void R_init_Biostrings(DllInfo *info)
{
/* Lots of code around assumes that sizeof(Rbyte) == sizeof(char) */
if (sizeof(Rbyte) != sizeof(char))
error("sizeof(Rbyte) != sizeof(char)");
_init_bytewise_match_tables();
R_registerRoutines(info, cMethods, NULL, NULL, NULL);
R_registerRoutines(info, NULL, callMethods, NULL, NULL);
/* XString_class.c */
REGISTER_CCALLABLE(_DNAencode);
REGISTER_CCALLABLE(_DNAdecode);
REGISTER_CCALLABLE(_RNAencode);
REGISTER_CCALLABLE(_RNAdecode);
/* XStringSet_class.c */
REGISTER_CCALLABLE(_get_XStringSet_length);
REGISTER_CCALLABLE(_get_XStringSet_xsbaseclassname);
REGISTER_CCALLABLE(_hold_XStringSet);
REGISTER_CCALLABLE(_get_length_from_XStringSet_holder);
REGISTER_CCALLABLE(_get_elt_from_XStringSet_holder);
REGISTER_CCALLABLE(_get_linear_subset_from_XStringSet_holder);
REGISTER_CCALLABLE(_set_XStringSet_names);
/* XStringSetList_class.c */
REGISTER_CCALLABLE(_hold_XStringSetList);
REGISTER_CCALLABLE(_get_length_from_XStringSetList_holder);
REGISTER_CCALLABLE(_get_elt_from_XStringSetList_holder);
/* match_reporting.c */
REGISTER_CCALLABLE(_init_match_reporting);
REGISTER_CCALLABLE(_set_active_PSpair);
REGISTER_CCALLABLE(_set_match_shift);
REGISTER_CCALLABLE(_report_match);
REGISTER_CCALLABLE(_drop_reported_matches);
REGISTER_CCALLABLE(_get_match_count);
REGISTER_CCALLABLE(_reported_matches_asSEXP);
/* MIndex_class.c */
REGISTER_CCALLABLE(_hold_MIndex);
REGISTER_CCALLABLE(_get_length_from_MIndex_holder);
REGISTER_CCALLABLE(_get_width0_elt_from_MIndex_holder);
REGISTER_CCALLABLE(_get_elt_from_MIndex_holder);
/* match_pattern_boyermoore.c */
REGISTER_CCALLABLE(_match_pattern_boyermoore);
return;
}
/**
* Library initialization.
*
* R calls this automatically on lib load/attach.
*/
extern "C" void R_init_stringi(DllInfo* dll)
{
R_registerRoutines(dll, NULL, cCallMethods, NULL, NULL);
// R_useDynamicSymbols(dll, Rboolean(FALSE)); // slower
if (!SUPPORT_UTF8) {
/* Rconfig.h states that all R platforms supports that */
Rf_error("R does not support UTF-8 encoding.");
}
stri_set_icu_data_directory((char*)*(char**)(dll) /* dll->path */);
#ifndef NDEBUG
fprintf(stdout, "!NDEBUG: ************************************************\n");
fprintf(stdout, "!NDEBUG: Dynamic library `stringi` loaded\n");
fprintf(stdout, "!NDEBUG: Check out http://stringi.rexamine.com\n");
fprintf(stdout, "!NDEBUG: \n");
fprintf(stdout, "!NDEBUG: Please send bug reports to [email protected] \n");
fprintf(stdout, "!NDEBUG: or at https://github.com/Rexamine/stringi/issues\n");
fprintf(stdout, "!NDEBUG: \n");
fprintf(stdout, "!NDEBUG: Have fun testing! :-)\n");
fprintf(stdout, "!NDEBUG: ************************************************\n");
// /* u_init: It is OK to simply use ICU services and functions without
// first having initialized ICU by calling u_init(). */
// UErrorCode status;
// u_init(&status);
// if (U_FAILURE(status))
// error("ICU init failed: %s", u_errorName(status));
#endif
}
R_init_graphics(DllInfo *dll)
{
R_registerRoutines(dll, NULL, CallEntries, NULL, ExtEntries);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
registerBase();
}
void R_init_xlsReadWrite(DllInfo *dll)
{
R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
Rprintf(crmsg);
Rprintf(cranmsg);
}
void
R_init_splines(DllInfo *dll)
{
R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
// R_forceSymbols(dll, TRUE); // too few to worry about, used in cobs*
}
