_FORCE GREP_OPTIONS ## --------------------- ## ## M4sh Shell Functions. ## ## --------------------- ## # as_fn_unset VAR # --------------- # Portably unset VAR. as_fn_unset () { { eval $1=; unset $1;} } as_unset=as_fn_unset # as_fn_set_status STATUS # ----------------------- # Set $? to STATUS, without forking. as_fn_set_status () { return $1 } # as_fn_set_status # as_fn_exit STATUS # ----------------- # Exit the shell with STATUS, even in a "trap 0" or "set -e" context. as_fn_exit () { set +e as_fn_set_status $1 exit $1 } # as_fn_exit # as_fn_mkdir_p # ------------- # Create "$as_dir" as a directory, including parents if necessary. as_fn_mkdir_p () { case $as_dir in #( -*) as_dir=./$as_dir;; esac test -d "$as_dir" || eval $as_mkdir_p || { as_dirs= while :; do case $as_dir in #( *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( *) as_qdir=$as_dir;; esac as_dirs="'$as_qdir' $as_dirs" as_dir=`$as_dirname -- "$as_dir" || $as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$as_dir" : 'X\(//\)[^/]' \| \ X"$as_dir" : 'X\(//\)$' \| \ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || $as_echo X"$as_dir" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q } /^X\(\/\/\)[^/].*/{ s//\1/ q } /^X\(\/\/\)$/{ s//\1/ q } /^X\(\/\).*/{ s//\1/ q } s/.*/./; q'` test -d "$as_dir" && break done test -z "$as_dirs" || eval "mkdir $as_dirs" } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" } # as_fn_mkdir_p # as_fn_executable_p FILE # ----------------------- # Test if FILE is an executable regular file. as_fn_executable_p () { test -f "$1" && test -x "$1" } # as_fn_executable_p # as_fn_append VAR VALUE # ---------------------- # Append the text in VALUE to the end of the definition contained in VAR. Take # advantage of any shell optimizations that allow amortized linear growth over # repeated appends, instead of the typical quadratic growth present in naive # implementations. if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : eval 'as_fn_append () { eval $1+=\$2 }' else as_fn_append () { eval $1=\$$1\$2 } fi # as_fn_append # as_fn_arith ARG... # ------------------ # Perform arithmetic evaluation on the ARGs, and store the result in the # global $as_val. Take advantage of shells that can avoid forks. The arguments # must be portable across $(()) and expr. if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : eval 'as_fn_arith () { as_val=$(( $* )) }' else as_fn_arith () { as_val=`expr "$@" || test $? -eq 1` } fi # as_fn_arith # as_fn_error STATUS ERROR [LINENO LOG_FD] # ---------------------------------------- # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are # provided, also output the error to LOG_FD, referencing LINENO. Then exit the # script with STATUS, using 1 if that was 0. as_fn_error () { as_status=$1; test $as_status -eq 0 && as_status=1 if test "$4"; then as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 fi $as_echo "$as_me: error: $2" >&2 as_fn_exit $as_status } # as_fn_error if expr a : '\(a\)' >/dev/null 2>&1 && test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr else as_expr=false fi if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then as_basename=basename else as_basename=false fi if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then as_dirname=dirname else as_dirname=false fi as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ X"$0" : 'X\(/\)' \| . 2>/dev/null || $as_echo X/"$0" | sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/ q } /^X\/\(\/\/\)$/{ s//\1/ q } /^X\/\(\/\).*/{ s//\1/ q } s/.*/./; q'` # Avoid depending upon Character Ranges. as_cr_letters='abcdefghijklmnopqrstuvwxyz' as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' as_cr_Letters=$as_cr_letters$as_cr_LETTERS as_cr_digits='0123456789' as_cr_alnum=$as_cr_Letters$as_cr_digits as_lineno_1=$LINENO as_lineno_1a=$LINENO as_lineno_2=$LINENO as_lineno_2a=$LINENO eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) sed -n ' p /[$]LINENO/= ' <$as_myself | sed ' s/[$]LINENO.*/&-/ t lineno b :lineno N :loop s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ t loop s/-\n.*// ' >$as_me.lineno && chmod +x "$as_me.lineno" || { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } # If we had to re-execute with $CONFIG_SHELL, we're ensured to have # already done that, so ensure we don't try to do so again and fall # in an infinite loop. This has already happened in practice. _as_can_reexec=no; export _as_can_reexec # Don't try to exec as it changes $[0], causing all sort of problems # (the dirname of $[0] is not the place where we might find the # original and so on. Autoconf is especially sensitive to this). . "./$as_me.lineno" # Exit status is that of the last command. exit } ECHO_C= ECHO_N= ECHO_T= case `echo -n x` in #((((( -n*) case `echo 'xy\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. xy) ECHO_C='\c';; *) echo `echo ksh88 bug on AIX 6.1` > /dev/null ECHO_T=' ';; esac;; *) ECHO_N='-n';; esac rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then rm -f conf$$.dir/conf$$.file else rm -f conf$$.dir mkdir conf$$.dir 2>/dev/null fi if (echo >conf$$.file) 2>/dev/null; then if ln -s conf$$.file conf$$ 2>/dev/null; then as_ln_s='ln -s' # ... but there are two gotchas: # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. # In both cases, we have to default to `cp -pR'. ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || as_ln_s='cp -pR' elif ln conf$$.file conf$$ 2>/dev/null; then as_ln_s=ln else as_ln_s='cp -pR' fi else as_ln_s='cp -pR' fi rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null if mkdir -p . 2>/dev/null; then as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false fi as_test_x='test -x' as_executable_p=as_fn_executable_p # Sed expression to map a string onto a valid CPP name. as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" # Sed expression to map a string onto a valid variable name. as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" test -n "$DJDIR" || exec 7<&0 &1 # Name of the host. # hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status, # so uname gets run too. ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q` # # Initializations. # ac_default_prefix=/usr/local ac_clean_files= ac_config_libobj_dir=. LIBOBJS= cross_compiling=no subdirs= MFLAGS= MAKEFLAGS= # Identity of this package. PACKAGE_NAME='rjags' PACKAGE_TARNAME='rjags' PACKAGE_VERSION='4' PACKAGE_STRING='rjags 4' PACKAGE_BUGREPORT='' PACKAGE_URL='' # Factoring default headers for most tests. ac_includes_default="\ #include #ifdef HAVE_SYS_TYPES_H # include #endif #ifdef HAVE_SYS_STAT_H # include #endif #ifdef STDC_HEADERS # include # include #else # ifdef HAVE_STDLIB_H # include # endif #endif #ifdef HAVE_STRING_H # if !defined STDC_HEADERS && defined HAVE_MEMORY_H # include # endif # include #endif #ifdef HAVE_STRINGS_H # include #endif #ifdef HAVE_INTTYPES_H # include #endif #ifdef HAVE_STDINT_H # include #endif #ifdef HAVE_UNISTD_H # include #endif" ac_subst_vars='LTLIBOBJS LIBOBJS JAGS_RPATH JAGS_MODDIR JAGS_CFLAGS JAGS_LIBS ac_ct_CC CFLAGS CC EGREP GREP CXXCPP OBJEXT EXEEXT ac_ct_CXX CPPFLAGS LDFLAGS CXXFLAGS CXX jags_bin_path PKG_CONFIG target_alias host_alias build_alias LIBS ECHO_T ECHO_N ECHO_C DEFS mandir localedir libdir psdir pdfdir dvidir htmldir infodir docdir oldincludedir includedir localstatedir sharedstatedir sysconfdir datadir datarootdir libexecdir sbindir bindir program_transform_name prefix exec_prefix PACKAGE_URL PACKAGE_BUGREPORT PACKAGE_STRING PACKAGE_VERSION PACKAGE_TARNAME PACKAGE_NAME PATH_SEPARATOR SHELL' ac_subst_files='' ac_user_opts=' enable_option_checking with_jags_prefix with_jags_includedir with_jags_libdir enable_rpath ' ac_precious_vars='build_alias host_alias target_alias CXX CXXFLAGS LDFLAGS LIBS CPPFLAGS CCC CXXCPP CC CFLAGS' # Initialize some variables set by options. ac_init_help= ac_init_version=false ac_unrecognized_opts= ac_unrecognized_sep= # The variables have the same names as the options, with # dashes changed to underlines. cache_file=/dev/null exec_prefix=NONE no_create= no_recursion= prefix=NONE program_prefix=NONE program_suffix=NONE program_transform_name=s,x,x, silent= site= srcdir= verbose= x_includes=NONE x_libraries=NONE # Installation directory options. # These are left unexpanded so users can "make install exec_prefix=/foo" # and all the variables that are supposed to be based on exec_prefix # by default will actually change. # Use braces instead of parens because sh, perl, etc. also accept them. # (The list follows the same order as the GNU Coding Standards.) bindir='${exec_prefix}/bin' sbindir='${exec_prefix}/sbin' libexecdir='${exec_prefix}/libexec' datarootdir='${prefix}/share' datadir='${datarootdir}' sysconfdir='${prefix}/etc' sharedstatedir='${prefix}/com' localstatedir='${prefix}/var' includedir='${prefix}/include' oldincludedir='/usr/include' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' infodir='${datarootdir}/info' htmldir='${docdir}' dvidir='${docdir}' pdfdir='${docdir}' psdir='${docdir}' libdir='${exec_prefix}/lib' localedir='${datarootdir}/locale' mandir='${datarootdir}/man' ac_prev= ac_dashdash= for ac_option do # If the previous option needs an argument, assign it. if test -n "$ac_prev"; then eval $ac_prev=\$ac_option ac_prev= continue fi case $ac_option in *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; *=) ac_optarg= ;; *) ac_optarg=yes ;; esac # Accept the important Cygnus configure options, so we can diagnose typos. case $ac_dashdash$ac_option in --) ac_dashdash=yes ;; -bindir | --bindir | --bindi | --bind | --bin | --bi) ac_prev=bindir ;; -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*) bindir=$ac_optarg ;; -build | --build | --buil | --bui | --bu) ac_prev=build_alias ;; -build=* | --build=* | --buil=* | --bui=* | --bu=*) build_alias=$ac_optarg ;; -cache-file | --cache-file | --cache-fil | --cache-fi \ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c) ac_prev=cache_file ;; -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*) cache_file=$ac_optarg ;; --config-cache | -C) cache_file=config.cache ;; -datadir | --datadir | --datadi | --datad) ac_prev=datadir ;; -datadir=* | --datadir=* | --datadi=* | --datad=*) datadir=$ac_optarg ;; -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \ | --dataroo | --dataro | --datar) ac_prev=datarootdir ;; -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \ | --dataroot=* | --dataroo=* | --dataro=* | --datar=*) datarootdir=$ac_optarg ;; -disable-* | --disable-*) ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && as_fn_error $? "invalid feature name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in *" "enable_$ac_useropt" "*) ;; *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig" ac_unrecognized_sep=', ';; esac eval enable_$ac_useropt=no ;; -docdir | --docdir | --docdi | --doc | --do) ac_prev=docdir ;; -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*) docdir=$ac_optarg ;; -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv) ac_prev=dvidir ;; -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*) dvidir=$ac_optarg ;; -enable-* | --enable-*) ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && as_fn_error $? "invalid feature name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in *" "enable_$ac_useropt" "*) ;; *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig" ac_unrecognized_sep=', ';; esac eval enable_$ac_useropt=\$ac_optarg ;; -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \ | --exec | --exe | --ex) ac_prev=exec_prefix ;; -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \ | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \ | --exec=* | --exe=* | --ex=*) exec_prefix=$ac_optarg ;; -gas | --gas | --ga | --g) # Obsolete; use --with-gas. with_gas=yes ;; -help | --help | --hel | --he | -h) ac_init_help=long ;; -help=r* | --help=r* | --hel=r* | --he=r* | -hr*) ac_init_help=recursive ;; -help=s* | --help=s* | --hel=s* | --he=s* | -hs*) ac_init_help=short ;; -host | --host | --hos | --ho) ac_prev=host_alias ;; -host=* | --host=* | --hos=* | --ho=*) host_alias=$ac_optarg ;; -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht) ac_prev=htmldir ;; -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \ | --ht=*) htmldir=$ac_optarg ;; -includedir | --includedir | --includedi | --included | --include \ | --includ | --inclu | --incl | --inc) ac_prev=includedir ;; -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \ | --includ=* | --inclu=* | --incl=* | --inc=*) includedir=$ac_optarg ;; -infodir | --infodir | --infodi | --infod | --info | --inf) ac_prev=infodir ;; -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*) infodir=$ac_optarg ;; -libdir | --libdir | --libdi | --libd) ac_prev=libdir ;; -libdir=* | --libdir=* | --libdi=* | --libd=*) libdir=$ac_optarg ;; -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \ | --libexe | --libex | --libe) ac_prev=libexecdir ;; -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \ | --libexe=* | --libex=* | --libe=*) libexecdir=$ac_optarg ;; -localedir | --localedir | --localedi | --localed | --locale) ac_prev=localedir ;; -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*) localedir=$ac_optarg ;; -localstatedir | --localstatedir | --localstatedi | --localstated \ | --localstate | --localstat | --localsta | --localst | --locals) ac_prev=localstatedir ;; -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \ | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*) localstatedir=$ac_optarg ;; -mandir | --mandir | --mandi | --mand | --man | --ma | --m) ac_prev=mandir ;; -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*) mandir=$ac_optarg ;; -nfp | --nfp | --nf) # Obsolete; use --without-fp. with_fp=no ;; -no-create | --no-create | --no-creat | --no-crea | --no-cre \ | --no-cr | --no-c | -n) no_create=yes ;; -no-recursion | --no-recursion | --no-recursio | --no-recursi \ | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r) no_recursion=yes ;; -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \ | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \ | --oldin | --oldi | --old | --ol | --o) ac_prev=oldincludedir ;; -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \ | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \ | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*) oldincludedir=$ac_optarg ;; -prefix | --prefix | --prefi | --pref | --pre | --pr | --p) ac_prev=prefix ;; -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*) prefix=$ac_optarg ;; -program-prefix | --program-prefix | --program-prefi | --program-pref \ | --program-pre | --program-pr | --program-p) ac_prev=program_prefix ;; -program-prefix=* | --program-prefix=* | --program-prefi=* \ | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*) program_prefix=$ac_optarg ;; -program-suffix | --program-suffix | --program-suffi | --program-suff \ | --program-suf | --program-su | --program-s) ac_prev=program_suffix ;; -program-suffix=* | --program-suffix=* | --program-suffi=* \ | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*) program_suffix=$ac_optarg ;; -program-transform-name | --program-transform-name \ | --program-transform-nam | --program-transform-na \ | --program-transform-n | --program-transform- \ | --program-transform | --program-transfor \ | --program-transfo | --program-transf \ | --program-trans | --program-tran \ | --progr-tra | --program-tr | --program-t) ac_prev=program_transform_name ;; -program-transform-name=* | --program-transform-name=* \ | --program-transform-nam=* | --program-transform-na=* \ | --program-transform-n=* | --program-transform-=* \ | --program-transform=* | --program-transfor=* \ | --program-transfo=* | --program-transf=* \ | --program-trans=* | --program-tran=* \ | --progr-tra=* | --program-tr=* | --program-t=*) program_transform_name=$ac_optarg ;; -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd) ac_prev=pdfdir ;; -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*) pdfdir=$ac_optarg ;; -psdir | --psdir | --psdi | --psd | --ps) ac_prev=psdir ;; -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*) psdir=$ac_optarg ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil) silent=yes ;; -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb) ac_prev=sbindir ;; -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \ | --sbi=* | --sb=*) sbindir=$ac_optarg ;; -sharedstatedir | --sharedstatedir | --sharedstatedi \ | --sharedstated | --sharedstate | --sharedstat | --sharedsta \ | --sharedst | --shareds | --shared | --share | --shar \ | --sha | --sh) ac_prev=sharedstatedir ;; -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \ | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \ | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \ | --sha=* | --sh=*) sharedstatedir=$ac_optarg ;; -site | --site | --sit) ac_prev=site ;; -site=* | --site=* | --sit=*) site=$ac_optarg ;; -srcdir | --srcdir | --srcdi | --srcd | --src | --sr) ac_prev=srcdir ;; -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*) srcdir=$ac_optarg ;; -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \ | --syscon | --sysco | --sysc | --sys | --sy) ac_prev=sysconfdir ;; -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \ | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*) sysconfdir=$ac_optarg ;; -target | --target | --targe | --targ | --tar | --ta | --t) ac_prev=target_alias ;; -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*) target_alias=$ac_optarg ;; -v | -verbose | --verbose | --verbos | --verbo | --verb) verbose=yes ;; -version | --version | --versio | --versi | --vers | -V) ac_init_version=: ;; -with-* | --with-*) ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && as_fn_error $? "invalid package name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in *" "with_$ac_useropt" "*) ;; *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig" ac_unrecognized_sep=', ';; esac eval with_$ac_useropt=\$ac_optarg ;; -without-* | --without-*) ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && as_fn_error $? "invalid package name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in *" "with_$ac_useropt" "*) ;; *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig" ac_unrecognized_sep=', ';; esac eval with_$ac_useropt=no ;; --x) # Obsolete; use --with-x. with_x=yes ;; -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \ | --x-incl | --x-inc | --x-in | --x-i) ac_prev=x_includes ;; -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \ | --x-incl=* | --x-inc=* | --x-in=* | --x-i=*) x_includes=$ac_optarg ;; -x-libraries | --x-libraries | --x-librarie | --x-librari \ | --x-librar | --x-libra | --x-libr | --x-lib | --x-li | --x-l) ac_prev=x_libraries ;; -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \ | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; -*) as_fn_error $? "unrecognized option: \`$ac_option' Try \`$0 --help' for more information" ;; *=*) ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='` # Reject names that are not valid shell variable names. case $ac_envvar in #( '' | [0-9]* | *[!