remove gropt from CRAN version due to LTO issues

jdtuck · Mar 6, 2020 · c5e1ff5 · c5e1ff5
1 parent f14a939
commit c5e1ff5
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Showing 5 changed files with 54 additions and 48 deletions.
diff --git a/R/optimum.reparam.R b/R/optimum.reparam.R
@@ -59,6 +59,7 @@ optimum.reparam <- function(Q1,T1,Q2,T2,lambda=0,method="DP",w=0.01,f1o=0.0,
         timet2 = (timet2-tmin)/(tmax-tmin)
         gam0 = simul_gam(u,out$g1,out$g2,timet2,out$s1,out$s2,timet2)
     } else if (method=="DP2") {
+        stop("Not implemented in CRAN version: please download and install from Github (https://github.com/jdtuck/fdasrvf_R)")
         opt = rep(0,n+1+1);
         swap = FALSE
         fopts = rep(0,5)
@@ -72,7 +73,8 @@ optimum.reparam <- function(Q1,T1,Q2,T2,lambda=0,method="DP",w=0.01,f1o=0.0,
         if (out$swap){
             gam0 = invertGamma(gam0);
         }
-    } else {
+    } else if (method == "RBFGS") {
+        stop("Not implemented in CRAN version: please download and install from Github (https://github.com/jdtuck/fdasrvf_R)")
         opt = rep(0,n+1+1);
         swap = FALSE
         fopts = rep(0,5)
@@ -92,6 +94,8 @@ optimum.reparam <- function(Q1,T1,Q2,T2,lambda=0,method="DP",w=0.01,f1o=0.0,
         if (out$swap){
             gam0 = invertGamma(gam0);
         }
+    } else {
+      stop("Invalid method chosen")
     }
 
     gam = (gam0-gam0[1])/(gam0[length(gam0)]-gam0[1])  # slight change on scale

diff --git a/R/reparam_curve.R b/R/reparam_curve.R
@@ -83,6 +83,7 @@ reparam_curve <- function(beta1,beta2,lambda=0,method="DP",w=0.01,rotated=T,
       dim(q2i) = c(M*n1)
       gam0 = .Call('DPQ', PACKAGE = 'fdasrvf', q1i, q2i, n1, M, lambda, 0, rep(0,M))
     } else if (method=="DP2") {
+      stop("Not implemented in CRAN version: please download and install from Github (https://github.com/jdtuck/fdasrvf_R)")
         c1 = t(beta1)
         dim(c1) = c(M*n1)
         c2 = t(beta2)
@@ -104,7 +105,8 @@ reparam_curve <- function(beta1,beta2,lambda=0,method="DP",w=0.01,rotated=T,
             R = t(R)
         }
 
-    } else {
+    } else if (method=="RBFGS") {
+        stop("Not implemented in CRAN version: please download and install from Github (https://github.com/jdtuck/fdasrvf_R)")
         c1 = t(beta1)
         dim(c1) = c(M*n1)
         c2 = t(beta2)
@@ -130,6 +132,8 @@ reparam_curve <- function(beta1,beta2,lambda=0,method="DP",w=0.01,rotated=T,
             gam0 = invertGamma(gam0);
             R = t(R)
         }
+    } else {
+      stop("Invalid method chosen")
     }
 