void R_init_xts(DllInfo *info)
{
SymbolShortcuts();
R_registerRoutines(info,
NULL,
callMethods,
NULL,
externalMethods);
R_useDynamicSymbols(info, TRUE);
/* used by external packages linking to internal xts code from C */
R_RegisterCCallable("xts","do_is_ordered",(DL_FUNC) &do_is_ordered);
R_RegisterCCallable("xts","coredata_xts", (DL_FUNC) &coredata_xts);
R_RegisterCCallable("xts","isXts", (DL_FUNC) &isXts);
R_RegisterCCallable("xts","tryXts", (DL_FUNC) &tryXts);
R_RegisterCCallable("xts","do_rbind_xts", (DL_FUNC) &do_rbind_xts);
R_RegisterCCallable("xts","naCheck", (DL_FUNC) &naCheck);
R_RegisterCCallable("xts","lagXts", (DL_FUNC) &lagXts);
R_RegisterCCallable("xts","make_index_unique", (DL_FUNC) &make_index_unique);
R_RegisterCCallable("xts","make_unique", (DL_FUNC) &make_unique);
R_RegisterCCallable("xts","endpoints", (DL_FUNC) &endpoints);
R_RegisterCCallable("xts","do_merge_xts", (DL_FUNC) &do_merge_xts);
R_RegisterCCallable("xts","na_omit_xts", (DL_FUNC) &na_omit_xts);
R_RegisterCCallable("xts","na_locf", (DL_FUNC) &na_locf);
/* used by xts (functions moved from xts to zoo) */
zoo_lag = (SEXP(*)(SEXP,SEXP,SEXP)) R_GetCCallable("zoo","zoo_lag");
zoo_coredata = (SEXP(*)(SEXP,SEXP)) R_GetCCallable("zoo","zoo_coredata");
}
void R_init_gtools(DllInfo *info)
{
/* Register C routines */
R_registerRoutines (info, cMethods, NULL, NULL, NULL);
R_useDynamicSymbols(info, FALSE);
R_forceSymbols (info, TRUE);
}
void R_init_grid(DllInfo *dll)
{
/* No .C, .Fortran, or .External routines => NULL
*/
R_registerRoutines(dll, NULL, callMethods, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
void R_init_sg(DllInfo *info)
#endif
{
/* There are four different external language call mechanisms available in R, namely:
* .C
* .Call
* .Fortran
* .External
*
* Currently shogun uses only the .External interface. */
R_CMethodDef cMethods[] = { {NULL, NULL, 0} };
R_FortranMethodDef fortranMethods[] = { {NULL, NULL, 0} };
#ifdef HAVE_ELWMS
R_ExternalMethodDef externalMethods[] = { {"elwms", (void*(*)()) &Rsg, 1}, {NULL, NULL, 0} };
#else
R_ExternalMethodDef externalMethods[] = { {"sg", (void*(*)()) &Rsg, 1}, {NULL, NULL, 0} };
#endif
R_CallMethodDef callMethods[] = { {NULL, NULL, 0} };
/* Register the routines saved in the callMethods structure so that they are available under R. */
R_registerRoutines(info, cMethods, callMethods, (R_FortranMethodDef*) fortranMethods, (R_ExternalMethodDef*) externalMethods);
}
void
R_init_lcd(DllInfo *info)
{
/* Register routines, allocate resources. */
R_registerRoutines(info, NULL, callEntries /*CallEntries*/,
NULL, NULL /*ExternEntries*/);
}
void registerAll()
{
// c methods
R_CMethodDef* pCMethods = NULL;
if (s_cMethods.size() > 0)
{
R_CMethodDef nullMethodDef ;
nullMethodDef.name = NULL ;
nullMethodDef.fun = NULL ;
nullMethodDef.numArgs = 0 ;
nullMethodDef.types = NULL;
nullMethodDef.styles = NULL;
s_cMethods.push_back(nullMethodDef);
pCMethods = &s_cMethods[0];
}
// call methods
R_CallMethodDef* pCallMethods = NULL;
if (s_callMethods.size() > 0)
{
R_CallMethodDef nullMethodDef ;
nullMethodDef.name = NULL ;
nullMethodDef.fun = NULL ;
nullMethodDef.numArgs = 0 ;
s_callMethods.push_back(nullMethodDef);
pCallMethods = &s_callMethods[0];
}
DllInfo *info = R_getEmbeddingDllInfo() ;
R_registerRoutines(info, pCMethods, pCallMethods, NULL, NULL) ;
}
/**************************************************************
*
* Register entry points...
