Cran submission

.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
   hooks:
   - id: cppcheck
     args: ["--platform=win64", "--language=c++", "--std=c++17", "--enable=warning", "--quiet", "--inline-suppr", "--library=googletest", "--library=tinyxml2"]
+    files: \.cpp$
 
 - repo: https://github.com/pre-commit/mirrors-clang-format
   rev: v16.0.6

configure

@@ -1,25 +1,14 @@
-: ${R_HOME=`R RHOME`}
-if test -z "${R_HOME}"; then
-  echo "could not determine R_HOME"
-  exit 1
-fi
+# Copy required arpack sources into src/arpack
+# and configure with ISO C bindings
 
-CC=`"${R_HOME}/bin/R" CMD config CC`
-CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
-CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
-LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
-FC=`"${R_HOME}/bin/R" CMD config FC`
-
-FSRC="z*.f icbazn.F90 debug.h stat.h"
+ZSRC="z*.f icbazn.F90 debug.h stat.h"
 USRC="icnteq.f icopy.f iset.f iswap.f dvout.f ivout.f second_NONE.f zvout.f zmout.f"
 FSRC_C="*.f icbazn.F90"
 
 tar -xf tools/arpack-ng-3.9.0.tar.gz -C tools/
-mkdir -p src/arpack
-for f in $FSRC; do cp tools/arpack-ng-3.9.0/SRC/$f src/arpack/; done
+
+for f in $ZSRC; do cp tools/arpack-ng-3.9.0/SRC/$f src/arpack/; done
 for f in $USRC; do cp tools/arpack-ng-3.9.0/UTIL/$f src/arpack/; done
 cat tools/arpack-ng-3.9.0/arpackdef.h.in | sed -e 's/@INTERFACE64@/0/g' > src/arpack/arpackdef.h
 cat tools/arpack-ng-3.9.0/arpackicb.h.in | sed -e 's/@INTERFACE64@/0/g' > src/arpack/arpackicb.h
 cp tools/arpack-ng-3.9.0/ICB/arpack.h src/arpack/
-cd src/arpack &&
-  for f in $FSRC_C; do ${FC} -c -fpic $f; done

configure.win

@@ -1,26 +1,14 @@
-: ${R_HOME=`R RHOME`}
-if test -z "${R_HOME}"; then
-  echo "could not determine R_HOME"
-  exit 1
-fi
-
-CC=`"${R_HOME}/bin/R" CMD config CC`
-CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
-CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
-LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
-FC=`"${R_HOME}/bin/R" CMD config FC`
+# Copy required arpack sources into src/arpack
+# and configure with ISO C bindings
 
 ZSRC="z*.f icbazn.F90 debug.h stat.h"
 USRC="icnteq.f icopy.f iset.f iswap.f dvout.f ivout.f second_NONE.f zvout.f zmout.f"
 FSRC_C="*.f icbazn.F90"
 
 tar -xf tools/arpack-ng-3.9.0.tar.gz -C tools/
-mkdir -p src/arpack
+
 for f in $ZSRC; do cp tools/arpack-ng-3.9.0/SRC/$f src/arpack/; done
 for f in $USRC; do cp tools/arpack-ng-3.9.0/UTIL/$f src/arpack/; done
 cat tools/arpack-ng-3.9.0/arpackdef.h.in | sed -e 's/@INTERFACE64@/0/g' > src/arpack/arpackdef.h
 cat tools/arpack-ng-3.9.0/arpackicb.h.in | sed -e 's/@INTERFACE64@/0/g' > src/arpack/arpackicb.h
 cp tools/arpack-ng-3.9.0/ICB/arpack.h src/arpack/
-cd src/arpack &&
-  for f in $FSRC_C; do ${FC} -c -fpic $f; done &&
-  ar cr libarpack.a *.o

src/Makevars

@@ -4,5 +4,14 @@
 # PKG_LIBS = -llapack -lblas -lgcov -L"arpack-ng-3.9.0/build" -l:libarpack.a
 # PKG_CFLAGS = -I"arpack-ng-3.9.0/ICB/" -I"arpack-ng-3.9.0/" -O0 --coverage
 # PKG_LIBS = -lblas -L"arpack-ng-3.9.0/build" -l:libarpack.a
-PKG_LIBS = arpack/*.o -lblas -llapack
+PKG_LIBS = -Larpack -larpack $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 PKG_CFLAGS = -I"arpack" -DUSING_R
+
+$(SHLIB): arpack/libarpack.a
+
+arpack/libarpack.a:
+	@(cd arpack && $(MAKE) libarpack.a \
+		FC="$(FC)" FFLAGS="$(FFLAGS) $(FPICFLAGS)" AR="$(AR)")
+
+# PKG_LIBS = arpack/*.o $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+# PKG_CFLAGS = -I"arpack" -DUSING_R

src/Makevars.win

@@ -1,2 +1,8 @@
-PKG_LIBS = arpack/*.o  -llapack -lblas -lgfortran -lquadmath
+PKG_LIBS = -Larpack -larpack -llapack $(BLAS_LIBS) $(FLIBS)
 PKG_CFLAGS = -I"arpack" -DUSING_R
+
+$(SHLIB): arpack/libarpack.a
+
+arpack/libarpack.a:
+	@(cd arpack && $(MAKE) libarpack.a \
+		FC="$(FC)" FFLAGS="$(FFLAGS) $(FPICFLAGS)" AR="$(AR)")