     gam = (gam0-gam0[1])/(gam0[length(gam0)]-gam0[1])  # slight change on scale

diff --git a/src/Makevars b/src/Makevars
@@ -1,6 +1,6 @@
 SOURCES1 = registerDynamicSymbol.cpp wrapper.cpp fdasrsf/DP.cpp fdasrsf/dp_grid.cpp fdasrsf/DynamicProgrammingQ2.cpp fdasrsf/misc_funcs.cpp fdasrsf/mlogit_warp_grad.cpp \
   fdasrsf/bayesian.cpp fdasrsf/pair_align_functions_expomap.cpp
-SOURCES2 = gropt/src/DriverElasticCurvesRO.cpp gropt/src/LowRank.cpp gropt/src/ProductManifold.cpp gropt/src/SolversTR.cpp \
+#SOURCES2 = gropt/src/DriverElasticCurvesRO.cpp gropt/src/LowRank.cpp gropt/src/ProductManifold.cpp gropt/src/SolversTR.cpp \
 	gropt/src/LowRankVariable.cpp gropt/src/randgen.cpp gropt/src/Sphere.cpp \
 	gropt/src/ElasticCurvesReparam.cpp gropt/src/LowRankVector.cpp gropt/src/RBFGS.cpp gropt/src/SphereVariable.cpp \
 	gropt/src/ElasticCurvesRO.cpp gropt/src/LRBFGS.cpp gropt/src/RBroydenFamily.cpp gropt/src/SphereVector.cpp \
@@ -18,7 +18,7 @@ SOURCES2 = gropt/src/DriverElasticCurvesRO.cpp gropt/src/LowRank.cpp gropt/src/P
 
 SOURCES3 = fdaqmap/src/myVector.cpp fdaqmap/src/UnitSquareImage.cpp
 
-SOURCES = $(SOURCES1) $(SOURCES2) $(SOURCES3)
+SOURCES = $(SOURCES1) $(SOURCES3)
 
 OBJECTS = $(SOURCES:.cpp=.o)
 

diff --git a/src/Makevars.win b/src/Makevars.win
@@ -1,7 +1,7 @@
 ##split sources to ensure the commands for linking are not too long!
 SOURCES1 = registerDynamicSymbol.cpp wrapper.cpp fdasrsf/DP.cpp fdasrsf/dp_grid.cpp fdasrsf/DynamicProgrammingQ2.cpp fdasrsf/misc_funcs.cpp fdasrsf/mlogit_warp_grad.cpp \
   fdasrsf/bayesian.cpp fdasrsf/pair_align_functions_expomap.cpp
-SOURCES2 = gropt/src/DriverElasticCurvesRO.cpp gropt/src/LowRank.cpp gropt/src/ProductManifold.cpp gropt/src/SolversTR.cpp \
+#SOURCES2 = gropt/src/DriverElasticCurvesRO.cpp gropt/src/LowRank.cpp gropt/src/ProductManifold.cpp gropt/src/SolversTR.cpp \
 	gropt/src/LowRankVariable.cpp gropt/src/randgen.cpp gropt/src/Sphere.cpp \
 	gropt/src/ElasticCurvesReparam.cpp gropt/src/LowRankVector.cpp gropt/src/RBFGS.cpp gropt/src/SphereVariable.cpp \
 	gropt/src/ElasticCurvesRO.cpp gropt/src/LRBFGS.cpp gropt/src/RBroydenFamily.cpp gropt/src/SphereVector.cpp \
@@ -20,21 +20,19 @@ SOURCES3 = fdaqmap/src/myVector.cpp fdaqmap/src/UnitSquareImage.cpp
 
 OBJECTS = wrapper.o
 OBJS1 = $(SOURCES1:.cpp=.o)
-OBJS2 = $(SOURCES2:.cpp=.o)
+#OBJS2 = $(SOURCES2:.cpp=.o)
 OBJS3 = $(SOURCES3:.cpp=.o)
 PKG_CPPFLAGS= -I. -Igropt/incl/ -Ifdaqmap/incl/
 CXX_STD = CXX11
-PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) libfdasrvf1.a libfdasrvf2.a libfdasrvf3.a
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) libfdasrvf1.a libfdasrvf3.a
 
-all: libfdasrvf1.a libfdasrvf2.a libfdasrvf3.a $(SHLIB)
+all: libfdasrvf1.a libfdasrvf3.a $(SHLIB)
 
-$(SHLIB): libfdasrvf1.a libfdasrvf2.a libfdasrvf3.a $(OBJECTS)
+$(SHLIB): libfdasrvf1.a libfdasrvf3.a $(OBJECTS)
 libfdasrvf1.a: $(OBJS1)
-libfdasrvf2.a: $(OBJS2)
 libfdasrvf3.a: $(OBJS3)
 
 clean:
 	@rm -f $(SHLIB) $(OBJECTS)
 	@rm -f $(OBJS1)
-	@rm -f $(OBJS2)
 	@rm -f $(OBJS3)
diff --git a/src/wrapper.cpp b/src/wrapper.cpp
@@ -1,5 +1,5 @@
 