*
**************************************************************/
void R_init_dREG(DllInfo *info) {
R_CallMethodDef callMethods[] = {
{"get_genomic_data_R", (DL_FUNC)&get_genomic_data_R, 5},
{NULL, NULL, 0}
};
R_registerRoutines(info, NULL, callMethods, NULL, NULL);
}
void R_init_foreign(DllInfo *dll)
{
R_registerRoutines(dll, CEntries, CallEntries, NULL, ExtEntries);
R_useDynamicSymbols(dll, FALSE);
#if defined(R_VERSION) && R_VERSION >= R_Version(3, 0, 0)
R_forceSymbols(dll, TRUE);
#endif
}
void R_init_lme4a(DllInfo *dll)
{
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, (Rboolean)FALSE);
M_R_cholmod_start(&c);
c.final_ll = 1; /* LL' form of simplicial factorization */
}
void
attribute_visible
R_init_frailtypack(DllInfo *dll)
{
R_registerRoutines(dll, NULL, NULL, FortEntries, NULL);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
}
void R_init_blme(DllInfo *dll)
{
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
M_R_cholmod_start(&cholmodCommon);
cholmodCommon.final_ll = 1; /* LL' form of simplicial factorization */
lme4_ASym = install("A");
lme4_CmSym = install("Cm");
lme4_CxSym = install("Cx");
lme4_DimSym = install("Dim");
lme4_GpSym = install("Gp");
lme4_LSym = install("L");
lme4_RXSym = install("RX");
lme4_RZXSym = install("RZX");
lme4_STSym = install("ST");
lme4_VSym = install("V");
lme4_XSym = install("X");
lme4_XstSym = install("Xst");
lme4_ZtSym = install("Zt");
lme4_devianceSym = install("deviance");
lme4_dimsSym = install("dims");
lme4_envSym = install("env");
lme4_etaSym = install("eta");
lme4_fixefSym = install("fixef");
lme4_flistSym = install("flist");
lme4_ghwSym = install("ghw");
lme4_ghxSym = install("ghx");
lme4_gradientSym = install("gradient");
lme4_iSym = install("i");
lme4_ncSym = install("nc");
lme4_nlmodelSym = install("nlmodel");
lme4_muEtaSym = install("muEta");
lme4_muSym = install("mu");
lme4_offsetSym = install("offset");
lme4_pSym = install("p");
lme4_permSym = install("perm");
lme4_pWtSym = install("pWt");
lme4_ranefSym = install("ranef");
lme4_residSym = install("resid");
lme4_sigmaSym = install("sigma");
lme4_sqrtrWtSym = install("sqrtrWt");
lme4_sqrtXWtSym = install("sqrtXWt");
lme4_uSym = install("u");
lme4_varSym = install("var");
lme4_xSym = install("x");
lme4_ySym = install("y");
blme_covariancePriorSym = install("cov.prior");
blme_unmodeledCoefficientPriorSym = install("fixef.prior");
blme_commonScalePriorSym = install("var.prior");
blme_prior_typeSym = install("type");
blme_prior_familiesSym = install("families");
blme_prior_scalesSym = install("scales");
blme_prior_hyperparametersSym = install("hyperparameters");
}
void
R_init_causalTree(DllInfo * dll)
{
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
#if defined(R_VERSION) && R_VERSION >= R_Version(2, 16, 0)
R_forceSymbols(dll, TRUE);
#endif
}
void R_init_myRoutines(DllInfo *info)
{
/* Register the .Call routines.
No .C .Fortran() or .External() routines,
so pass those arrays as NULL.