_$as_cr_alnum]* ) as_fn_error $? "invalid variable name: \`$ac_envvar'" ;; esac eval $ac_envvar=\$ac_optarg export $ac_envvar ;; *) # FIXME: should be removed in autoconf 3.0. $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2 expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null && $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2 : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}" ;; esac done if test -n "$ac_prev"; then ac_option=--`echo $ac_prev | sed 's/_/-/g'` as_fn_error $? "missing argument to $ac_option" fi if test -n "$ac_unrecognized_opts"; then case $enable_option_checking in no) ;; fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;; *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac fi # Check all directory arguments for consistency. for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ datadir sysconfdir sharedstatedir localstatedir includedir \ oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ libdir localedir mandir do eval ac_val=\$$ac_var # Remove trailing slashes. case $ac_val in */ ) ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'` eval $ac_var=\$ac_val;; esac # Be sure to have absolute directory names. case $ac_val in [\\/$]* | ?:[\\/]* ) continue;; NONE | '' ) case $ac_var in *prefix ) continue;; esac;; esac as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val" done # There might be people who depend on the old broken behavior: `$host' # used to hold the argument of --host etc. # FIXME: To remove some day. build=$build_alias host=$host_alias target=$target_alias # FIXME: To remove some day. if test "x$host_alias" != x; then if test "x$build_alias" = x; then cross_compiling=maybe elif test "x$build_alias" != "x$host_alias"; then cross_compiling=yes fi fi ac_tool_prefix= test -n "$host_alias" && ac_tool_prefix=$host_alias- test "$silent" = yes && exec 6>/dev/null ac_pwd=`pwd` && test -n "$ac_pwd" && ac_ls_di=`ls -di .` && ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || as_fn_error $? "working directory cannot be determined" test "X$ac_ls_di" = "X$ac_pwd_ls_di" || as_fn_error $? "pwd does not report name of working directory" # Find the source files, if location was not specified. if test -z "$srcdir"; then ac_srcdir_defaulted=yes # Try the directory containing this script, then the parent directory. ac_confdir=`$as_dirname -- "$as_myself" || $as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$as_myself" : 'X\(//\)[^/]' \| \ X"$as_myself" : 'X\(//\)$' \| \ X"$as_myself" : 'X\(/\)' \| . 2>/dev/null || $as_echo X"$as_myself" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q } /^X\(\/\/\)[^/].*/{ s//\1/ q } /^X\(\/\/\)$/{ s//\1/ q } /^X\(\/\).*/{ s//\1/ q } s/.*/./; q'` srcdir=$ac_confdir if test ! -r "$srcdir/$ac_unique_file"; then srcdir=.. fi else ac_srcdir_defaulted=no fi if test ! -r "$srcdir/$ac_unique_file"; then test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir" fi ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" ac_abs_confdir=`( cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg" pwd)` # When building in place, set srcdir=. if test "$ac_abs_confdir" = "$ac_pwd"; then srcdir=. fi # Remove unnecessary trailing slashes from srcdir. # Double slashes in file names in object file debugging info # mess up M-x gdb in Emacs. case $srcdir in */) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;; esac for ac_var in $ac_precious_vars; do eval ac_env_${ac_var}_set=\${${ac_var}+set} eval ac_env_${ac_var}_value=\$${ac_var} eval ac_cv_env_${ac_var}_set=\${${ac_var}+set} eval ac_cv_env_${ac_var}_value=\$${ac_var} done # # Report the --help message. # if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF \`configure' configures rjags 4 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... To assign environment variables (e.g., CC, CFLAGS...), specify them as VAR=VALUE. See below for descriptions of some of the useful variables. Defaults for the options are specified in brackets. Configuration: -h, --help display this help and exit --help=short display options specific to this package --help=recursive display the short help of all the included packages -V, --version display version information and exit -q, --quiet, --silent do not print \`checking ...' messages --cache-file=FILE cache test results in FILE [disabled] -C, --config-cache alias for \`--cache-file=config.cache' -n, --no-create do not create output files --srcdir=DIR find the sources in DIR [configure dir or \`..'] Installation directories: --prefix=PREFIX install architecture-independent files in PREFIX [$ac_default_prefix] --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX [PREFIX] By default, \`make install' will install all the files in \`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify an installation prefix other than \`$ac_default_prefix' using \`--prefix', for instance \`--prefix=\$HOME'. For better control, use the options below. Fine tuning of the installation directories: --bindir=DIR user executables [EPREFIX/bin] --sbindir=DIR system admin executables [EPREFIX/sbin] --libexecdir=DIR program executables [EPREFIX/libexec] --sysconfdir=DIR read-only single-machine data [PREFIX/etc] --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] --localstatedir=DIR modifiable single-machine data [PREFIX/var] --libdir=DIR object code libraries [EPREFIX/lib] --includedir=DIR C header files [PREFIX/include] --oldincludedir=DIR C header files for non-gcc [/usr/include] --datarootdir=DIR read-only arch.-independent data root [PREFIX/share] --datadir=DIR read-only architecture-independent data [DATAROOTDIR] --infodir=DIR info documentation [DATAROOTDIR/info] --localedir=DIR locale-dependent data [DATAROOTDIR/locale] --mandir=DIR man documentation [DATAROOTDIR/man] --docdir=DIR documentation root [DATAROOTDIR/doc/rjags] --htmldir=DIR html documentation [DOCDIR] --dvidir=DIR dvi documentation [DOCDIR] --pdfdir=DIR pdf documentation [DOCDIR] --psdir=DIR ps documentation [DOCDIR] _ACEOF cat <<\_ACEOF _ACEOF fi if test -n "$ac_init_help"; then case $ac_init_help in short | recursive ) echo "Configuration of rjags 4:";; esac cat <<\_ACEOF Optional Features: --disable-option-checking ignore unrecognized --enable/--with options --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no) --enable-FEATURE[=ARG] include FEATURE [ARG=yes] --enable-rpath Hard link the location of the JAGS library Optional Packages: --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) --with-jags-prefix=PREFIX_PATH Prefix used when JAGS was installed --with-jags-includedir=INCLUDE_PATH the value of includedir used when JAGS was installed --with-jags-libdir=LIB_PATH the value of libdir used when JAGS was installed Some influential environment variables: CXX C++ compiler command CXXFLAGS C++ compiler flags LDFLAGS linker flags, e.g. -L if you have libraries in a nonstandard directory LIBS libraries to pass to the linker, e.g. -l CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I if you have headers in a nonstandard directory CXXCPP C++ preprocessor CC C compiler command CFLAGS C compiler flags Use these variables to override the choices made by `configure' or to help it to find libraries and programs with nonstandard names/locations. Report bugs to the package provider. _ACEOF ac_status=$? fi if test "$ac_init_help" = "recursive"; then # If there are subdirs, report their specific --help. for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue test -d "$ac_dir" || { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } || continue ac_builddir=. case "$ac_dir" in .) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; *) ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` # A ".." for each directory in $ac_dir_suffix. ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` case $ac_top_builddir_sub in "") ac_top_builddir_sub=. ac_top_build_prefix= ;; *) ac_top_build_prefix=$ac_top_builddir_sub/ ;; esac ;; esac ac_abs_top_builddir=$ac_pwd ac_abs_builddir=$ac_pwd$ac_dir_suffix # for backward compatibility: ac_top_builddir=$ac_top_build_prefix case $srcdir in .) # We are building in place. ac_srcdir=. ac_top_srcdir=$ac_top_builddir_sub ac_abs_top_srcdir=$ac_pwd ;; [\\/]* | ?:[\\/]* ) # Absolute name. ac_srcdir=$srcdir$ac_dir_suffix; ac_top_srcdir=$srcdir ac_abs_top_srcdir=$srcdir ;; *) # Relative name. ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix ac_top_srcdir=$ac_top_build_prefix$srcdir ac_abs_top_srcdir=$ac_pwd/$srcdir ;; esac ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix cd "$ac_dir" || { ac_status=$?; continue; } # Check for guested configure. if test -f "$ac_srcdir/configure.gnu"; then echo && $SHELL "$ac_srcdir/configure.gnu" --help=recursive elif test -f "$ac_srcdir/configure"; then echo && $SHELL "$ac_srcdir/configure" --help=recursive else $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2 fi || ac_status=$? cd "$ac_pwd" || { ac_status=$?; break; } done fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF rjags configure 4 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. This configure script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it. _ACEOF exit fi ## ------------------------ ## ## Autoconf initialization. ## ## ------------------------ ## # ac_fn_cxx_try_compile LINENO # ---------------------------- # Try to compile conftest.$ac_ext, and return whether this succeeded. ac_fn_cxx_try_compile () { as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack rm -f conftest.$ac_objext if { { ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_compile") 2>conftest.err ac_status=$? if test -s conftest.err; then grep -v '^ *+' conftest.err >conftest.er1 cat conftest.er1 >&5 mv -f conftest.er1 conftest.err fi $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && { test -z "$ac_cxx_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then : ac_retval=0 else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_retval=1 fi eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno as_fn_set_status $ac_retval } # ac_fn_cxx_try_compile # ac_fn_cxx_try_cpp LINENO # ------------------------ # Try to preprocess conftest.$ac_ext, and return whether this succeeded. ac_fn_cxx_try_cpp () { as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack if { { ac_try="$ac_cpp conftest.$ac_ext" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err ac_status=$? if test -s conftest.err; then grep -v '^ *+' conftest.err >conftest.er1 cat conftest.er1 >&5 mv -f conftest.er1 conftest.err fi $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } > conftest.i && { test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" || test ! -s conftest.err }; then : ac_retval=0 else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_retval=1 fi eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno as_fn_set_status $ac_retval } # ac_fn_cxx_try_cpp # ac_fn_cxx_check_header_mongrel LINENO HEADER VAR INCLUDES # --------------------------------------------------------- # Tests whether HEADER exists, giving a warning if it cannot be compiled using # the include files in INCLUDES and setting the cache variable VAR # accordingly. ac_fn_cxx_check_header_mongrel () { as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack if eval \${$3+:} false; then : { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 $as_echo_n "checking for $2... " >&6; } if eval \${$3+:} false; then : $as_echo_n "(cached) " >&6 fi eval ac_res=\$$3 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 $as_echo "$ac_res" >&6; } else # Is the header compilable? { $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5 $as_echo_n "checking $2 usability... " >&6; } cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ $4 #include <$2> _ACEOF if ac_fn_cxx_try_compile "$LINENO"; then : ac_header_compiler=yes else ac_header_compiler=no fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5 $as_echo "$ac_header_compiler" >&6; } # Is the header present? { $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5 $as_echo_n "checking $2 presence... " >&6; } cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include <$2> _ACEOF if ac_fn_cxx_try_cpp "$LINENO"; then : ac_header_preproc=yes else ac_header_preproc=no fi rm -f conftest.err conftest.i conftest.$ac_ext { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5 $as_echo "$ac_header_preproc" >&6; } # So? What about this header? case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in #(( yes:no: ) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5 $as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5 $as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;} ;; no:yes:* ) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5 $as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5 $as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5 $as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5 $as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5 $as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;} ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 $as_echo_n "checking for $2... " >&6; } if eval \${$3+:} false; then : $as_echo_n "(cached) " >&6 else eval "$3=\$ac_header_compiler" fi eval ac_res=\$$3 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 $as_echo "$ac_res" >&6; } fi eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno } # ac_fn_cxx_check_header_mongrel # ac_fn_cxx_try_run LINENO # ------------------------ # Try to link conftest.$ac_ext, and return whether this succeeded. Assumes # that executables *can* be run. ac_fn_cxx_try_run () { as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack if { { ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_link") 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && { ac_try='./conftest$ac_exeext' { { case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_try") 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; }; then : ac_retval=0 else $as_echo "$as_me: program exited with status $ac_status" >&5 $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_retval=$ac_status fi rm -rf conftest.dSYM conftest_ipa8_conftest.oo eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno as_fn_set_status $ac_retval } # ac_fn_cxx_try_run # ac_fn_cxx_check_header_compile LINENO HEADER VAR INCLUDES # --------------------------------------------------------- # Tests whether HEADER exists and can be compiled using the include files in # INCLUDES, setting the cache variable VAR accordingly. ac_fn_cxx_check_header_compile () { as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 $as_echo_n "checking for $2... " >&6; } if eval \${$3+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ $4 #include <$2> _ACEOF if ac_fn_cxx_try_compile "$LINENO"; then : eval "$3=yes" else eval "$3=no" fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi eval ac_res=\$$3 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 $as_echo "$ac_res" >&6; } eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno } # ac_fn_cxx_check_header_compile # ac_fn_c_try_compile LINENO # -------------------------- # Try to compile conftest.$ac_ext, and return whether this succeeded. ac_fn_c_try_compile () { as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack rm -f conftest.$ac_objext if { { ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_compile") 2>conftest.err ac_status=$? if test -s conftest.err; then grep -v '^ *+' conftest.err >conftest.er1 cat conftest.er1 >&5 mv -f conftest.er1 conftest.err fi $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then : ac_retval=0 else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_retval=1 fi eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno as_fn_set_status $ac_retval } # ac_fn_c_try_compile # ac_fn_c_try_link LINENO # ----------------------- # Try to link conftest.$ac_ext, and return whether this succeeded. ac_fn_c_try_link () { as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack rm -f conftest.$ac_objext conftest$ac_exeext if { { ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_link") 2>conftest.err ac_status=$? if test -s conftest.err; then grep -v '^ *+' conftest.err >conftest.er1 cat conftest.er1 >&5 mv -f conftest.er1 conftest.err fi $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest$ac_exeext && { test "$cross_compiling" = yes || test -x conftest$ac_exeext }; then : ac_retval=0 else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_retval=1 fi # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would # interfere with the next link command; also delete a directory that is # left behind by Apple's compiler. We do this before executing the actions. rm -rf conftest.dSYM conftest_ipa8_conftest.oo eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno as_fn_set_status $ac_retval } # ac_fn_c_try_link cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by rjags $as_me 4, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ _ACEOF exec 5>>config.log { cat <<_ASUNAME ## --------- ## ## Platform. ## ## --------- ## hostname = `(hostname || uname -n) 2>/dev/null | sed 1q` uname -m = `(uname -m) 2>/dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown` /bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown` /bin/arch = `(/bin/arch) 2>/dev/null || echo unknown` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown` /usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown` /bin/machine = `(/bin/machine) 2>/dev/null || echo unknown` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown` /bin/universe = `(/bin/universe) 2>/dev/null || echo unknown` _ASUNAME as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. $as_echo "PATH: $as_dir" done IFS=$as_save_IFS } >&5 cat >&5 <<_ACEOF ## ----------- ## ## Core tests. ## ## ----------- ## _ACEOF # Keep a trace of the command line. # Strip out --no-create and --no-recursion so they do not pile up. # Strip out --silent because we don't want to record it for future runs. # Also quote any args containing shell meta-characters. # Make two passes to allow for proper duplicate-argument suppression. ac_configure_args= ac_configure_args0= ac_configure_args1= ac_must_keep_next=false for ac_pass in 1 2 do for ac_arg do case $ac_arg in -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil) continue ;; *\'*) ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; esac case $ac_pass in 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; 2) as_fn_append ac_configure_args1 " '$ac_arg'" if test $ac_must_keep_next = true; then ac_must_keep_next=false # Got value, back to normal. else case $ac_arg in *=* | --config-cache | -C | -disable-* | --disable-* \ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \ | -with-* | --with-* | -without-* | --without-* | --x) case "$ac_configure_args0 " in "$ac_configure_args1"*" '$ac_arg' "* ) continue ;; esac ;; -* ) ac_must_keep_next=true ;; esac fi as_fn_append ac_configure_args " '$ac_arg'" ;; esac done done { ac_configure_args0=; unset ac_configure_args0;} { ac_configure_args1=; unset ac_configure_args1;} # When interrupted or exit'd, cleanup temporary files, and complete # config.log. We remove comments because anyway the quotes in there # would cause problems or look ugly. # WARNING: Use '\'' to represent an apostrophe within the trap. # WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug. trap 'exit_status=$? # Save into config.log some information that might help in debugging. { echo $as_echo "## ---------------- ## ## Cache variables. ## ## ---------------- ##" echo # The following way of writing the cache mishandles newlines in values, ( for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do eval ac_val=\$$ac_var case $ac_val in #( *${as_nl}*) case $ac_var in #( *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( *) { eval $ac_var=; unset $ac_var;} ;; esac ;; esac done (set) 2>&1 | case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #( *${as_nl}ac_space=\ *) sed -n \ "s/'\''/'\''\\\\'\'''\''/g; s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p" ;; #( *) sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p" ;; esac | sort ) echo $as_echo "## ----------------- ## ## Output variables. ## ## ----------------- ##" echo for ac_var in $ac_subst_vars do eval ac_val=\$$ac_var case $ac_val in *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; esac $as_echo "$ac_var='\''$ac_val'\''" done | sort echo if test -n "$ac_subst_files"; then $as_echo "## ------------------- ## ## File substitutions. ## ## ------------------- ##" echo for ac_var in $ac_subst_files do eval ac_val=\$$ac_var case $ac_val in *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; esac $as_echo "$ac_var='\''$ac_val'\''" done | sort echo fi if test -s confdefs.h; then $as_echo "## ----------- ## ## confdefs.h. ## ## ----------- ##" echo cat confdefs.h echo fi test "$ac_signal" != 0 && $as_echo "$as_me: caught signal $ac_signal" $as_echo "$as_me: exit $exit_status" } >&5 rm -f core *.core core.conftest.