-#include "gropt/incl/ElasticCurvesReparam.h"
+// #include "gropt/incl/ElasticCurvesReparam.h"
 #include "fdasrsf/DynamicProgrammingQ2.h"
 #include "fdasrsf/mlogit_warp_grad.h"
 #include "fdasrsf/DP.h"
@@ -89,39 +89,39 @@ RcppExport SEXP DPQ(SEXP Q1, SEXP Q2, SEXP n1, SEXP N1, SEXP lam1, SEXP Disp, SE
   return(yyi);
 }
 
-RcppExport SEXP opt_reparam(SEXP C1, SEXP C2, SEXP n, SEXP d, SEXP w,
-                            SEXP onlyDP, SEXP rotated, SEXP isclosed,
-                            SEXP skipm, SEXP autoselectC, SEXP opt, SEXP swap,
-                            SEXP fopts, SEXP comtime){
-
-    NumericVector C1i(C1);
-    NumericVector C2i(C2);
-    NumericVector opti(opt);
-    NumericVector foptsi(fopts);
-    NumericVector comtimei(comtime);
-
-    double *_C1i = &C1i[0];
-    double *_C2i = &C2i[0];
-    double *_opti = &opti[0];
-    double *_foptsi = &foptsi[0];
-    double *_comtimei = &comtimei[0];
-
-    int _n = as<int>(n);
-    int _d = as<int>(d);
-    double _w = as<double>(w);
-    bool _onlyDP = as<bool>(onlyDP);
-    bool _rotated = as<bool>(rotated);
-    bool _isclosed = as<bool>(isclosed);
-    int _skipm = as<int>(skipm);
-    int _autoselectC = as<int>(autoselectC);
-    bool _swap = as<bool>(swap);
-
-
-    optimum_reparam(_C1i, _C2i, _n, _d, _w, _onlyDP, _rotated, _isclosed,
-                    _skipm, _autoselectC, _opti, _swap, _foptsi, _comtimei);
-
-    List ret; ret["opt"] = opti; ret["fopts"] = foptsi;
-    ret["comtime"] = comtimei; ret["swap"] = wrap(_swap);
-
-    return(ret);
-}
+// RcppExport SEXP opt_reparam(SEXP C1, SEXP C2, SEXP n, SEXP d, SEXP w,
+//                             SEXP onlyDP, SEXP rotated, SEXP isclosed,
+//                             SEXP skipm, SEXP autoselectC, SEXP opt, SEXP swap,
+//                             SEXP fopts, SEXP comtime){
+// 
+//     NumericVector C1i(C1);
+//     NumericVector C2i(C2);
+//     NumericVector opti(opt);
+//     NumericVector foptsi(fopts);
+//     NumericVector comtimei(comtime);
+// 
+//     double *_C1i = &C1i[0];
+//     double *_C2i = &C2i[0];
+//     double *_opti = &opti[0];
+//     double *_foptsi = &foptsi[0];
+//     double *_comtimei = &comtimei[0];
+// 
+//     int _n = as<int>(n);
+//     int _d = as<int>(d);
+//     double _w = as<double>(w);
+//     bool _onlyDP = as<bool>(onlyDP);
+//     bool _rotated = as<bool>(rotated);
+//     bool _isclosed = as<bool>(isclosed);
+//     int _skipm = as<int>(skipm);
+//     int _autoselectC = as<int>(autoselectC);
+//     bool _swap = as<bool>(swap);
+// 
+// 
+//     optimum_reparam(_C1i, _C2i, _n, _d, _w, _onlyDP, _rotated, _isclosed,
+//                     _skipm, _autoselectC, _opti, _swap, _foptsi, _comtimei);
+// 
+//     List ret; ret["opt"] = opti; ret["fopts"] = foptsi;
+//     ret["comtime"] = comtimei; ret["swap"] = wrap(_swap);
+// 
+//     return(ret);
+// }