*/
R_registerRoutines(info, NULL, callMethods, NULL, NULL);
R_useDynamicSymbols(info, TRUE);
}
// this is called by R_init_Rcpp that is in Module.cpp
void init_Rcpp_routines(DllInfo *info){
/* Register routines, allocate resources. */
R_registerRoutines(info,
NULL /* .C*/,
callEntries /*.Call*/,
NULL /* .Fortran */,
extEntries /*.External*/
);
}
void attribute_visible R_init_aster(DllInfo *info)
{
R_registerRoutines(info, cMethods, callMethods, NULL, NULL);
R_useDynamicSymbols(info, FALSE);
R_forceSymbols(info, TRUE);
R_RegisterCCallable("aster", "aster_mlogl_sat_unco",
(DL_FUNC) aster_mlogl_sat_unco);
R_RegisterCCallable("aster", "aster_mlogl_sat_cond",
(DL_FUNC) aster_mlogl_sat_cond);
}
R_init_rgeos(DllInfo *dll) {
// SEXP INIT;
R_registerRoutines(dll, CEntries, CallEntries, NULL, NULL); // RSB FIXME
R_useDynamicSymbols(dll, FALSE);
// INIT = rgeos_Init();
}
void attribute_visible R_init_stats(DllInfo *dll)
{
R_registerRoutines(dll, CEntries, CallEntries, FortEntries, ExtEntries);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
R_RegisterCCallable("stats", "nlminb_iterate", (DL_FUNC) nlminb_iterate);
R_RegisterCCallable("stats", "nlsb_iterate", (DL_FUNC) nlsb_iterate);
R_RegisterCCallable("stats", "Rf_divset", (DL_FUNC) Rf_divset);
}
void R_init_networkDynamic(DllInfo *dll)
{
R_registerRoutines(dll,CEntries,CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
/* Callable functions from other packages' C code */
#define RREGDEF(name) R_RegisterCCallable("network", #name, (DL_FUNC) name)
/* Register network functions */
netRegisterFunctions();
}
void R_init_survival(DllInfo *dll){
R_registerRoutines(dll, Centries, Callentries, NULL, NULL);
/* My take on the documentation is that adding the following line
will make symbols available ONLY through the above tables.
Anyone who then tried to link to my C code would be SOL.
It also wouldn't work with .C("whatever", ....) which I use in
my test directory.
*/
/* R_useDynamicSymbols(dll, FALSE); */
}
void R_init_expm(DllInfo *dll)
{
R_registerRoutines(dll, NULL, CallEntries, FortEntries, NULL);
R_useDynamicSymbols(dll, FALSE);
/* callable C code from other packages C code :*/
R_RegisterCCallable("expm", "expm", (DL_FUNC) expm);
R_RegisterCCallable("matpow", "matpow", (DL_FUNC) matpow);
R_RegisterCCallable("expm_eigen", "expm_eigen", (DL_FUNC) expm_eigen);
R_RegisterCCallable("logm_eigen", "logm_eigen", (DL_FUNC) logm_eigen);
R_RegisterCCallable("matexp_MH09", "matexp_MH09", (DL_FUNC) matexp_MH09);
}
void R_init_VA(DllInfo *info)
{
/* Register the .C and .Call routines.
No .Fortran() or .External() routines,
so pass those arrays as NULL.
*/
R_registerRoutines(info,
cMethods, NULL,
NULL, NULL);
}
void R_init_jsClientLib(DllInfo *info)
{
static R_CallMethodDef callMethods[] = {
{ "jsClientLib_jsclient_callback_sync_", (DL_FUNC)&jsClientLib_jsclient_callback_sync_, 2},
{ "jsClientLib_jsclient_callback_", (DL_FUNC)&jsClientLib_jsclient_callback_, 3},
{ "jsClientLib_jsclient_device_resize_", (DL_FUNC)&jsClientLib_jsclient_device_resize_, 4},
{ "jsClientLib_jsclient_device_", (DL_FUNC)&jsClientLib_jsclient_device_, 5},
{ NULL, NULL, 0 }
};
R_registerRoutines( info, NULL, callMethods, NULL, NULL);
}
void R_init_IRanges(DllInfo *info)
{
R_registerRoutines(info, NULL, callMethods, NULL, NULL);
/* Ranges_comparison.c */
REGISTER_CCALLABLE(_overlap_code);
REGISTER_CCALLABLE(_invert_overlap_code);
/* IRanges_class.c */
REGISTER_CCALLABLE(_get_IRanges_start);
REGISTER_CCALLABLE(_get_IRanges_width);
REGISTER_CCALLABLE(_get_IRanges_names);