* && rm -f -r conftest* confdefs* conf$$* $ac_clean_files && exit $exit_status ' 0 for ac_signal in 1 2 13 15; do trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal done ac_signal=0 # confdefs.h avoids OS command line length limits that DEFS can exceed. rm -f -r conftest* confdefs.h $as_echo "/* confdefs.h */" > confdefs.h # Predefined preprocessor variables. cat >>confdefs.h <<_ACEOF #define PACKAGE_NAME "$PACKAGE_NAME" _ACEOF cat >>confdefs.h <<_ACEOF #define PACKAGE_TARNAME "$PACKAGE_TARNAME" _ACEOF cat >>confdefs.h <<_ACEOF #define PACKAGE_VERSION "$PACKAGE_VERSION" _ACEOF cat >>confdefs.h <<_ACEOF #define PACKAGE_STRING "$PACKAGE_STRING" _ACEOF cat >>confdefs.h <<_ACEOF #define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" _ACEOF cat >>confdefs.h <<_ACEOF #define PACKAGE_URL "$PACKAGE_URL" _ACEOF # Let the site file select an alternate cache file if it wants to. # Prefer an explicitly selected file to automatically selected ones. ac_site_file1=NONE ac_site_file2=NONE if test -n "$CONFIG_SITE"; then # We do not want a PATH search for config.site. case $CONFIG_SITE in #(( -*) ac_site_file1=./$CONFIG_SITE;; */*) ac_site_file1=$CONFIG_SITE;; *) ac_site_file1=./$CONFIG_SITE;; esac elif test "x$prefix" != xNONE; then ac_site_file1=$prefix/share/config.site ac_site_file2=$prefix/etc/config.site else ac_site_file1=$ac_default_prefix/share/config.site ac_site_file2=$ac_default_prefix/etc/config.site fi for ac_site_file in "$ac_site_file1" "$ac_site_file2" do test "x$ac_site_file" = xNONE && continue if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 $as_echo "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 . "$ac_site_file" \ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "failed to load site script $ac_site_file See \`config.log' for more details" "$LINENO" 5; } fi done if test -r "$cache_file"; then # Some versions of bash will fail to source /dev/null (special files # actually), so we avoid doing that. DJGPP emulates it as a regular file. if test /dev/null != "$cache_file" && test -f "$cache_file"; then { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5 $as_echo "$as_me: loading cache $cache_file" >&6;} case $cache_file in [\\/]* | ?:[\\/]* ) . "$cache_file";; *) . "./$cache_file";; esac fi else { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5 $as_echo "$as_me: creating cache $cache_file" >&6;} >$cache_file fi # Check that the precious variables saved in the cache have kept the same # value. ac_cache_corrupted=false for ac_var in $ac_precious_vars; do eval ac_old_set=\$ac_cv_env_${ac_var}_set eval ac_new_set=\$ac_env_${ac_var}_set eval ac_old_val=\$ac_cv_env_${ac_var}_value eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; *) if test "x$ac_old_val" != "x$ac_new_val"; then # differences in whitespace do not lead to failure. ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 $as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 $as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 $as_echo "$as_me: former value: \`$ac_old_val'" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac # Pass precious variables to config.status. if test "$ac_new_set" = set; then case $ac_new_val in *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; *) ac_arg=$ac_var=$ac_new_val ;; esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. *) as_fn_append ac_configure_args " '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 fi ## -------------------- ## ## Main body of script. ## ## -------------------- ## ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -z "${R_HOME}"; then as_fn_error $? "\"R_HOME is not defined\"" "$LINENO" 5 fi CC=`"${R_HOME}/bin/R" CMD config CC` CXX=`"${R_HOME}/bin/R" CMD config CXX` CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS` CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS` CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS` # Try using pkg-config to set compiler flags PKG_CONFIG_OK="FALSE" # Extract the first word of "pkg-config", so it can be a program name with args. set dummy pkg-config; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_path_PKG_CONFIG+:} false; then : $as_echo_n "(cached) " >&6 else case $PKG_CONFIG in [\\/]* | ?:[\\/]*) ac_cv_path_PKG_CONFIG="$PKG_CONFIG" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR as_dummy="$PATH:/usr/local/bin" for as_dir in $as_dummy do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_PKG_CONFIG="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi PKG_CONFIG=$ac_cv_path_PKG_CONFIG if test -n "$PKG_CONFIG"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PKG_CONFIG" >&5 $as_echo "$PKG_CONFIG" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test -n "${PKG_CONFIG}" ; then if `${PKG_CONFIG} --exists jags`; then if `${PKG_CONFIG} --exists --atleast-version=${PACKAGE_VERSION}.0.0 jags` && `${PKG_CONFIG} --exists --max-version=${PACKAGE_VERSION}.99.99 jags`; then JAGS_LIBS=`${PKG_CONFIG} --libs jags` JAGS_CFLAGS=`${PKG_CONFIG} --cflags jags` JAGS_LIBDIR=`${PKG_CONFIG} --variable libdir jags` if test -z "${JAGS_LIBS}" -a -z "${JAGS_CFLAGS}" ; then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Cannot get information about jags ${PACKAGE_VERSION} from pkg-config" >&5 $as_echo "$as_me: WARNING: Cannot get information about jags ${PACKAGE_VERSION} from pkg-config" >&2;} else { $as_echo "$as_me:${as_lineno-$LINENO}: Setting compile and link flags according to pkg-config" >&5 $as_echo "$as_me: Setting compile and link flags according to pkg-config" >&6;} { $as_echo "$as_me:${as_lineno-$LINENO}: Compile flags are $JAGS_CFLAGS" >&5 $as_echo "$as_me: Compile flags are $JAGS_CFLAGS" >&6;} { $as_echo "$as_me:${as_lineno-$LINENO}: Link flags are $JAGS_LIBS" >&5 $as_echo "$as_me: Link flags are $JAGS_LIBS" >&6;} PKG_CONFIG_OK="TRUE" fi else jags_installed_version=`${PKG_CONFIG} --modversion jags` as_fn_error $? "pkg-config found JAGS ${jags_installed_version} but rjags requires JAGS ${PACKAGE_VERSION}.x.y" "$LINENO" 5 fi else { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: pkg-config file for jags ${PACKAGE_VERSION} unavailable" >&5 $as_echo "$as_me: WARNING: pkg-config file for jags ${PACKAGE_VERSION} unavailable" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Consider adding the directory containing \`jags.pc\`" >&5 $as_echo "$as_me: WARNING: Consider adding the directory containing \`jags.pc\`" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: to the PKG_CONFIG_PATH environment variable" >&5 $as_echo "$as_me: WARNING: to the PKG_CONFIG_PATH environment variable" >&2;} fi fi ########################## Begin legacy configuration ##################### if test "${PKG_CONFIG_OK}" != TRUE; then { $as_echo "$as_me:${as_lineno-$LINENO}: Attempting legacy configuration of rjags" >&5 $as_echo "$as_me: Attempting legacy configuration of rjags" >&6;} # Set JAGS_PREFIX # # For installations in a non-standard location, set the prefix for # JAGS manually, using either option --with-jags-prefix or environment # variable JAGS_PREFIX. Otherwise we get the prefix from the jags # executable. # Check whether --with-jags-prefix was given. if test "${with_jags_prefix+set}" = set; then : withval=$with_jags_prefix; jags_prefix_path=$withval else jags_prefix_path="" fi if test -n "$jags_prefix_path" ; then JAGS_PREFIX=${jags_prefix_path} else if test -z "${JAGS_PREFIX}" ; then # Extract the first word of "jags", so it can be a program name with args. set dummy jags; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_path_jags_bin_path+:} false; then : $as_echo_n "(cached) " >&6 else case $jags_bin_path in [\\/]* | ?:[\\/]*) ac_cv_path_jags_bin_path="$jags_bin_path" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_jags_bin_path="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi jags_bin_path=$ac_cv_path_jags_bin_path if test -n "$jags_bin_path"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $jags_bin_path" >&5 $as_echo "$jags_bin_path" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test -n "$jags_bin_path"; then jags_bin_path=`$as_dirname -- "$jags_bin_path" || $as_expr X"$jags_bin_path" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$jags_bin_path" : 'X\(//\)[^/]' \| \ X"$jags_bin_path" : 'X\(//\)$' \| \ X"$jags_bin_path" : 'X\(/\)' \| . 2>/dev/null || $as_echo X"$jags_bin_path" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q } /^X\(\/\/\)[^/].*/{ s//\1/ q } /^X\(\/\/\)$/{ s//\1/ q } /^X\(\/\).*/{ s//\1/ q } s/.*/./; q'` JAGS_PREFIX=`$as_dirname -- "$jags_bin_path" || $as_expr X"$jags_bin_path" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$jags_bin_path" : 'X\(//\)[^/]' \| \ X"$jags_bin_path" : 'X\(//\)$' \| \ X"$jags_bin_path" : 'X\(/\)' \| . 2>/dev/null || $as_echo X"$jags_bin_path" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q } /^X\(\/\/\)[^/].*/{ s//\1/ q } /^X\(\/\/\)$/{ s//\1/ q } /^X\(\/\).*/{ s//\1/ q } s/.*/./; q'` else as_fn_error $? "\"automatic detection of JAGS failed. Please use pkg-config to locate the JAGS library. See the INSTALL file for details.\"" "$LINENO" 5 fi fi fi # Set include path with option --with-jags-includedir or environment # variable JAGS_INCLUDEDIR. By default, this is determined from # JAGS_PREFIX. # Check whether --with-jags-includedir was given. if test "${with_jags_includedir+set}" = set; then : withval=$with_jags_includedir; jags_include_path=$withval else jags_include_path="" fi if test -n "$jags_include_path" ; then JAGS_INCLUDEDIR=${jags_include_path} else if test -z "${JAGS_INCLUDEDIR}" ; then JAGS_INCLUDEDIR=${JAGS_PREFIX}/include fi fi JAGS_PKGINCLUDEDIR=${JAGS_INCLUDEDIR}/JAGS ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu OCPPFLAGS=${CPPFLAGS} CPPFLAGS=-I${JAGS_PKGINCLUDEDIR} ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu if test -z "$CXX"; then if test -n "$CCC"; then CXX=$CCC else if test -n "$ac_tool_prefix"; then for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_CXX+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then ac_cv_prog_CXX="$CXX" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 $as_echo "$CXX" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$CXX" && break done fi if test -z "$CXX"; then ac_ct_CXX=$CXX for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_CXX+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CXX="$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 $as_echo "$ac_ct_CXX" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$ac_ct_CXX" && break done if test "x$ac_ct_CXX" = x; then CXX="g++" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac CXX=$ac_ct_CXX fi fi fi fi # Provide some information about the compiler. $as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5 set X $ac_compile ac_compiler=$2 for ac_option in --version -v -V -qversion; do { { ac_try="$ac_compiler $ac_option >&5" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? if test -s conftest.err; then sed '10a\ ... rest of stderr output deleted ... 10q' conftest.err >conftest.er1 cat conftest.er1 >&5 fi rm -f conftest.er1 conftest.err $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } done cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out" # Try to create an executable without -o first, disregard a.out. # It will help us diagnose broken compilers, and finding out an intuition # of exeext. { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler works" >&5 $as_echo_n "checking whether the C++ compiler works... " >&6; } ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` # The possible output files: ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*" ac_rmfiles= for ac_file in $ac_files do case $ac_file in *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; * ) ac_rmfiles="$ac_rmfiles $ac_file";; esac done rm -f $ac_rmfiles if { { ac_try="$ac_link_default" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_link_default") 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then : # Autoconf-2.13 could set the ac_cv_exeext variable to `no'. # So ignore a value of `no', otherwise this would lead to `EXEEXT = no' # in a Makefile. We should not override ac_cv_exeext if it was cached, # so that the user can short-circuit this test for compilers unknown to # Autoconf. for ac_file in $ac_files '' do test -f "$ac_file" || continue case $ac_file in *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; [ab].out ) # We found the default executable, but exeext='' is most # certainly right. break;; *.* ) if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; then :; else ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` fi # We set ac_cv_exeext here because the later test for it is not # safe: cross compilers may not add the suffix if given an `-o' # argument, so we may need to know it at that point already. # Even if this section looks crufty: it has the advantage of # actually working. break;; * ) break;; esac done test "$ac_cv_exeext" = no && ac_cv_exeext= else ac_file='' fi if test -z "$ac_file"; then : { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error 77 "C++ compiler cannot create executables See \`config.log' for more details" "$LINENO" 5; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler default output file name" >&5 $as_echo_n "checking for C++ compiler default output file name... " >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5 $as_echo "$ac_file" >&6; } ac_exeext=$ac_cv_exeext rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out ac_clean_files=$ac_clean_files_save { $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5 $as_echo_n "checking for suffix of executables... " >&6; } if { { ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_link") 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then : # If both `conftest.exe' and `conftest' are `present' (well, observable) # catch `conftest.exe'. For instance with Cygwin, `ls conftest' will # work properly (i.e., refer to `conftest.exe'), while it won't with # `rm'. for ac_file in conftest.exe conftest conftest.*; do test -f "$ac_file" || continue case $ac_file in *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` break;; * ) break;; esac done else { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "cannot compute suffix of executables: cannot compile and link See \`config.log' for more details" "$LINENO" 5; } fi rm -f conftest conftest$ac_cv_exeext { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5 $as_echo "$ac_cv_exeext" >&6; } rm -f conftest.$ac_ext EXEEXT=$ac_cv_exeext ac_exeext=$EXEEXT cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main () { FILE *f = fopen ("conftest.out", "w"); return ferror (f) || fclose (f) != 0; ; return 0; } _ACEOF ac_clean_files="$ac_clean_files conftest.out" # Check that the compiler produces executables we can run. If not, either # the compiler is broken, or we cross compile. { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5 $as_echo_n "checking whether we are cross compiling... " >&6; } if test "$cross_compiling" != yes; then { { ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_link") 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } if { ac_try='./conftest$ac_cv_exeext' { { case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_try") 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; }; then cross_compiling=no else if test "$cross_compiling" = maybe; then cross_compiling=yes else { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "cannot run C++ compiled programs. If you meant to cross compile, use \`--host'. See \`config.log' for more details" "$LINENO" 5; } fi fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5 $as_echo "$cross_compiling" >&6; } rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out ac_clean_files=$ac_clean_files_save { $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5 $as_echo_n "checking for suffix of object files... " >&6; } if ${ac_cv_objext+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.o conftest.obj if { { ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_compile") 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then : for ac_file in conftest.o conftest.obj conftest.*; do test -f "$ac_file" || continue; case $ac_file in *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;; *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` break;; esac done else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "cannot compute suffix of object files: cannot compile See \`config.log' for more details" "$LINENO" 5; } fi rm -f conftest.$ac_cv_objext conftest.$ac_ext fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5 $as_echo "$ac_cv_objext" >&6; } OBJEXT=$ac_cv_objext ac_objext=$OBJEXT { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5 $as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; } if ${ac_cv_cxx_compiler_gnu+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { #ifndef __GNUC__ choke me #endif ; return 0; } _ACEOF if ac_fn_cxx_try_compile "$LINENO"; then : ac_compiler_gnu=yes else ac_compiler_gnu=no fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 $as_echo "$ac_cv_cxx_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GXX=yes else GXX= fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 $as_echo_n "checking whether $CXX accepts -g... " >&6; } if ${ac_cv_prog_cxx_g+:} false; then : $as_echo_n "(cached) " >&6 else ac_save_cxx_werror_flag=$ac_cxx_werror_flag ac_cxx_werror_flag=yes ac_cv_prog_cxx_g=no CXXFLAGS="-g" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_prog_cxx_g=yes else CXXFLAGS="" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_cxx_try_compile "$LINENO"; then : else ac_cxx_werror_flag=$ac_save_cxx_werror_flag CXXFLAGS="-g" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_prog_cxx_g=yes fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cxx_werror_flag=$ac_save_cxx_werror_flag fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 $as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS elif test $ac_cv_prog_cxx_g = yes; then if test "$GXX" = yes; then CXXFLAGS="-g -O2" else CXXFLAGS="-g" fi else if test "$GXX" = yes; then CXXFLAGS="-O2" else CXXFLAGS= fi fi ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C++ preprocessor" >&5 $as_echo_n "checking how to run the C++ preprocessor... " >&6; } if test -z "$CXXCPP"; then if ${ac_cv_prog_CXXCPP+:} false; then : $as_echo_n "(cached) " >&6 else # Double quotes because CXXCPP needs to be expanded for CXXCPP in "$CXX -E" "/lib/cpp" do ac_preproc_ok=false for ac_cxx_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # Prefer to if __STDC__ is defined, since # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include #else # include #endif Syntax error _ACEOF if ac_fn_cxx_try_cpp "$LINENO"; then : else # Broken: fails on valid input. continue fi rm -f conftest.err conftest.i conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if ac_fn_cxx_try_cpp "$LINENO"; then : # Broken: success on invalid input. continue else # Passes both tests. ac_preproc_ok=: break fi rm -f conftest.err conftest.i conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.i conftest.err conftest.$ac_ext if $ac_preproc_ok; then : break fi done ac_cv_prog_CXXCPP=$CXXCPP fi CXXCPP=$ac_cv_prog_CXXCPP else ac_cv_prog_CXXCPP=$CXXCPP fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXXCPP" >&5 $as_echo "$CXXCPP" >&6; } ac_preproc_ok=false for ac_cxx_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # Prefer to if __STDC__ is defined, since # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include #else # include #endif Syntax error _ACEOF if ac_fn_cxx_try_cpp "$LINENO"; then : else # Broken: fails on valid input. continue fi rm -f conftest.err conftest.i conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if ac_fn_cxx_try_cpp "$LINENO"; then : # Broken: success on invalid input. continue else # Passes both tests. ac_preproc_ok=: break fi rm -f conftest.err conftest.i conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.i conftest.err conftest.$ac_ext if $ac_preproc_ok; then : else { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "C++ preprocessor \"$CXXCPP\" fails sanity check See \`config.log' for more details" "$LINENO" 5; } fi ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu { $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 $as_echo_n "checking for grep that handles long lines and -e... " >&6; } if ${ac_cv_path_GREP+:} false; then : $as_echo_n "(cached) " >&6 else if test -z "$GREP"; then ac_path_GREP_found=false # Loop through the user's path and test for each of PROGNAME-LIST as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_prog in grep ggrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext" as_fn_executable_p "$ac_path_GREP" || continue # Check for GNU ac_path_GREP and select it if it is found. # Check for GNU $ac_path_GREP case `"$ac_path_GREP" --version 2>&1` in *GNU*) ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;; *) ac_count=0 $as_echo_n 0123456789 >"conftest.in" while : do cat "conftest.in" "conftest.in" >"conftest.tmp" mv "conftest.tmp" "conftest.in" cp "conftest.in" "conftest.nl" $as_echo 'GREP' >> "conftest.nl" "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break as_fn_arith $ac_count + 1 && ac_count=$as_val if test $ac_count -gt ${ac_path_GREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_max=$ac_count fi # 10*(2^10) chars as input seems more than enough test $ac_count -gt 10 && break done rm -f conftest.in conftest.tmp conftest.nl conftest.out;; esac $ac_path_GREP_found && break 3 done done done IFS=$as_save_IFS if test -z "$ac_cv_path_GREP"; then as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 fi else ac_cv_path_GREP=$GREP fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5 $as_echo "$ac_cv_path_GREP" >&6; } GREP="$ac_cv_path_GREP" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5 $as_echo_n "checking for egrep... " >&6; } if ${ac_cv_path_EGREP+:} false; then : $as_echo_n "(cached) " >&6 else if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 then ac_cv_path_EGREP="$GREP -E" else if test -z "$EGREP"; then ac_path_EGREP_found=false # Loop through the user's path and test for each of PROGNAME-LIST as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_prog in egrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext" as_fn_executable_p "$ac_path_EGREP" || continue # Check for GNU ac_path_EGREP and select it if it is found. # Check for GNU $ac_path_EGREP case `"$ac_path_EGREP" --version 2>&1` in *GNU*) ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;; *) ac_count=0 $as_echo_n 0123456789 >"conftest.in" while : do cat "conftest.in" "conftest.in" >"conftest.tmp" mv "conftest.tmp" "conftest.in" cp "conftest.in" "conftest.nl" $as_echo 'EGREP' >> "conftest.nl" "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break as_fn_arith $ac_count + 1 && ac_count=$as_val if test $ac_count -gt ${ac_path_EGREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_max=$ac_count fi # 10*(2^10) chars as input seems more than enough test $ac_count -gt 10 && break done rm -f conftest.in conftest.tmp conftest.nl conftest.out;; esac $ac_path_EGREP_found && break 3 done done done IFS=$as_save_IFS if test -z "$ac_cv_path_EGREP"; then as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 fi else ac_cv_path_EGREP=$EGREP fi fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5 $as_echo "$ac_cv_path_EGREP" >&6; } EGREP="$ac_cv_path_EGREP" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 $as_echo_n "checking for ANSI C header files... " >&6; } if ${ac_cv_header_stdc+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include #include #include int main () { ; return 0; } _ACEOF if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_header_stdc=yes else ac_cv_header_stdc=no fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | $EGREP "memchr" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | $EGREP "free" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. if test "$cross_compiling" = yes; then : : else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include #if ((' ' & 0x0FF) == 0x020) # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #else # define ISLOWER(c) \ (('a' <= (c) && (c) <= 'i') \ || ('j' <= (c) && (c) <= 'r') \ || ('s' <= (c) && (c) <= 'z')) # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) #endif #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main () { int i; for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) return 2; return 0; } _ACEOF if ac_fn_cxx_try_run "$LINENO"; then : else ac_cv_header_stdc=no fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then $as_echo "#define STDC_HEADERS 1" >>confdefs.h fi # On IRIX 5.3, sys/types and inttypes.h are conflicting. for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h do : as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` ac_fn_cxx_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default " if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi done ac_fn_cxx_check_header_mongrel "$LINENO" "Console.h" "ac_cv_header_Console_h" "$ac_includes_default" if test "x$ac_cv_header_Console_h" = xyes; then : else as_fn_error $? "\"cannot find header file ${JAGS_PKGINCLUDEDIR}/Console.h. Please use pkg-config to locate the JAGS library. See the INSTALL file for details.\"" "$LINENO" 5 fi CPPFLAGS=${OCPPFLAGS} ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu # There is no consensus on where 64- versus 32-bit libraries should be # installed. We take a hint from R, assuming that if R is installed # in, say, /usr/LIBnn/R then we can find the jags library in # ${JAGS_PREFIX}/LIBnn. # # This is a reasonable assumption if both JAGS and R have been # properly packaged, but may not be true if either has been manually # installed. The user can set the environment variable LIBnn to # override this. if test -z "${LIBnn}"; then LIBnn=`"${R_HOME}/bin/R" CMD config LIBnn` fi # Set optional library path with option --with-jags-libdir or # environment variable JAGS_LIBDIR. By default this is determined by # JAGS_PREFIX and LIBnn. # Check whether --with-jags-libdir was given. if test "${with_jags_libdir+set}" = set; then : withval=$with_jags_libdir; jags_lib_path=$withval fi if test -n "$jags_lib_path" ; then JAGS_LIBDIR=$jags_lib_path else if test -z "${JAGS_LIBDIR}" ; then JAGS_LIBDIR=${JAGS_PREFIX}/${LIBnn} fi fi JAGS_CFLAGS="-I${JAGS_PKGINCLUDEDIR}" JAGS_LIBS="-L${JAGS_LIBDIR} -ljags" { $as_echo "$as_me:${as_lineno-$LINENO}: Compile flags are $JAGS_CFLAGS" >&5 $as_echo "$as_me: Compile flags are $JAGS_CFLAGS" >&6;} { $as_echo "$as_me:${as_lineno-$LINENO}: Link flags are $JAGS_LIBS" >&5 $as_echo "$as_me: Link flags are $JAGS_LIBS" >&6;} fi ####################### END legacy configuration ########################## # Support for private installations of JAGS. If the jags library is not # on the linker path then it helps to hard-code the location of JAGS into # the DSO for rjags. Suggested by Doug Bates, April 2011. # Check whether --enable-rpath was given. if test "${enable_rpath+set}" = set; then : enableval=$enable_rpath; fi if test "x$enable_rpath" = "xyes"; then JAGS_RPATH="-Wl,-rpath ${JAGS_LIBDIR}" fi # Sanity checks. OLDFLAGS=${LDFLAGS} OCFLAGS=${CFLAGS} ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu CFLAGS=${JAGS_CFLAGS} # Can we link to the library? LDFLAGS="-L${JAGS_LIBDIR}" ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. set dummy ${ac_tool_prefix}gcc; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_CC+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}gcc" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 $as_echo "$CC" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "gcc", so it can be a program name with args. set dummy gcc; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_CC+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="gcc" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 $as_echo "$ac_ct_CC" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_CC" = x; then CC="" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac CC=$ac_ct_CC fi else CC="$ac_cv_prog_CC" fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. set dummy ${ac_tool_prefix}cc; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_CC+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}cc" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 $as_echo "$CC" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi fi if test -z "$CC"; then # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_CC+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else ac_prog_rejected=no as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then ac_prog_rejected=yes continue fi ac_cv_prog_CC="cc" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS if test $ac_prog_rejected = yes; then # We found a bogon in the path, so make sure we never use it. set dummy $ac_cv_prog_CC shift if test $# != 0; then # We chose a different compiler from the bogus one. # However, it has the same basename, so the bogon will be chosen # first if we set CC to just the basename; use the full file name. shift ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" fi fi fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 $as_echo "$CC" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then for ac_prog in cl.exe do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_CC+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 $as_echo "$CC" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$CC" && break done fi if test -z "$CC"; then ac_ct_CC=$CC for ac_prog in cl.exe do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_CC+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 $as_echo "$ac_ct_CC" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$ac_ct_CC" && break done if test "x$ac_ct_CC" = x; then CC="" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac CC=$ac_ct_CC fi fi fi test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "no acceptable C compiler found in \$PATH See \`config.log' for more details" "$LINENO" 5; } # Provide some information about the compiler. $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 set X $ac_compile ac_compiler=$2 for ac_option in --version -v -V -qversion; do { { ac_try="$ac_compiler $ac_option >&5" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" $as_echo "$ac_try_echo"; } >&5 (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? if test -s conftest.err; then sed '10a\ ... rest of stderr output deleted ... 10q' conftest.err >conftest.er1 cat conftest.er1 >&5 fi rm -f conftest.er1 conftest.err $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } done { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 $as_echo_n "checking whether we are using the GNU C compiler... " >&6; } if ${ac_cv_c_compiler_gnu+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { #ifndef __GNUC__ choke me #endif ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : ac_compiler_gnu=yes else ac_compiler_gnu=no fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_c_compiler_gnu=$ac_compiler_gnu fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 $as_echo "$ac_cv_c_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GCC=yes else GCC= fi ac_test_CFLAGS=${CFLAGS+set} ac_save_CFLAGS=$CFLAGS { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 $as_echo_n "checking whether $CC accepts -g... " >&6; } if ${ac_cv_prog_cc_g+:} false; then : $as_echo_n "(cached) " >&6 else ac_save_c_werror_flag=$ac_c_werror_flag ac_c_werror_flag=yes ac_cv_prog_cc_g=no CFLAGS="-g" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_g=yes else CFLAGS="" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : else ac_c_werror_flag=$ac_save_c_werror_flag CFLAGS="-g" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_g=yes fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_c_werror_flag=$ac_save_c_werror_flag fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 $as_echo "$ac_cv_prog_cc_g" >&6; } if test "$ac_test_CFLAGS" = set; then CFLAGS=$ac_save_CFLAGS elif test $ac_cv_prog_cc_g = yes; then if test "$GCC" = yes; then CFLAGS="-g -O2" else CFLAGS="-g" fi else if test "$GCC" = yes; then CFLAGS="-O2" else CFLAGS= fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 $as_echo_n "checking for $CC option to accept ISO C89... " >&6; } if ${ac_cv_prog_cc_c89+:} false; then : $as_echo_n "(cached) " >&6 else ac_cv_prog_cc_c89=no ac_save_CC=$CC cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include struct stat; /* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ struct buf { int x; }; FILE * (*rcsopen) (struct buf *, struct stat *, int); static char *e (p, i) char **p; int i; { return p[i]; } static char *f (char * (*g) (char **, int), char **p, ...) { char *s; va_list v; va_start (v,p); s = g (p, va_arg (v,int)); va_end (v); return s; } /* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has function prototypes and stuff, but not '\xHH' hex character constants. These don't provoke an error unfortunately, instead are silently treated as 'x'. The following induces an error, until -std is added to get proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an array size at least. It's necessary to write '\x00'==0 to get something that's true only with -std. */ int osf4_cc_array ['\x00' == 0 ? 1 : -1]; /* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters inside strings and character constants. */ #define FOO(x) 'x' int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); int argc; char **argv; int main () { return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; ; return 0; } _ACEOF for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_c89=$ac_arg fi rm -f core conftest.err conftest.$ac_objext test "x$ac_cv_prog_cc_c89" != "xno" && break done rm -f conftest.$ac_ext CC=$ac_save_CC fi # AC_CACHE_VAL case "x$ac_cv_prog_cc_c89" in x) { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 $as_echo "none needed" >&6; } ;; xno) { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 $as_echo "unsupported" >&6; } ;; *) CC="$CC $ac_cv_prog_cc_c89" { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 $as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac if test "x$ac_cv_prog_cc_c89" != xno; then : fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu { $as_echo "$as_me:${as_lineno-$LINENO}: checking for jags_version in -ljags" >&5 $as_echo_n "checking for jags_version in -ljags... " >&6; } if ${ac_cv_lib_jags_jags_version+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ljags $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char jags_version (); int main () { return jags_version (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_jags_jags_version=yes else ac_cv_lib_jags_jags_version=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_jags_jags_version" >&5 $as_echo "$ac_cv_lib_jags_jags_version" >&6; } if test "x$ac_cv_lib_jags_jags_version" = xyes; then : cat >>confdefs.h <<_ACEOF #define HAVE_LIBJAGS 1 _ACEOF LIBS="-ljags $LIBS" else as_fn_error $? "\"cannot link to JAGS library in ${JAGS_LIBDIR}.\"" "$LINENO" 5 fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu CFLAGS=${OCFLAGS} # Does the library have the correct major version number? ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu OCXXFLAGS=${CXXFLAGS} CXXFLAGS=${JAGS_CFLAGS} LDFLAGS="${JAGS_LIBS} ${JAGS_RPATH}" { $as_echo "$as_me:${as_lineno-$LINENO}: checking version of JAGS library" >&5 $as_echo_n "checking version of JAGS library... " >&6; } # Need to run this trivial test program first to detect runtime linkage problems if test "$cross_compiling" = yes; then : { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "cannot run test program while cross compiling See \`config.log' for more details" "$LINENO" 5; } else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main() { return 0; } _ACEOF if ac_fn_cxx_try_run "$LINENO"; then : else { $as_echo "$as_me:${as_lineno-$LINENO}: result: link error" >&5 $as_echo "link error" >&6; } as_fn_error $? "Runtime link error: See the INSTALL file for help" "$LINENO" 5 fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi # Now we can test if test "$cross_compiling" = yes; then : { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "cannot run test program while cross compiling See \`config.log' for more details" "$LINENO" 5; } else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main() { return JAGS_MAJOR == ${PACKAGE_VERSION} ? 