REGISTER_CCALLABLE(_get_IRanges_length);
REGISTER_CCALLABLE(_hold_IRanges);
REGISTER_CCALLABLE(_get_length_from_IRanges_holder);
REGISTER_CCALLABLE(_get_width_elt_from_IRanges_holder);
REGISTER_CCALLABLE(_get_start_elt_from_IRanges_holder);
REGISTER_CCALLABLE(_get_end_elt_from_IRanges_holder);
REGISTER_CCALLABLE(_get_names_elt_from_IRanges_holder);
REGISTER_CCALLABLE(_get_linear_subset_from_IRanges_holder);
REGISTER_CCALLABLE(_set_IRanges_names);
REGISTER_CCALLABLE(_copy_IRanges_slots);
REGISTER_CCALLABLE(_new_IRanges);
REGISTER_CCALLABLE(_new_IRanges_from_IntPairAE);
REGISTER_CCALLABLE(_new_list_of_IRanges_from_IntPairAEAE);
REGISTER_CCALLABLE(_alloc_IRanges);
/* Grouping_class.c */
REGISTER_CCALLABLE(_get_H2LGrouping_high2low);
REGISTER_CCALLABLE(_get_H2LGrouping_low2high);
REGISTER_CCALLABLE(_get_Partitioning_names);
REGISTER_CCALLABLE(_get_PartitioningByEnd_end);
REGISTER_CCALLABLE(_new_PartitioningByEnd);
/* CompressedList_class.c */
REGISTER_CCALLABLE(_get_CompressedList_unlistData);
REGISTER_CCALLABLE(_get_CompressedList_partitioning);
REGISTER_CCALLABLE(_get_CompressedList_length);
REGISTER_CCALLABLE(_get_CompressedList_names);
REGISTER_CCALLABLE(_new_CompressedList);
REGISTER_CCALLABLE(_hold_CompressedIntegerList);
REGISTER_CCALLABLE(_get_length_from_CompressedIntsList_holder);
REGISTER_CCALLABLE(_get_elt_from_CompressedIntsList_holder);
/* CompressedIRangesList_class.c */
REGISTER_CCALLABLE(_hold_CompressedIRangesList);
REGISTER_CCALLABLE(_get_elt_from_CompressedIRangesList_holder);
/* RangedData_class.c */
REGISTER_CCALLABLE(_new_RangedData);
return;
}
void R_init_lme4(DllInfo *dll)
{
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
M_R_cholmod_start(&c);
c.final_ll = 1; /* LL' form of simplicial factorization */
/* need own error handler, that resets final_ll (after *_defaults()) : */
c.error_handler = lme4_R_cholmod_error;
lme4_ASym = install("A");
lme4_CmSym = install("Cm");
lme4_CxSym = install("Cx");
lme4_DimSym = install("Dim");
lme4_GpSym = install("Gp");
lme4_LSym = install("L");
lme4_RXSym = install("RX");
lme4_RZXSym = install("RZX");
lme4_STSym = install("ST");
lme4_VSym = install("V");
lme4_XSym = install("X");
lme4_XstSym = install("Xst");
lme4_ZtSym = install("Zt");
lme4_devianceSym = install("deviance");
lme4_dimsSym = install("dims");
lme4_envSym = install("env");
lme4_etaSym = install("eta");
lme4_fixefSym = install("fixef");
lme4_flistSym = install("flist");
lme4_ghwSym = install("ghw");
lme4_ghxSym = install("ghx");
lme4_gradientSym = install("gradient");
lme4_iSym = install("i");
lme4_ncSym = install("nc");
lme4_nlmodelSym = install("nlmodel");
lme4_muEtaSym = install("muEta");
lme4_muSym = install("mu");
lme4_offsetSym = install("offset");
lme4_pSym = install("p");
lme4_permSym = install("perm");
lme4_pWtSym = install("pWt");
lme4_ranefSym = install("ranef");
lme4_residSym = install("resid");
lme4_sigmaSym = install("sigma");
lme4_sqrtrWtSym = install("sqrtrWt");
lme4_sqrtXWtSym = install("sqrtXWt");
lme4_uSym = install("u");
lme4_varSym = install("var");
lme4_xSym = install("x");
lme4_ySym = install("y");
}
void R_init_fastcluster(DllInfo * const info)
{
R_CallMethodDef callMethods[] = {
{"fastcluster", (DL_FUNC) &fastcluster, 4},
{"emp_means", (DL_FUNC) &emp_means, 5},
{"emp_diffs", (DL_FUNC) &emp_diffs, 6},
{"fastcluster_correlation_distances", (DL_FUNC) &fastcluster_correlation_distances, 4},
{"fastcluster_vector", (DL_FUNC) &fastcluster_vector, 5},
{NULL, NULL, 0}
};
R_registerRoutines(info, NULL, callMethods, NULL, NULL);
}