0 : 1; } _ACEOF if ac_fn_cxx_try_run "$LINENO"; then : { $as_echo "$as_me:${as_lineno-$LINENO}: result: OK" >&5 $as_echo "OK" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: wrong version" >&5 $as_echo "wrong version" >&6; } as_fn_error $? "rjags requires JAGS version ${PACKAGE_VERSION}.x.y" "$LINENO" 5 fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu LDFLAGS=${OLDFLAGS} CXXFLAGS=${OCXXFLAGS} # Set location of modules JAGS_MODDIR=${JAGS_LIBDIR}/JAGS/modules-${PACKAGE_VERSION} ac_config_files="$ac_config_files src/Makevars" cat >confcache <<\_ACEOF # This file is a shell script that caches the results of configure # tests run on this system so they can be shared between configure # scripts and configure runs, see configure's option --config-cache. # It is not useful on other systems. If it contains results you don't # want to keep, you may remove or edit it. # # config.status only pays attention to the cache file if you give it # the --recheck option to rerun configure. # # `ac_cv_env_foo' variables (set or unset) will be overridden when # loading this file, other *unset* `ac_cv_foo' will be assigned the # following values. _ACEOF # The following way of writing the cache mishandles newlines in values, # but we know of no workaround that is simple, portable, and efficient. # So, we kill variables containing newlines. # Ultrix sh set writes to stderr and can't be redirected directly, # and sets the high bit in the cache file unless we assign to the vars. ( for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do eval ac_val=\$$ac_var case $ac_val in #( *${as_nl}*) case $ac_var in #( *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( *) { eval $ac_var=; unset $ac_var;} ;; esac ;; esac done (set) 2>&1 | case $as_nl`(ac_space=' '; set) 2>&1` in #( *${as_nl}ac_space=\ *) # `set' does not quote correctly, so add quotes: double-quote # substitution turns \\\\ into \\, and sed turns \\ into \. sed -n \ "s/'/'\\\\''/g; s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" ;; #( *) # `set' quotes correctly as required by POSIX, so do not add quotes. sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p" ;; esac | sort ) | sed ' /^ac_cv_env_/b end t clear :clear s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/ t end s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/ :end' >>confcache if diff "$cache_file" confcache >/dev/null 2>&1; then :; else if test -w "$cache_file"; then if test "x$cache_file" != "x/dev/null"; then { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 $as_echo "$as_me: updating cache $cache_file" >&6;} if test ! -f "$cache_file" || test -h "$cache_file"; then cat confcache >"$cache_file" else case $cache_file in #( */* | ?:*) mv -f confcache "$cache_file"$$ && mv -f "$cache_file"$$ "$cache_file" ;; #( *) mv -f confcache "$cache_file" ;; esac fi fi else { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} fi fi rm -f confcache test "x$prefix" = xNONE && prefix=$ac_default_prefix # Let make expand exec_prefix. test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' # Transform confdefs.h into DEFS. # Protect against shell expansion while executing Makefile rules. # Protect against Makefile macro expansion. # # If the first sed substitution is executed (which looks for macros that # take arguments), then branch to the quote section. Otherwise, # look for a macro that doesn't take arguments. ac_script=' :mline /\\$/{ N s,\\\n,, b mline } t clear :clear s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g t quote s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g t quote b any :quote s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g s/\[/\\&/g s/\]/\\&/g s/\$/$$/g H :any ${ g s/^\n// s/\n/ /g p } ' DEFS=`sed -n "$ac_script" confdefs.h` ac_libobjs= ac_ltlibobjs= U= for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue # 1. Remove the extension, and $U if already installed. ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' ac_i=`$as_echo "$ac_i" | sed "$ac_script"` # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR # will be set to the directory where LIBOBJS objects are built. as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' done LIBOBJS=$ac_libobjs LTLIBOBJS=$ac_ltlibobjs : "${CONFIG_STATUS=./config.status}" ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" { $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 $as_echo "$as_me: creating $CONFIG_STATUS" >&6;} as_write_fail=0 cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 #! $SHELL # Generated by $as_me. # Run this file to recreate the current configuration. # Compiler output produced by configure, useful for debugging # configure, is in config.log if it exists. debug=false ac_cs_recheck=false ac_cs_silent=false SHELL=\${CONFIG_SHELL-$SHELL} export SHELL _ASEOF cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 ## -------------------- ## ## M4sh Initialization. ## ## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else case `(set -o) 2>/dev/null` in #( *posix*) : set -o posix ;; #( *) : ;; esac fi as_nl=' ' export as_nl # Printing a long string crashes Solaris 7 /usr/bin/printf. as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo # Prefer a ksh shell builtin over an external printf program on Solaris, # but without wasting forks for bash or zsh. if test -z "$BASH_VERSION$ZSH_VERSION" \ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='print -r --' as_echo_n='print -rn --' elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' as_echo_n='/usr/ucb/echo -n' else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; case $arg in #( *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; esac; expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" ' export as_echo_n_body as_echo_n='sh -c $as_echo_n_body as_echo' fi export as_echo_body as_echo='sh -c $as_echo_body as_echo' fi # The user is always right. if test "${PATH_SEPARATOR+set}" != set; then PATH_SEPARATOR=: (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || PATH_SEPARATOR=';' } fi # IFS # We need space, tab and new line, in precisely that order. Quoting is # there to prevent editors from complaining about space-tab. # (If _AS_PATH_WALK were called with IFS unset, it would disable word # splitting by setting IFS to empty value.) IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. as_myself= case $0 in #(( *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break done IFS=$as_save_IFS ;; esac # We did not find ourselves, most probably we were run as `sh COMMAND' # in which case we are not to be found in the path. if test "x$as_myself" = x; then as_myself=$0 fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 exit 1 fi # Unset variables that we do not need and which cause bugs (e.g. in # pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" # suppresses any "Segmentation fault" message there. '((' could # trigger a bug in pdksh 5.2.14. for as_var in BASH_ENV ENV MAIL MAILPATH do eval test x\${$as_var+set} = xset \ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : done PS1='$ ' PS2='> ' PS4='+ ' # NLS nuisances. LC_ALL=C export LC_ALL LANGUAGE=C export LANGUAGE # CDPATH. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH # as_fn_error STATUS ERROR [LINENO LOG_FD] # ---------------------------------------- # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are # provided, also output the error to LOG_FD, referencing LINENO. Then exit the # script with STATUS, using 1 if that was 0. as_fn_error () { as_status=$1; test $as_status -eq 0 && as_status=1 if test "$4"; then as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 fi $as_echo "$as_me: error: $2" >&2 as_fn_exit $as_status } # as_fn_error # as_fn_set_status STATUS # ----------------------- # Set $? to STATUS, without forking. as_fn_set_status () { return $1 } # as_fn_set_status # as_fn_exit STATUS # ----------------- # Exit the shell with STATUS, even in a "trap 0" or "set -e" context. as_fn_exit () { set +e as_fn_set_status $1 exit $1 } # as_fn_exit # as_fn_unset VAR # --------------- # Portably unset VAR. as_fn_unset () { { eval $1=; unset $1;} } as_unset=as_fn_unset # as_fn_append VAR VALUE # ---------------------- # Append the text in VALUE to the end of the definition contained in VAR. Take # advantage of any shell optimizations that allow amortized linear growth over # repeated appends, instead of the typical quadratic growth present in naive # implementations. if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : eval 'as_fn_append () { eval $1+=\$2 }' else as_fn_append () { eval $1=\$$1\$2 } fi # as_fn_append # as_fn_arith ARG... # ------------------ # Perform arithmetic evaluation on the ARGs, and store the result in the # global $as_val. Take advantage of shells that can avoid forks. The arguments # must be portable across $(()) and expr. if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : eval 'as_fn_arith () { as_val=$(( $* )) }' else as_fn_arith () { as_val=`expr "$@" || test $? -eq 1` } fi # as_fn_arith if expr a : '\(a\)' >/dev/null 2>&1 && test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr else as_expr=false fi if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then as_basename=basename else as_basename=false fi if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then as_dirname=dirname else as_dirname=false fi as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ X"$0" : 'X\(/\)' \| . 2>/dev/null || $as_echo X/"$0" | sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/ q } /^X\/\(\/\/\)$/{ s//\1/ q } /^X\/\(\/\).*/{ s//\1/ q } s/.*/./; q'` # Avoid depending upon Character Ranges. as_cr_letters='abcdefghijklmnopqrstuvwxyz' as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' as_cr_Letters=$as_cr_letters$as_cr_LETTERS as_cr_digits='0123456789' as_cr_alnum=$as_cr_Letters$as_cr_digits ECHO_C= ECHO_N= ECHO_T= case `echo -n x` in #((((( -n*) case `echo 'xy\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. xy) ECHO_C='\c';; *) echo `echo ksh88 bug on AIX 6.1` > /dev/null ECHO_T=' ';; esac;; *) ECHO_N='-n';; esac rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then rm -f conf$$.dir/conf$$.file else rm -f conf$$.dir mkdir conf$$.dir 2>/dev/null fi if (echo >conf$$.file) 2>/dev/null; then if ln -s conf$$.file conf$$ 2>/dev/null; then as_ln_s='ln -s' # ... but there are two gotchas: # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. # In both cases, we have to default to `cp -pR'. ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || as_ln_s='cp -pR' elif ln conf$$.file conf$$ 2>/dev/null; then as_ln_s=ln else as_ln_s='cp -pR' fi else as_ln_s='cp -pR' fi rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null # as_fn_mkdir_p # ------------- # Create "$as_dir" as a directory, including parents if necessary. as_fn_mkdir_p () { case $as_dir in #( -*) as_dir=./$as_dir;; esac test -d "$as_dir" || eval $as_mkdir_p || { as_dirs= while :; do case $as_dir in #( *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( *) as_qdir=$as_dir;; esac as_dirs="'$as_qdir' $as_dirs" as_dir=`$as_dirname -- "$as_dir" || $as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$as_dir" : 'X\(//\)[^/]' \| \ X"$as_dir" : 'X\(//\)$' \| \ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || $as_echo X"$as_dir" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q } /^X\(\/\/\)[^/].*/{ s//\1/ q } /^X\(\/\/\)$/{ s//\1/ q } /^X\(\/\).*/{ s//\1/ q } s/.*/./; q'` test -d "$as_dir" && break done test -z "$as_dirs" || eval "mkdir $as_dirs" } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" } # as_fn_mkdir_p if mkdir -p . 2>/dev/null; then as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false fi # as_fn_executable_p FILE # ----------------------- # Test if FILE is an executable regular file. as_fn_executable_p () { test -f "$1" && test -x "$1" } # as_fn_executable_p as_test_x='test -x' as_executable_p=as_fn_executable_p # Sed expression to map a string onto a valid CPP name. as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" # Sed expression to map a string onto a valid variable name. as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" exec 6>&1 ## ----------------------------------- ## ## Main body of $CONFIG_STATUS script. ## ## ----------------------------------- ## _ASEOF test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # Save the log message, to keep $0 and so on meaningful, and to # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" This file was extended by rjags $as_me 4, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS CONFIG_LINKS = $CONFIG_LINKS CONFIG_COMMANDS = $CONFIG_COMMANDS $ $0 $@ on `(hostname || uname -n) 2>/dev/null | sed 1q` " _ACEOF case $ac_config_files in *" "*) set x $ac_config_files; shift; ac_config_files=$*;; esac cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 # Files that config.status was made for. config_files="$ac_config_files" _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ \`$as_me' instantiates files and other configuration actions from templates according to the current configuration. Unless the files and actions are specified as TAGs, all are instantiated by default. Usage: $0 [OPTION]... [TAG]... -h, --help print this help, then exit -V, --version print version number and configuration settings, then exit --config print configuration, then exit -q, --quiet, --silent do not print progress messages -d, --debug don't remove temporary files --recheck update $as_me by reconfiguring in the same conditions --file=FILE[:TEMPLATE] instantiate the configuration file FILE Configuration files: $config_files Report bugs to the package provider." _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ rjags config.status 4 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" Copyright (C) 2012 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." ac_pwd='$ac_pwd' srcdir='$srcdir' test -n "\$AWK" || AWK=awk _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # The default lists apply if the user does not specify any file. ac_need_defaults=: while test $# != 0 do case $1 in --*=?*) ac_option=`expr "X$1" : 'X\([^=]*\)='` ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` ac_shift=: ;; --*=) ac_option=`expr "X$1" : 'X\([^=]*\)='` ac_optarg= ac_shift=: ;; *) ac_option=$1 ac_optarg=$2 ac_shift=shift ;; esac case $ac_option in # Handling of the options. -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r) ac_cs_recheck=: ;; --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) $as_echo "$ac_cs_version"; exit ;; --config | --confi | --conf | --con | --co | --c ) $as_echo "$ac_cs_config"; exit ;; --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; '') as_fn_error $? "missing file argument" ;; esac as_fn_append CONFIG_FILES " '$ac_optarg'" ac_need_defaults=false;; --he | --h | --help | --hel | -h ) $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil | --si | --s) ac_cs_silent=: ;; # This is an error. -*) as_fn_error $? "unrecognized option: \`$1' Try \`$0 --help' for more information." ;; *) as_fn_append ac_config_targets " $1" ac_need_defaults=false ;; esac shift done ac_configure_extra_args= if $ac_cs_silent; then exec 6>/dev/null ac_configure_extra_args="$ac_configure_extra_args --silent" fi _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 if \$ac_cs_recheck; then set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion shift \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6 CONFIG_SHELL='$SHELL' export CONFIG_SHELL exec "\$@" fi _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 exec 5>>config.log { echo sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX ## Running $as_me. ## _ASBOX $as_echo "$ac_log" } >&5 _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # Handling of arguments. for ac_config_target in $ac_config_targets do case $ac_config_target in "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;; *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;; esac done # If the user did not use the arguments to specify the items to instantiate, # then the envvar interface is used. Set only those that are not. # We use the long form for the default assignment because of an extremely # bizarre bug on SunOS 4.1.3. if $ac_need_defaults; then test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files fi # Have a temporary directory for convenience. Make it in the build tree # simply because there is no reason against having it here, and in addition, # creating and moving files from /tmp can sometimes cause problems. # Hook for its removal unless debugging. # Note that there is a small window in which the directory will not be cleaned: # after its creation but before its name has been assigned to `$tmp'. $debug || { tmp= ac_tmp= trap 'exit_status=$? : "${ac_tmp:=$tmp}" { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status ' 0 trap 'as_fn_exit 1' 1 2 13 15 } # Create a (secure) tmp directory for tmp files. { tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` && test -d "$tmp" } || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") } || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 ac_tmp=$tmp # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. # This happens for instance with `./config.status config.h'. if test -n "$CONFIG_FILES"; then ac_cr=`echo X | tr X '\015'` # On cygwin, bash can eat \r inside `` if the user requested igncr. # But we know of no other shell where ac_cr would be empty at this # point, so we can use a bashism as a fallback. if test "x$ac_cr" = x; then eval ac_cr=\$\'\\r\' fi ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then ac_cs_awk_cr='\\r' else ac_cs_awk_cr=$ac_cr fi echo 'BEGIN {' >"$ac_tmp/subs1.awk" && _ACEOF { echo "cat >conf$$subs.awk <<_ACEOF" && echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && echo "_ACEOF" } >conf$$subs.sh || as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'` ac_delim='%!_!# ' for ac_last_try in false false false false false :; do . ./conf$$subs.sh || as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` if test $ac_delim_n = $ac_delim_num; then break elif $ac_last_try; then as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi done rm -f conf$$subs.sh cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK && _ACEOF sed -n ' h s/^/S["/; s/!.*/"]=/ p g s/^[^!]*!// :repl t repl s/'"$ac_delim"'$// t delim :nl h s/\(.\{148\}\)..*/\1/ t more1 s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ p n b repl :more1 s/["\\]/\\&/g; s/^/"/; s/$/"\\/ p g s/.\{148\}// t nl :delim h s/\(.\{148\}\)..*/\1/ t more2 s/["\\]/\\&/g; s/^/"/; s/$/"/ p b :more2 s/["\\]/\\&/g; s/^/"/; s/$/"\\/ p g s/.\{148\}// t delim ' >$CONFIG_STATUS || ac_write_fail=1 rm -f conf$$subs.awk cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACAWK cat >>"\$ac_tmp/subs1.awk" <<_ACAWK && for (key in S) S_is_set[key] = 1 FS = "" } { line = $ 0 nfields = split(line, field, "@") substed = 0 len = length(field[1]) for (i = 2; i < nfields; i++) { key = field[i] keylen = length(key) if (S_is_set[key]) { value = S[key] line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3) len += length(value) + length(field[++i]) substed = 1 } else len += 1 + keylen } print line } _ACAWK _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g" else cat fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 _ACEOF # VPATH may cause trouble with some makes, so we remove sole $(srcdir), # ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and # trailing colons and then remove the whole line if VPATH becomes empty # (actually we leave an empty line to preserve line numbers). if test "x$srcdir" = x.; then ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{ h s/// s/^/:/ s/[ ]*$/:/ s/:\$(srcdir):/:/g s/:\${srcdir}:/:/g s/:@srcdir@:/:/g s/^:*// s/:*$// x s/\(=[ ]*\).*/\1/ G s/\n// s/^[^=]*=[ ]*$// }' fi cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 fi # test -n "$CONFIG_FILES" eval set X " :F $CONFIG_FILES " shift for ac_tag do case $ac_tag in :[FHLC]) ac_mode=$ac_tag; continue;; esac case $ac_mode$ac_tag in :[FHL]*:*);; :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac ac_save_IFS=$IFS IFS=: set x $ac_tag IFS=$ac_save_IFS shift ac_file=$1 shift case $ac_mode in :L) ac_source=$1;; :[FH]) ac_file_inputs= for ac_f do case $ac_f in -) ac_f="$ac_tmp/stdin";; *) # Look for the file first in the build tree, then in the source tree # (if the path is not absolute). The absolute path cannot be DOS-style, # because $ac_f cannot contain `:'. test -f "$ac_f" || case $ac_f in [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac as_fn_append ac_file_inputs " '$ac_f'" done # Let's still pretend it is `configure' which instantiates (i.e., don't # use $as_me), people would be surprised to read: # /* config.h. Generated by config.status. */ configure_input='Generated from '` $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g' `' by configure.' if test x"$ac_file" != x-; then configure_input="$ac_file. $configure_input" { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 $as_echo "$as_me: creating $ac_file" >&6;} fi # Neutralize special characters interpreted by sed in replacement strings. case $configure_input in #( *\&* | *\|* | *\\* ) ac_sed_conf_input=`$as_echo "$configure_input" | sed 's/[\\\\&|]/\\\\&/g'`;; #( *) ac_sed_conf_input=$configure_input;; esac case $ac_tag in *:-:* | *:-) cat >"$ac_tmp/stdin" \ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; esac ;; esac ac_dir=`$as_dirname -- "$ac_file" || $as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$ac_file" : 'X\(//\)[^/]' \| \ X"$ac_file" : 'X\(//\)$' \| \ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null || $as_echo X"$ac_file" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q } /^X\(\/\/\)[^/].*/{ s//\1/ q } /^X\(\/\/\)$/{ s//\1/ q } /^X\(\/\).*/{ s//\1/ q } s/.*/./; q'` as_dir="$ac_dir"; as_fn_mkdir_p ac_builddir=. case "$ac_dir" in .) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; *) ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` # A ".." for each directory in $ac_dir_suffix. ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` case $ac_top_builddir_sub in "") ac_top_builddir_sub=. ac_top_build_prefix= ;; *) ac_top_build_prefix=$ac_top_builddir_sub/ ;; esac ;; esac ac_abs_top_builddir=$ac_pwd ac_abs_builddir=$ac_pwd$ac_dir_suffix # for backward compatibility: ac_top_builddir=$ac_top_build_prefix case $srcdir in .) # We are building in place. ac_srcdir=. ac_top_srcdir=$ac_top_builddir_sub ac_abs_top_srcdir=$ac_pwd ;; [\\/]* | ?:[\\/]* ) # Absolute name. ac_srcdir=$srcdir$ac_dir_suffix; ac_top_srcdir=$srcdir ac_abs_top_srcdir=$srcdir ;; *) # Relative name. ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix ac_top_srcdir=$ac_top_build_prefix$srcdir ac_abs_top_srcdir=$ac_pwd/$srcdir ;; esac ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix case $ac_mode in :F) # # CONFIG_FILE # _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # If the template does not know about datarootdir, expand it. # FIXME: This hack should be removed a few years after 2.60. ac_datarootdir_hack=; ac_datarootdir_seen= ac_sed_dataroot=' /datarootdir/ { p q } /@datadir@/p /@docdir@/p /@infodir@/p /@localedir@/p /@mandir@/p' case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in *datarootdir*) ac_datarootdir_seen=yes;; *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_datarootdir_hack=' s&@datadir@&$datadir&g s&@docdir@&$docdir&g s&@infodir@&$infodir&g s&@localedir@&$localedir&g s&@mandir@&$mandir&g s&\\\${datarootdir}&$datarootdir&g' ;; esac _ACEOF # Neutralize VPATH when `$srcdir' = `.'. # Shell code in configure.ac might set extrasub. # FIXME: do we really want to maintain this feature? cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_sed_extra="$ac_vpsub $extrasub _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 :t /@[a-zA-Z_][a-zA-Z_0-9]*@/!b s|@configure_input@|$ac_sed_conf_input|;t t s&@top_builddir@&$ac_top_builddir_sub&;t t s&@top_build_prefix@&$ac_top_build_prefix&;t t s&@srcdir@&$ac_srcdir&;t t s&@abs_srcdir@&$ac_abs_srcdir&;t t s&@top_srcdir@&$ac_top_srcdir&;t t s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t s&@builddir@&$ac_builddir&;t t s&@abs_builddir@&$ac_abs_builddir&;t t s&@abs_top_builddir@&$ac_abs_top_builddir&;t t $ac_datarootdir_hack " eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \ "$ac_tmp/out"`; test -z "$ac_out"; } && { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&2;} rm -f "$ac_tmp/stdin" case $ac_file in -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";; *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";; esac \ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; esac done # for ac_tag as_fn_exit 0 _ACEOF ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 # configure is writing to config.log, and then calls config.status. # config.status does its own redirection, appending to config.log. # Unfortunately, on DOS this fails, as config.log is still kept open # by configure, so config.status won't be able to write to it; its # output is simply discarded. So we exec the FD to /dev/null, # effectively closing config.log, so it can be properly (re)opened and # appended to by config.status. When coming back to configure, we # need to make the FD available again. if test "$no_create" != yes; then ac_cs_success=: ac_config_status_args= test "$silent" = yes && ac_config_status_args="$ac_config_status_args --quiet" exec 5>/dev/null $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. $ac_cs_success || as_fn_exit 1 fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi ac_config_files="$ac_config_files R/unix/zzz.R" cat >confcache <<\_ACEOF # This file is a shell script that caches the results of configure # tests run on this system so they can be shared between configure # scripts and configure runs, see configure's option --config-cache. # It is not useful on other systems. If it contains results you don't # want to keep, you may remove or edit it. # # config.status only pays attention to the cache file if you give it # the --recheck option to rerun configure. # # `ac_cv_env_foo' variables (set or unset) will be overridden when # loading this file, other *unset* `ac_cv_foo' will be assigned the # following values. _ACEOF # The following way of writing the cache mishandles newlines in values, # but we know of no workaround that is simple, portable, and efficient. # So, we kill variables containing newlines. # Ultrix sh set writes to stderr and can't be redirected directly, # and sets the high bit in the cache file unless we assign to the vars. ( for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do eval ac_val=\$$ac_var case $ac_val in #( *${as_nl}*) case $ac_var in #( *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( *) { eval $ac_var=; unset $ac_var;} ;; esac ;; esac done (set) 2>&1 | case $as_nl`(ac_space=' '; set) 2>&1` in #( *${as_nl}ac_space=\ *) # `set' does not quote correctly, so add quotes: double-quote # substitution turns \\\\ into \\, and sed turns \\ into \. sed -n \ "s/'/'\\\\''/g; s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" ;; #( *) # `set' quotes correctly as required by POSIX, so do not add quotes. sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p" ;; esac | sort ) | sed ' /^ac_cv_env_/b end t clear :clear s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/ t end s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/ :end' >>confcache if diff "$cache_file" confcache >/dev/null 2>&1; then :; else if test -w "$cache_file"; then if test "x$cache_file" != "x/dev/null"; then { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 $as_echo "$as_me: updating cache $cache_file" >&6;} if test ! -f "$cache_file" || test -h "$cache_file"; then cat confcache >"$cache_file" else case $cache_file in #( */* | ?:*) mv -f confcache "$cache_file"$$ && mv -f "$cache_file"$$ "$cache_file" ;; #( *) mv -f confcache "$cache_file" ;; esac fi fi else { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} fi fi rm -f confcache test "x$prefix" = xNONE && prefix=$ac_default_prefix # Let make expand exec_prefix. test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' # Transform confdefs.h into DEFS. # Protect against shell expansion while executing Makefile rules. # Protect against Makefile macro expansion. # # If the first sed substitution is executed (which looks for macros that # take arguments), then branch to the quote section. Otherwise, # look for a macro that doesn't take arguments. ac_script=' :mline /\\$/{ N s,\\\n,, b mline } t clear :clear s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g t quote s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g t quote b any :quote s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g s/\[/\\&/g s/\]/\\&/g s/\$/$$/g H :any ${ g s/^\n// s/\n/ /g p } ' DEFS=`sed -n "$ac_script" confdefs.h` ac_libobjs= ac_ltlibobjs= U= for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue # 1. Remove the extension, and $U if already installed. ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' ac_i=`$as_echo "$ac_i" | sed "$ac_script"` # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR # will be set to the directory where LIBOBJS objects are built. as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' done LIBOBJS=$ac_libobjs LTLIBOBJS=$ac_ltlibobjs : "${CONFIG_STATUS=./config.status}" ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" { $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 $as_echo "$as_me: creating $CONFIG_STATUS" >&6;} as_write_fail=0 cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 #! $SHELL # Generated by $as_me. # Run this file to recreate the current configuration. # Compiler output produced by configure, useful for debugging # configure, is in config.log if it exists. debug=false ac_cs_recheck=false ac_cs_silent=false SHELL=\${CONFIG_SHELL-$SHELL} export SHELL _ASEOF cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 ## -------------------- ## ## M4sh Initialization. ## ## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else case `(set -o) 2>/dev/null` in #( *posix*) : set -o posix ;; #( *) : ;; esac fi as_nl=' ' export as_nl # Printing a long string crashes Solaris 7 /usr/bin/printf. as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo # Prefer a ksh shell builtin over an external printf program on Solaris, # but without wasting forks for bash or zsh. if test -z "$BASH_VERSION$ZSH_VERSION" \ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='print -r --' as_echo_n='print -rn --' elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' as_echo_n='/usr/ucb/echo -n' else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; case $arg in #( *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; esac; expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" ' export as_echo_n_body as_echo_n='sh -c $as_echo_n_body as_echo' fi export as_echo_body as_echo='sh -c $as_echo_body as_echo' fi # The user is always right. if test "${PATH_SEPARATOR+set}" != set; then PATH_SEPARATOR=: (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || PATH_SEPARATOR=';' } fi # IFS # We need space, tab and new line, in precisely that order. Quoting is # there to prevent editors from complaining about space-tab. # (If _AS_PATH_WALK were called with IFS unset, it would disable word # splitting by setting IFS to empty value.) IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. as_myself= case $0 in #(( *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break done IFS=$as_save_IFS ;; esac # We did not find ourselves, most probably we were run as `sh COMMAND' # in which case we are not to be found in the path. if test "x$as_myself" = x; then as_myself=$0 fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 exit 1 fi # Unset variables that we do not need and which cause bugs (e.g. in # pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" # suppresses any "Segmentation fault" message there. '((' could # trigger a bug in pdksh 5.2.14. for as_var in BASH_ENV ENV MAIL MAILPATH do eval test x\${$as_var+set} = xset \ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : done PS1='$ ' PS2='> ' PS4='+ ' # NLS nuisances. LC_ALL=C export LC_ALL LANGUAGE=C export LANGUAGE # CDPATH. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH # as_fn_error STATUS ERROR [LINENO LOG_FD] # ---------------------------------------- # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are # provided, also output the error to LOG_FD, referencing LINENO. Then exit the # script with STATUS, using 1 if that was 0. as_fn_error () { as_status=$1; test $as_status -eq 0 && as_status=1 if test "$4"; then as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 fi $as_echo "$as_me: error: $2" >&2 as_fn_exit $as_status } # as_fn_error # as_fn_set_status STATUS # ----------------------- # Set $? to STATUS, without forking. as_fn_set_status () { return $1 } # as_fn_set_status # as_fn_exit STATUS # ----------------- # Exit the shell with STATUS, even in a "trap 0" or "set -e" context. as_fn_exit () { set +e as_fn_set_status $1 exit $1 } # as_fn_exit # as_fn_unset VAR # --------------- # Portably unset VAR. as_fn_unset () { { eval $1=; unset $1;} } as_unset=as_fn_unset # as_fn_append VAR VALUE # ---------------------- # Append the text in VALUE to the end of the definition contained in VAR. Take # advantage of any shell optimizations that allow amortized linear growth over # repeated appends, instead of the typical quadratic growth present in naive # implementations. if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : eval 'as_fn_append () { eval $1+=\$2 }' else as_fn_append () { eval $1=\$$1\$2 } fi # as_fn_append # as_fn_arith ARG... # ------------------ # Perform arithmetic evaluation on the ARGs, and store the result in the # global $as_val. Take advantage of shells that can avoid forks. The arguments # must be portable across $(()) and expr. if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : eval 'as_fn_arith () { as_val=$(( $* )) }' else as_fn_arith () { as_val=`expr "$@" || test $? -eq 1` } fi # as_fn_arith if expr a : '\(a\)' >/dev/null 2>&1 && test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr else as_expr=false fi if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then as_basename=basename else as_basename=false fi if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then as_dirname=dirname else as_dirname=false fi as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ X"$0" : 'X\(/\)' \| . 2>/dev/null || $as_echo X/"$0" | sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/ q } /^X\/\(\/\/\)$/{ s//\1/ q } /^X\/\(\/\).*/{ s//\1/ q } s/.*/./; q'` # Avoid depending upon Character Ranges. as_cr_letters='abcdefghijklmnopqrstuvwxyz' as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' as_cr_Letters=$as_cr_letters$as_cr_LETTERS as_cr_digits='0123456789' as_cr_alnum=$as_cr_Letters$as_cr_digits ECHO_C= ECHO_N= ECHO_T= case `echo -n x` in #((((( -n*) case `echo 'xy\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. xy) ECHO_C='\c';; *) echo `echo ksh88 bug on AIX 6.1` > /dev/null ECHO_T=' ';; esac;; *) ECHO_N='-n';; esac rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then rm -f conf$$.dir/conf$$.file else rm -f conf$$.dir mkdir conf$$.dir 2>/dev/null fi if (echo >conf$$.file) 2>/dev/null; then if ln -s conf$$.file conf$$ 2>/dev/null; then as_ln_s='ln -s' # ... but there are two gotchas: # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. # In both cases, we have to default to `cp -pR'. ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || as_ln_s='cp -pR' elif ln conf$$.file conf$$ 2>/dev/null; then as_ln_s=ln else as_ln_s='cp -pR' fi else as_ln_s='cp -pR' fi rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null # as_fn_mkdir_p # ------------- # Create "$as_dir" as a directory, including parents if necessary. as_fn_mkdir_p () { case $as_dir in #( -*) as_dir=./$as_dir;; esac test -d "$as_dir" || eval $as_mkdir_p || { as_dirs= while :; do case $as_dir in #( *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( *) as_qdir=$as_dir;; esac as_dirs="'$as_qdir' $as_dirs" as_dir=`$as_dirname -- "$as_dir" || $as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$as_dir" : 'X\(//\)[^/]' \| \ X"$as_dir" : 'X\(//\)$' \| \ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || $as_echo X"$as_dir" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q } /^X\(\/\/\)[^/].*/{ s//\1/ q } /^X\(\/\/\)$/{ s//\1/ q } /^X\(\/\).*/{ s//\1/ q } s/.*/./; q'` test -d "$as_dir" && break done test -z "$as_dirs" || eval "mkdir $as_dirs" } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" } # as_fn_mkdir_p if mkdir -p . 2>/dev/null; then as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false fi # as_fn_executable_p FILE # ----------------------- # Test if FILE is an executable regular file. as_fn_executable_p () { test -f "$1" && test -x "$1" } # as_fn_executable_p as_test_x='test -x' as_executable_p=as_fn_executable_p # Sed expression to map a string onto a valid CPP name. as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" # Sed expression to map a string onto a valid variable name. as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" exec 6>&1 ## ----------------------------------- ## ## Main body of $CONFIG_STATUS script. ## ## ----------------------------------- ## _ASEOF test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # Save the log message, to keep $0 and so on meaningful, and to # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" This file was extended by rjags $as_me 4, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS CONFIG_LINKS = $CONFIG_LINKS CONFIG_COMMANDS = $CONFIG_COMMANDS $ $0 $@ on `(hostname || uname -n) 2>/dev/null | sed 1q` " _ACEOF case $ac_config_files in *" "*) set x $ac_config_files; shift; ac_config_files=$*;; esac cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 # Files that config.status was made for. config_files="$ac_config_files" _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ \`$as_me' instantiates files and other configuration actions from templates according to the current configuration. Unless the files and actions are specified as TAGs, all are instantiated by default. Usage: $0 [OPTION]... [TAG]... -h, --help print this help, then exit -V, --version print version number and configuration settings, then exit --config print configuration, then exit -q, --quiet, --silent do not print progress messages -d, --debug don't remove temporary files --recheck update $as_me by reconfiguring in the same conditions --file=FILE[:TEMPLATE] instantiate the configuration file FILE Configuration files: $config_files Report bugs to the package provider." _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ rjags config.status 4 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" Copyright (C) 2012 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." ac_pwd='$ac_pwd' srcdir='$srcdir' test -n "\$AWK" || AWK=awk _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # The default lists apply if the user does not specify any file. ac_need_defaults=: while test $# != 0 do case $1 in --*=?*) ac_option=`expr "X$1" : 'X\([^=]*\)='` ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` ac_shift=: ;; --*=) ac_option=`expr "X$1" : 'X\([^=]*\)='` ac_optarg= ac_shift=: ;; *) ac_option=$1 ac_optarg=$2 ac_shift=shift ;; esac case $ac_option in # Handling of the options. -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r) ac_cs_recheck=: ;; --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) $as_echo "$ac_cs_version"; exit ;; --config | --confi | --conf | --con | --co | --c ) $as_echo "$ac_cs_config"; exit ;; --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; '') as_fn_error $? "missing file argument" ;; esac as_fn_append CONFIG_FILES " '$ac_optarg'" ac_need_defaults=false;; --he | --h | --help | --hel | -h ) $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil | --si | --s) ac_cs_silent=: ;; # This is an error. -*) as_fn_error $? "unrecognized option: \`$1' Try \`$0 --help' for more information." ;; *) as_fn_append ac_config_targets " $1" ac_need_defaults=false ;; esac shift done ac_configure_extra_args= if $ac_cs_silent; then exec 6>/dev/null ac_configure_extra_args="$ac_configure_extra_args --silent" fi _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 if \$ac_cs_recheck; then set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion shift \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6 CONFIG_SHELL='$SHELL' export CONFIG_SHELL exec "\$@" fi _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 exec 5>>config.log { echo sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX ## Running $as_me. ## _ASBOX $as_echo "$ac_log" } >&5 _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # Handling of arguments. for ac_config_target in $ac_config_targets do case $ac_config_target in "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;; "R/unix/zzz.R") CONFIG_FILES="$CONFIG_FILES R/unix/zzz.R" ;; *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;; esac done # If the user did not use the arguments to specify the items to instantiate, # then the envvar interface is used. Set only those that are not. # We use the long form for the default assignment because of an extremely # bizarre bug on SunOS 4.1.3. if $ac_need_defaults; then test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files fi # Have a temporary directory for convenience. Make it in the build tree # simply because there is no reason against having it here, and in addition, # creating and moving files from /tmp can sometimes cause problems. # Hook for its removal unless debugging. # Note that there is a small window in which the directory will not be cleaned: # after its creation but before its name has been assigned to `$tmp'. $debug || { tmp= ac_tmp= trap 'exit_status=$? : "${ac_tmp:=$tmp}" { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status ' 0 trap 'as_fn_exit 1' 1 2 13 15 } # Create a (secure) tmp directory for tmp files. { tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` && test -d "$tmp" } || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") } || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 ac_tmp=$tmp # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. # This happens for instance with `./config.status config.h'. if test -n "$CONFIG_FILES"; then ac_cr=`echo X | tr X '\015'` # On cygwin, bash can eat \r inside `` if the user requested igncr. # But we know of no other shell where ac_cr would be empty at this # point, so we can use a bashism as a fallback. if test "x$ac_cr" = x; then eval ac_cr=\$\'\\r\' fi ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then ac_cs_awk_cr='\\r' else ac_cs_awk_cr=$ac_cr fi echo 'BEGIN {' >"$ac_tmp/subs1.awk" && _ACEOF { echo "cat >conf$$subs.awk <<_ACEOF" && echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && echo "_ACEOF" } >conf$$subs.sh || as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'` ac_delim='%!_!# ' for ac_last_try in false false false false false :; do . ./conf$$subs.sh || as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` if test $ac_delim_n = $ac_delim_num; then break elif $ac_last_try; then as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi done rm -f conf$$subs.sh cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK && _ACEOF sed -n ' h s/^/S["/; s/!.*/"]=/ p g s/^[^!]*!// :repl t repl s/'"$ac_delim"'$// t delim :nl h s/\(.\{148\}\)..*/\1/ t more1 s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ p n b repl :more1 s/["\\]/\\&/g; s/^/"/; s/$/"\\/ p g s/.\{148\}// t nl :delim h s/\(.\{148\}\)..*/\1/ t more2 s/["\\]/\\&/g; s/^/"/; s/$/"/ p b :more2 s/["\\]/\\&/g; s/^/"/; s/$/"\\/ p g s/.\{148\}// t delim ' >$CONFIG_STATUS || ac_write_fail=1 rm -f conf$$subs.awk cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACAWK cat >>"\$ac_tmp/subs1.awk" <<_ACAWK && for (key in S) S_is_set[key] = 1 FS = "" } { line = $ 0 nfields = split(line, field, "@") substed = 0 len = length(field[1]) for (i = 2; i < nfields; i++) { key = field[i] keylen = length(key) if (S_is_set[key]) { value = S[key] line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3) len += length(value) + length(field[++i]) substed = 1 } else len += 1 + keylen } print line } _ACAWK _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g" else cat fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 _ACEOF # VPATH may cause trouble with some makes, so we remove sole $(srcdir), # ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and # trailing colons and then remove the whole line if VPATH becomes empty # (actually we leave an empty line to preserve line numbers). if test "x$srcdir" = x.; then ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{ h s/// s/^/:/ s/[ ]*$/:/ s/:\$(srcdir):/:/g s/:\${srcdir}:/:/g s/:@srcdir@:/:/g s/^:*// s/:*$// x s/\(=[ ]*\).*/\1/ G s/\n// s/^[^=]*=[ ]*$// }' fi cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 fi # test -n "$CONFIG_FILES" eval set X " :F $CONFIG_FILES " shift for ac_tag do case $ac_tag in :[FHLC]) ac_mode=$ac_tag; continue;; esac case $ac_mode$ac_tag in :[FHL]*:*);; :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac ac_save_IFS=$IFS IFS=: set x $ac_tag IFS=$ac_save_IFS shift ac_file=$1 shift case $ac_mode in :L) ac_source=$1;; :[FH]) ac_file_inputs= for ac_f do case $ac_f in -) ac_f="$ac_tmp/stdin";; *) # Look for the file first in the build tree, then in the source tree # (if the path is not absolute). The absolute path cannot be DOS-style, # because $ac_f cannot contain `:'. test -f "$ac_f" || case $ac_f in [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac as_fn_append ac_file_inputs " '$ac_f'" done # Let's still pretend it is `configure' which instantiates (i.e., don't # use $as_me), people would be surprised to read: # /* config.h. Generated by config.status. */ configure_input='Generated from '` $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g' `' by configure.' if test x"$ac_file" != x-; then configure_input="$ac_file. $configure_input" { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 $as_echo "$as_me: creating $ac_file" >&6;} fi # Neutralize special characters interpreted by sed in replacement strings. case $configure_input in #( *\&* | *\|* | *\\* ) ac_sed_conf_input=`$as_echo "$configure_input" | sed 's/[\\\\&|]/\\\\&/g'`;; #( *) ac_sed_conf_input=$configure_input;; esac case $ac_tag in *:-:* | *:-) cat >"$ac_tmp/stdin" \ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; esac ;; esac ac_dir=`$as_dirname -- "$ac_file" || $as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$ac_file" : 'X\(//\)[^/]' \| \ X"$ac_file" : 'X\(//\)$' \| \ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null || $as_echo X"$ac_file" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q } /^X\(\/\/\)[^/].*/{ s//\1/ q } /^X\(\/\/\)$/{ s//\1/ q } /^X\(\/\).*/{ s//\1/ q } s/.*/./; q'` as_dir="$ac_dir"; as_fn_mkdir_p ac_builddir=. case "$ac_dir" in .) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; *) ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` # A ".." for each directory in $ac_dir_suffix. ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` case $ac_top_builddir_sub in "") ac_top_builddir_sub=. ac_top_build_prefix= ;; *) ac_top_build_prefix=$ac_top_builddir_sub/ ;; esac ;; esac ac_abs_top_builddir=$ac_pwd ac_abs_builddir=$ac_pwd$ac_dir_suffix # for backward compatibility: ac_top_builddir=$ac_top_build_prefix case $srcdir in .) # We are building in place. ac_srcdir=. ac_top_srcdir=$ac_top_builddir_sub ac_abs_top_srcdir=$ac_pwd ;; [\\/]* | ?:[\\/]* ) # Absolute name. ac_srcdir=$srcdir$ac_dir_suffix; ac_top_srcdir=$srcdir ac_abs_top_srcdir=$srcdir ;; *) # Relative name. ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix ac_top_srcdir=$ac_top_build_prefix$srcdir ac_abs_top_srcdir=$ac_pwd/$srcdir ;; esac ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix case $ac_mode in :F) # # CONFIG_FILE # _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # If the template does not know about datarootdir, expand it. # FIXME: This hack should be removed a few years after 2.60. ac_datarootdir_hack=; ac_datarootdir_seen= ac_sed_dataroot=' /datarootdir/ { p q } /@datadir@/p /@docdir@/p /@infodir@/p /@localedir@/p /@mandir@/p' case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in *datarootdir*) ac_datarootdir_seen=yes;; *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_datarootdir_hack=' s&@datadir@&$datadir&g s&@docdir@&$docdir&g s&@infodir@&$infodir&g s&@localedir@&$localedir&g s&@mandir@&$mandir&g s&\\\${datarootdir}&$datarootdir&g' ;; esac _ACEOF # Neutralize VPATH when `$srcdir' = `.'. # Shell code in configure.ac might set extrasub. # FIXME: do we really want to maintain this feature? cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_sed_extra="$ac_vpsub $extrasub _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 :t /@[a-zA-Z_][a-zA-Z_0-9]*@/!b s|@configure_input@|$ac_sed_conf_input|;t t s&@top_builddir@&$ac_top_builddir_sub&;t t s&@top_build_prefix@&$ac_top_build_prefix&;t t s&@srcdir@&$ac_srcdir&;t t s&@abs_srcdir@&$ac_abs_srcdir&;t t s&@top_srcdir@&$ac_top_srcdir&;t t s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t s&@builddir@&$ac_builddir&;t t s&@abs_builddir@&$ac_abs_builddir&;t t s&@abs_top_builddir@&$ac_abs_top_builddir&;t t $ac_datarootdir_hack " eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \ "$ac_tmp/out"`; test -z "$ac_out"; } && { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&2;} rm -f "$ac_tmp/stdin" case $ac_file in -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";; *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";; esac \ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; esac done # for ac_tag as_fn_exit 0 _ACEOF ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 # configure is writing to config.log, and then calls config.status. # config.status does its own redirection, appending to config.log. # Unfortunately, on DOS this fails, as config.log is still kept open # by configure, so config.status won't be able to write to it; its # output is simply discarded. So we exec the FD to /dev/null, # effectively closing config.log, so it can be properly (re)opened and # appended to by config.status. When coming back to configure, we # need to make the FD available again. if test "$no_create" != yes; then ac_cs_success=: ac_config_status_args= test "$silent" = yes && ac_config_status_args="$ac_config_status_args --quiet" exec 5>/dev/null $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. $ac_cs_success || as_fn_exit 1 fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi rjags/man/0000755000175100001440000000000012611462760012156 5ustar hornikusersrjags/man/dic.samples.Rd0000644000175100001440000000604412611461563014653 0ustar hornikusers\name{dic.samples} \alias{dic} \alias{dic.samples} %- Also NEED an '\alias' for EACH other topic documented here. \title{Generate penalized deviance samples} \description{ Function to extract random samples of the penalized deviance from a \code{jags} model. } \usage{ dic.samples(model, n.iter, thin = 1, type, ...) } %- maybe also 'usage' for other objects documented here. \arguments{ \item{model}{a jags model object} \item{n.iter}{number of iterations to monitor} \item{thin}{thinning interval for monitors} \item{type}{type of penalty to use} \item{...}{optional arguments passed to the update method for jags model objects} } \details{ The \code{dic.samples} function generates penalized deviance statistics for use in model comparison. The two alternative penalized deviance statistics generated by \code{dic.samples} are the deviance information criterion (DIC) and the penalized expected deviance. These are chosen by giving the values ``pD'' and ``popt'' respectively as the \code{type} argument. DIC (Spiegelhalter et al 2002) is calculated by adding the ``effective number of parameters'' (\code{pD}) to the expected deviance. The definition of \code{pD} used by \code{dic.samples} is the one proposed by Plummer (2002) and requires two or more parallel chains in the model. DIC is an approximation to the penalized plug-in deviance, which is used when only a point estimate of the parameters is of interest. The DIC approximation only holds asymptotically when the effective number of parameters is much smaller than the sample size, and the model parameters have a normal posterior distribution. The penalized expected deviance (Plummer 2008) is calculated by adding the optimism (\code{popt}) to the expected deviance. The \code{popt} penalty is at least twice the size of the \code{pD} penalty, and penalizes complex models more severely. } \value{ An object of class ``dic''. This is a list containing the following elements: \item{deviance}{A numeric vector, with one element for each observed stochastic node, containing the mean deviance for that node} \item{penalty}{A numeric vector, with one element for each observed stochastic node, containing an estimate of the contribution towards the penalty} \item{type}{A string identifying the type of penalty: ``pD'' or ``popt''} } \note{ The \code{popt} penalty is estimated by importance weighting, and may be numerically unstable. } \author{Martyn Plummer} \references{ Spiegelhalter, D., N. Best, B. Carlin, and A. van der Linde (2002), Bayesian measures of model complexity and fit (with discussion). \emph{Journal of the Royal Statistical Society Series B} \bold{64}, 583-639. Plummer, M. (2002), Discussion of the paper by Spiegelhalter et al. \emph{Journal of the Royal Statistical Society Series B} \bold{64}, 620. Plummer, M. (2008) Penalized loss functions for Bayesian model comparison. \emph{Biostatistics} doi: 10.1093/biostatistics/kxm049 } \seealso{\code{\link{diffdic}}} \keyword{models} rjags/man/coda.samples.Rd0000644000175100001440000000353412611461563015023 0ustar hornikusers\name{coda.samples} \alias{coda.samples} \title{Generate posterior samples in mcmc.list format} \description{ This is a wrapper function for \code{jags.samples} which sets a trace monitor for all requested nodes, updates the model, and coerces the output to a single \code{mcmc.list} object. } \usage{ coda.samples(model, variable.names, n.iter, thin = 1, na.rm=TRUE, ...) } \arguments{ \item{model}{a jags model object} \item{variable.names}{a character vector giving the names of variables to be monitored} \item{n.iter}{number of iterations to monitor} \item{thin}{thinning interval for monitors} \item{na.rm}{logical flag that indicates whether variables containing missing values should be omitted. See details.} \item{...}{optional arguments that are passed to the update method for jags model objects} } \value{ An \code{mcmc.list} object. } \details{ If \code{na.rm=TRUE} (the default) then elements of a variable that are missing (\code{NA}) for any iteration in at least one chain will be dropped. This argument was added to handle incompletely defined variables. From JAGS version 4.0.0, users may monitor variables that are not completely defined in the BUGS language description of the model, e.g. if \code{y[i]} is defined in a \code{for} loop starting from \code{i=3} then \code{y[1], y[2]} are not defined. The user may still monitor variable \code{y} and the monitored values corresponding to \code{y[1], y[2]} will have value \code{NA} for all iterations in all chains. Most of the functions in the \pkg{coda} package cannot handle missing values so these variables are dropped by default. } \examples{ data(LINE) LINE$recompile() LINE.out <- coda.samples(LINE, c("alpha","beta","sigma"), n.iter=1000) summary(LINE.out) } \author{Martyn Plummer} \seealso{\code{\link{jags.samples}}} \keyword{models} rjags/man/read.jagsdata.Rd0000644000175100001440000000332512611461563015140 0ustar hornikusers\name{read.jagsdata} \alias{read.jagsdata} \alias{read.bugsdata} \title{Read data files for jags models} \description{ Read data for a JAGS model from a file. } \usage{ read.jagsdata(file) read.bugsdata(file) } \arguments{ \item{file}{name of a file containing a text repesentation of the data for a jags model} } \value{ A named list of numeric vectors or arrays. } \details{ The command line interface for JAGS reads data and initial values from a text file. The data format used for jags data files is the same as the R \code{dump} function. Thus the data values can be read into an R session using the \code{source} function, but this will create objects in the global environment. The \code{read.jagsdata} function is a simple wrapper that reads the data into a list instead. OpenBUGS also reads data and initial values from a text file. The format of these files is described as "S-PLUS" format by the OpenBUGS authors. It superficially resembles the format used by the \code{dput} function (and in fact can be parsed by the \code{dget} function). However, in BUGS "S-PLUS" format, arrays are stored in row-major order instead of the column-major order used by R. The \code{read.bugsdata} function reads OpenBUGS "S-PLUS" format files and permutes the elements of arrays so that they appear in the correct order. Either function returns a list which can be used as the \code{data} or \code{inits} argument of \code{jags.model}. } \note{ Earlier versions of the rjags package had a \code{read.data} function which read data in either format, but the function name was ambiguous (There are many data file format in R) so this is now deprecated. } \author{Martyn Plummer} \keyword{file} rjags/man/adapt.Rd0000644000175100001440000000352512611461731013540 0ustar hornikusers\name{adapt} \alias{adapt} \title{Adaptive phase for JAGS models} \description{ Update the model in adaptive mode. } \usage{ adapt(object, n.iter, end.adaptation=FALSE, \ldots) } \arguments{ \item{object}{a \code{jags} model object} \item{n.iter}{length of the adaptive phase} \item{end.adaptation}{logical flag. If \code{TRUE} then adaptive mode will be turned off on exit.} \item{\ldots}{additional arguments to the update method} } \value{ Returns \code{TRUE} if all the samplers in the model have successfully adapted their behaviour to optimum performance and \code{FALSE} otherwise. } \details{ This function is not normally called by the user. It is called by the \code{jags.model} function when the model object is created. When a JAGS model is compiled, it may require an initial sampling phase during which the samplers adapt their behaviour to maximize their efficiency (e.g. a Metropolis-Hastings random walk algorithm may change its step size). The sequence of samples generated during this adaptive phase is not a Markov chain, and therefore may not be used for posterior inference on the model. The \code{adapt} function updates the model for \code{n.iter} iterations in adaptive mode. Then each sampler reports whether it has acheived optimal performance (e.g. whether the rejection rate of a Metropolis-Hasting sampler is close to the theoretical optimum). If any sampler reports failure of this test then \code{adapt} returns \code{FALSE}. If \code{end.adaptation = TRUE}, then adaptive mode is turned off on exit, and further calls to \code{adapt()} do nothing. The model may be maintained in adaptive mode with the default option \code{end.adaptation = FALSE} so that successive calls to \code{adapt()} may be made until adaptation is satisfactory. } \author{Martyn Plummer} \keyword{models} rjags/man/rjags-package.Rd0000644000175100001440000000452012611461563015145 0ustar hornikusers\name{rjags-package} \alias{rjags-package} \alias{rjags} \docType{package} \title{ Bayesian graphical models using MCMC } \description{ The rjags package provides an interface from R to the JAGS library for Bayesian data analysis. JAGS uses Markov Chain Monte Carlo (MCMC) to generate a sequence of dependent samples from the posterior distribution of the parameters. } \details{ JAGS is a clone of BUGS (Bayesian analysis Using Gibbs Sampling). See Lunn et al (2009) for a history of the BUGS project. Note that the rjags package does not include a copy of the JAGS library: you must install this separately. For instructions on downloading JAGS, see the home page at \url{http://mcmc-jags.sourceforge.net}. To fully understand how JAGS works, you need to read the \href{http://sourceforge.net/projects/mcmc-jags/files/Manuals/3.x/jags_user_manual.pdf}{JAGS User Manual}. The manual explains the basics of modelling with JAGS and shows the functions and distributions available in the dialect of the BUGS language used by JAGS. It also describes the command line interface. The \pkg{rjags} package does not use the command line interface but provides equivalent functionality using R functions. Analysis using the \pkg{rjags} package proceeds in steps: \enumerate{ \item Define the model using the BUGS language in a separate file. \item Read in the model file using the \code{jags.model} function. This creates an object of class \dQuote{jags}. \item Update the model using the \code{update} method for \dQuote{jags} objects. This constitutes a \sQuote{burn-in} period. \item Extract samples from the model object using the \code{coda.samples} function. This creates an object of class \dQuote{mcmc.list} which can be used to summarize the posterior distribution. The \pkg{coda} package also provides convergence diagnostics to check that the output is valid for analysis (see Plummer et al 2006). } } \author{ Martyn Plummer } \references{ Lunn D, Spiegelhalter D, Thomas A, Best N. (2009) The BUGS project: Evolution, critique and future directions. \emph{Statistics in Medicine}, \bold{28}:3049-67. Plummer M, Best N, Cowles K, Vines K (2006). CODA: Convergence Diagnosis and Output Analysis for MCMC, \emph{R News}, \bold{6}:7-11. } \keyword{ package } %\examples{ % %} rjags/man/update.Rd0000644000175100001440000000312312611461563013726 0ustar hornikusers\name{update} \alias{update.jags} \title{Update jags models} \description{ Update the Markov chain associated with the model. } \usage{ \method{update}{jags}(object, n.iter=1, by, progress.bar, \ldots) } \arguments{ \item{object}{a \code{jags} model object} \item{n.iter}{number of iterations of the Markov chain to run} \item{by}{refresh frequency for progress bar. See Details} \item{progress.bar}{type of progress bar. Possible values are \code{"text"}, \code{"gui"}, and \code{"none"}. See Details.} \item{\ldots}{additional arguments to the update method (ignored)} } \value{ The \code{update} method for \code{jags} model objects modifies the original object and returns \code{NULL}. } \details{ Since MCMC calculations are typically long, a progress bar is displayed during the call to \code{update}. The type of progress bar is determined by the \code{progress.bar} argument. Type \code{"text"} is displayed on the R console. Type \code{"gui"} is a graphical progress bar in a new window. The progress bar is suppressed if \code{progress.bar} is \code{"none"} or \code{NULL}, if the update is less than 100 iterations, or if R is not running interactively. The default progress bar type is taken from the option \code{jags.pb}. The progress bar is refreshed every \code{by} iterations. The update can only be interrupted when the progress bar is refreshed. Therefore it is advisable not to set \code{by} to a very large value. By default \code{by} is either \code{n.iter/50} or \code{100}, whichever is smaller. } \author{Martyn Plummer} \keyword{models} rjags/man/parallel.Rd0000644000175100001440000000313112611461563014237 0ustar hornikusers\name{parallel} \alias{parallel.seeds} \title{Get initial values for parallel RNGs} \description{ On a multi-processor system, you may wish to run parallel chains using multiple \code{jags.model} objects, each running a single chain on a separate processor. This function returns a list of values that may be used to initialize the random number generator of each chain. } \usage{ parallel.seeds(factory, nchain) } \arguments{ \item{factory}{Name of the RNG factory to use.} \item{nchain}{Number of chains for which to initialize RNGs.} } \value{ \code{parallel.seeds} returns a list of RNG states. Each element is a list of length 2 with the following elements: \item{.RNG.name}{The name of the RNG} \item{.RNG.state}{An integer vector giving the state of the RNG.} } \note{ It is not yet possible to make the results of \code{parallel.seeds} reproducible. This will be fixed in a future version of JAGS. } \examples{ ##The BaseRNG factory generates up to four distinct types of RNG. If ##more than 4 chains are requested, it will recycle the RNG types, but ##use different initial values parallel.seeds("base::BaseRNG", 3) ## The lecuyer module provides the RngStream factory, which allows large ## numbers of independent parallel RNGs to be generated. load.module("lecuyer") list.factories(type="rng") parallel.seeds("lecuyer::RngStream", 5); } \author{Martyn Plummer} \seealso{ \code{\link{jags.model}}, section \dQuote{Random number generators}, for further details on RNG initialization; \code{\link{list.factories}} to find the names of available RNG factories. } \keyword{models} rjags/man/mcarray.object.Rd0000644000175100001440000000322212611461563015347 0ustar hornikusers\name{mcarray.object} \alias{mcarray.object} \alias{print.mcarray} \alias{summary.mcarray} \alias{as.mcmc.list.mcarray} \title{Objects for representing MCMC output} \description{ An \code{mcarray} object is used by the \code{jags.samples} function to represent MCMC output from a JAGS model. It is an array with named dimensions, for which the dimensions "iteration" and "chain" have a special status } \usage{ \method{summary}{mcarray}(object, FUN, \ldots) \method{print}{mcarray}(x, \ldots) \method{as.mcmc.list}{mcarray}(x, \ldots) } \arguments{ \item{object,x}{an \code{mcarray} object} \item{FUN}{a function to be used to generate summary statistics} \item{\ldots}{additional arguments to the call} } \value{ The \code{summary} method for \code{mcarray} objects applies the given function to the array, marginalizing the "chain" and "iteration" dimensions. The \code{print} method applies the summary function with \code{FUN=mean}. The \code{as.mcmc.list} method coerces an \code{mcarray} to an \code{mcmc.list} object so that the diagnostics provided by the \code{coda} package can be applied to the MCMC output it represents. } \details{ The \code{coda} package defines \code{mcmc} objects for representing output from an MCMC sampler, and \code{mcmc.list} for representing output from multiple parallel chains. These objects emphasize the time-series aspect of the MCMC output, but lose the original array structure of the variables they represent. The \code{mcarray} class attempts to rectify this by preserving the dimensions of the original node array defined in the JAGS model. } \author{Martyn Plummer} \keyword{models} rjags/man/jags.object.Rd0000644000175100001440000000262212611461563014640 0ustar hornikusers\name{jags.object} \alias{variable.names.jags} \alias{coef.jags} \alias{list.samplers} \title{Functions for manipulating jags model objects} \description{ A \code{jags} object represents a Bayesian graphical model described using the BUGS language. } \usage{ \method{coef}{jags}(object, chain=1, \ldots) \method{variable.names}{jags}(object, \ldots) list.samplers(object) } \arguments{ \item{object}{a \code{jags} model object} \item{chain}{chain number to query} \item{\ldots}{additional arguments to the call (ignored)} } \value{ The \code{coef} function returns a list with an entry for each Node array that contains an unobserved Node. Elements corresponding to observed Nodes or deterministic Nodes are given missing values. The \code{variable.names} function returns a character vector of names of node arrays used in the model. The \code{list.samplers} function returns a named list with an entry for each Sampler used by the model. Each list element is a character vector containing the names of stochastic Nodes that are updated together in a block. The names of the list elements indicate the sampling methods that are used to update each block. Stochastic nodes that are updated by forward sampling from the prior are not listed. } \examples{ data(LINE) LINE$recompile() coef(LINE) variable.names(LINE) list.samplers(LINE) } \author{Martyn Plummer} \keyword{models} rjags/man/diffdic.Rd0000644000175100001440000000307112611461563014036 0ustar hornikusers\name{diffdic} \alias{diffdic} \title{Differences in penalized deviance} \description{ Compare two models by the difference of two \code{dic} objects. } \usage{ \special{dic1 - dic2} diffdic(dic1, dic2) } \arguments{ \item{dic1, dic2}{Objects inheriting from class ``dic''} } \details{ A \code{diffdic} object represents the difference in penalized deviance between two models. A negative value indicates that \code{dic1} is preferred and vice versa. } \value{ An object of class ``diffdic''. This is a numeric vector with an element for each observed stochastic node in the model. The \code{diffdic} class has its own print method, which will display the sum of the differences, and its sample standard deviation. } \note{ The problem of determining what is a noteworthy difference in DIC (or other penalized deviance) between two models is currently unsolved. Following the results of Ripley (1996) on the Akaike Information Criterion, Plummer (2008) argues that there is no absolute scale for comparison of two penalized deviance statistics, and proposes that the difference should be calibrated with respect to the sample standard deviation of the individual contributions from each observed stochastic node. } \author{Martyn Plummer} \references{ Ripley, B. (1996) \emph{Statistical Pattern Recognition and Neural Networks.} Cambridge University Press. Plummer, M. (2008) Penalized loss functions for Bayesian model comparison. \emph{Biostatistics} doi: 10.1093/biostatistics/kxm049 } \seealso{\code{\link{dic}}} \keyword{models} rjags/man/line.Rd0000644000175100001440000000052412611461563013375 0ustar hornikusers\name{line} \docType{data} \alias{LINE} \title{Linear regression example} \description{ The LINE model is a trivial linear regression model with only 5 observations. It's main use is to allow automated checks of the \pkg{rjags} package. } \format{ A \code{jags.model} object, which must be recompiled before use. } \keyword{datasets} rjags/man/jags.module.Rd0000644000175100001440000000153212611461563014656 0ustar hornikusers\name{jags.module} \alias{load.module} \alias{unload.module} \alias{list.modules} \title{Dynamically load JAGS modules} \description{ A JAGS module is a dynamically loaded library that extends the functionality of JAGS. These functions load and unload JAGS modules and show the names of the currently loaded modules. } \usage{ load.module(name, path, quiet=FALSE) unload.module(name, quiet=FALSE) list.modules() } \arguments{ \item{name}{name of the load module to be loaded} \item{path}{file path to the location of the DLL. If omitted, the option \code{jags.moddir} is used to locate the modules} \item{quiet}{a logical. If \code{TRUE}, no message will be printed about loading the package} } \examples{ list.modules() load.module("glm") list.modules() unload.module("glm") list.modules() } \author{Martyn Plummer} \keyword{interface} rjags/man/control.Rd0000644000175100001440000000266612611461563014137 0ustar hornikusers\name{control} \alias{list.factories} \alias{set.factory} \title{Advanced control over JAGS} \description{ JAGS modules contain factory objects for samplers, monitors, and random number generators for a JAGS model. These functions allow fine-grained control over which factories are active. } \usage{ list.factories(type) set.factory(name, type, state) } \arguments{ \item{name}{name of the factory to set} \item{type}{type of factory to query or set. Possible values are \code{"sampler"}, \code{"monitor"}, or \code{"rng"}} \item{state}{a logical. If \code{TRUE} then the factory will be active, otherwise the factory will become inactive.} } \value{ \code{list.factories} returns a data frame with two columns, the first column shows the names of the factory objects in the currently loaded modules, and the second column is a logical vector indicating whether the corresponding factory is active or not. \code{set.factory} is called to change the future behaviour of factory objects. If a factory is set to inactive then it will be skipped. } \note{ When a module is loaded, all of its factory objects are active. This is also true if a module is unloaded and then reloaded. } \examples{ list.factories("sampler") list.factories("monitor") list.factories("rng") set.factory("base::Slice", "sampler", FALSE) list.factories("sampler") set.factory("base::Slice", "sampler", TRUE) } \author{Martyn Plummer} \keyword{models} rjags/man/rjags-deprecated.Rd0000644000175100001440000000124012611461563015646 0ustar hornikusers\name{rjags-deprecated} \alias{rjags-deprecated} \alias{read.data} \title{Deprecated Functions in the rjags package} \description{ These functions are provided for compatibility with older versions of the rjags package and will soon be defunct. } \usage{ read.data(file, format=c("jags","bugs")) } \arguments{ \item{file}{name of a file containing a text repesentation of the data for a jags model} \item{format}{format of the data} } \details{ \code{read.data} with \code{format="jags"} is a deprecated synonym for \code{\link{read.jagsdata}} and with \code{format="bugs"} is a deprecated synonym for \code{\link{read.bugsdata}}. } \keyword{misc} rjags/man/jags.model.Rd0000644000175100001440000001244712611462760014500 0ustar hornikusers\name{jags.model} \alias{jags.model} \title{Create a JAGS model object} \description{ \code{jags.model} is used to create an object representing a Bayesian graphical model, specified with a BUGS-language description of the prior distribution, and a set of data. } \usage{ jags.model(file, data, inits, n.chains = 1, n.adapt=1000, quiet=FALSE) } \arguments{ \item{file}{the name of the file containing a description of the model in the JAGS dialect of the BUGS language. Alternatively, \code{file} can be a readable text-mode connection, or a complete URL.} \item{data}{a list or environment containing the data. Any numeric objects in \code{data} corresponding to node arrays used in \code{file} are taken to represent the values of observed nodes in the model.} \item{inits}{optional specification of initial values in the form of a list or a function (see \code{Initialization} below). If omitted, initial values will be generated automatically. It is an error to supply an initial value for an observed node.} \item{n.chains}{the number of parallel chains for the model} \item{n.adapt}{the number of iterations for adaptation. See \code{\link{adapt}} for details. If \code{n.adapt = 0} then no adaptation takes place.} \item{quiet}{if \code{TRUE} then messages generated during compilation will be suppressed, as well as the progress bar during adaptation.} } \value{ \code{jags.model} returns an object inheriting from class \code{jags} which can be used to generate dependent samples from the posterior distribution of the parameters An object of class \code{jags} is a list of functions that share a common environment. This environment encapsulates the state of the model, and the functions can be used to query or modify the model state. \item{ptr()}{Returns an external pointer to an object created by the JAGS library} \item{data()}{Returns a list containing the data that define the observed nodes in the model} \item{model()}{Returns a character vector containing the BUGS-language representation of the model} \item{state(internal=FALSE)}{Returns a list of length equal to the number of parallel chains in the model. Each element of the list is itself a list containing the current parameter values in that chain. if \code{internal=TRUE} then the returned lists also include the RNG names (\code{.RNG.name}) and states (\code{.RNG.state}). This is not the user-level interface: use the \code{\link{coef.jags}} method instead.} \item{update(n.iter)}{Updates the model by \code{n.iter} iterations. This is not the user-level interface: use the \code{\link{update.jags}} method instead.} } \section{Initialization}{ There are various ways to specify initial values for a JAGS model. If no initial values are supplied, then they will be generated automatically by JAGS. See the JAGS User Manual for details. Otherwise, the options are as follows: \enumerate{ \item A list of numeric values. Initial values for a single chain may supplied as a named list of numeric values. If there are multiple parallel chains then the same list is re-used for each chain. \item A list of lists. Distinct initial values for each chain may be given as a list of lists. In this case, the list should have the same length as the number of chains in the model. \item A function. A function may be supplied that returns a list of initial values. The function is called repeatedly to generate initial values for each chain. Normally this function should call some random number generating functions so that it returns different values every time it is called. The function should either have no arguments, or have a single argument named \code{chain}. In the latter case, the supplied function is called with the chain number as argument. In this way, initial values may be generated that depend systematically on the chain number. } } \section{Random number generators}{ Each chain in a model has its own random number generator (RNG). RNGs and their initial seed values are assigned automatically when the model is created. The automatic seeds are calculated from the current time. If you wish to make the output from the model reproducible, you may specify the RNGs to be used for each chain, and their starting seeds as part of the \code{inits} argument (see \code{Initialization} above). This is done by supplementing the list of initial parameter values for a given chain with two additional elements named \dQuote{.RNG.name}, and \dQuote{.RNG.seed}: \describe{ \item{\code{.RNG.name}}{a character vector of length 1. The names of the RNGs supplied in the base module are: \itemize{ \item \dQuote{base::Wichmann-Hill} \item \dQuote{base::Marsaglia-Multicarry} \item \dQuote{base::Super-Duper} \item \dQuote{base::Mersenne-Twister} } If the lecuyer module is loaded, it provides \dQuote{lecuyer::RngStream} } \item{\code{.RNG.seed}}{a numeric vector of length 1 containing an integer value.} } Note that it is also possible to specify \dQuote{.RNG.state} rather than \dQuote{.RNG.seed} - see for example the output of \code{\link{parallel.seeds}} } \author{Martyn Plummer} \keyword{models} rjags/man/jags.samples.Rd0000644000175100001440000000226612611461563015042 0ustar hornikusers\name{jags.samples} \alias{jags.samples} \title{Generate posterior samples} \description{ Function to extract random samples from the posterior distribution of the parameters of a \code{jags} model. } \usage{ jags.samples(model, variable.names, n.iter, thin = 1, type="trace", ...) } \arguments{ \item{model}{a jags model object} \item{variable.names}{a character vector giving the names of variables to be monitored} \item{n.iter}{number of iterations to monitor} \item{thin}{thinning interval for monitors} \item{type}{type of monitor} \item{...}{optional arguments passed to the update method for jags model objects} } \details{ The \code{jags.samples} function creates monitors for the given variables, runs the model for \code{n.iter} iterations and returns the monitored samples. } \value{ A list of \code{mcarray} objects, with one element for each element of the \code{variable.names} argument. } \examples{ data(LINE) LINE$recompile() LINE.samples <- jags.samples(LINE, c("alpha","beta","sigma"), n.iter=1000) LINE.samples } \author{Martyn Plummer} \seealso{\code{\link{jags.model}}, \code{\link{coda.samples}}} \keyword{models} rjags/configure.win0000644000175100001440000000000012611461563014071 0ustar hornikusersrjags/cleanup0000755000175100001440000000006012611461563012754 0ustar hornikusers#!/bin/sh rm -f src/Makevars rm -f R/unix/zzz.R