src/arpack/Makefile

@@ -0,0 +1,18 @@
+ARPACK_SOURCES = $(wildcard *.f *.F90)
+ARPACK_OBJECTS = $(ARPACK_SOURCES:.f=.o)
+ARPACK_OBJECTS := $(ARPACK_OBJECTS:.F90=.o)
+ARPACK_FFLAGS = $(filter-out -pedantic, $(FFLAGS) $(FPICFLAGS))
+
+libarpack.a: $(ARPACK_OBJECTS)
+	$(AR) rcs $@ $^
+
+%.o: %.f
+	$(FC) $(ARPACK_FFLAGS) -c $< -o $@
+
+%.o: %.F90
+	$(FC) $(ARPACK_FFLAGS) -c $< -o $@
+
+clean:
+	rm -f *.o $(LIBRARY)
+
+.PHONY: clean

src/dpca.c

@@ -78,7 +78,7 @@ SEXP R_dpca
     fourier_transform(covs, nrx, nrx, freqs, nfreqs, lags, nlags,
                       (double _Complex *)COMPLEX(spec));
 
-
+    SEXP hl_select;
     if (select_q) { // chose q ( number of dynamic factors) using Hallin & Liska (2007) method
 
         int lps = length(r_penalty_scales);
@@ -127,6 +127,21 @@ SEXP R_dpca
         R_Free(temp_evecs);
         R_Free(temp_evals);
 
+        hl_select = PROTECT(allocVector(VECSXP, 5));
+        SEXP chosen_q = PROTECT(allocVector(INTSXP, 1));
+        *INTEGER(chosen_q) = q;
+        SET_VECTOR_ELT(hl_select, 0, unpenalized_ic_vals);
+        SET_VECTOR_ELT(hl_select, 1, sample_var);
+        SET_VECTOR_ELT(hl_select, 2, chosen_q);
+        SET_VECTOR_ELT(hl_select, 3, info);
+        SET_VECTOR_ELT(hl_select, 4, q_path);
+        SEXP nms_hl_select = PROTECT(allocVector(STRSXP, 5));
+        SET_STRING_ELT(nms_hl_select, 0, mkChar("unpenalized_ic_vals"));
+        SET_STRING_ELT(nms_hl_select, 1, mkChar("sample_var"));
+        SET_STRING_ELT(nms_hl_select, 2, mkChar("q"));
+        SET_STRING_ELT(nms_hl_select, 3, mkChar("info"));
+        SET_STRING_ELT(nms_hl_select, 4, mkChar("q_path"));
+        setAttrib(hl_select, R_NamesSymbol, nms_hl_select);
     } else { // user-specfied q
         q = *INTEGER(r_q);
         evecs = PROTECT(alloc3DArray(CPLXSXP, q, nrx, nfreqs));
@@ -165,6 +180,7 @@ SEXP R_dpca
                 }
             }
         }
+        hl_select = PROTECT(allocVector(VECSXP, 0));
     }
 
     for (int i = 0; i < nfreqs; i++) {
@@ -211,27 +227,6 @@ SEXP R_dpca
     SET_STRING_ELT(nms_filter, 1, mkChar("dcc"));
     setAttrib(filter, R_NamesSymbol, nms_filter);
 
-    SEXP hl_select;
-    if (select_q) {
-        hl_select = PROTECT(allocVector(VECSXP, 5));
-        SEXP chosen_q = PROTECT(allocVector(INTSXP, 1));
-        *INTEGER(chosen_q) = q;
-        SET_VECTOR_ELT(hl_select, 0, unpenalized_ic_vals);
-        SET_VECTOR_ELT(hl_select, 1, sample_var);
-        SET_VECTOR_ELT(hl_select, 2, chosen_q);
-        SET_VECTOR_ELT(hl_select, 3, info);
-        SET_VECTOR_ELT(hl_select, 4, q_path);
-        SEXP nms_hl_select = PROTECT(allocVector(STRSXP, 5));
-        SET_STRING_ELT(nms_hl_select, 0, mkChar("unpenalized_ic_vals"));
-        SET_STRING_ELT(nms_hl_select, 1, mkChar("sample_var"));
-        SET_STRING_ELT(nms_hl_select, 2, mkChar("q"));
-        SET_STRING_ELT(nms_hl_select, 3, mkChar("info"));
-        SET_STRING_ELT(nms_hl_select, 4, mkChar("q_path"));
-        setAttrib(hl_select, R_NamesSymbol, nms_hl_select);
-    } else {
-        hl_select = PROTECT(allocVector(VECSXP, 0));
-    }
-
     SEXP res = PROTECT(allocVector(VECSXP, 7));
     SET_VECTOR_ELT(res, 0, spec);
     SET_VECTOR_ELT(res, 1, eig);

src/eigs.c

@@ -89,7 +89,6 @@ void arnoldi_eigs(double _Complex *mat, int dim, int ldm, int q,
 
   int cnt = 0;
   while (ido != 99) {
-    /* call arpack like you would have, but, use znaupd_c instead of znaupd_ */
     znaupd_c(&ido, bmat, N, which, nev, tol, resid, ncv, V, ldv, iparam, ipntr,
              workd, workl, lworkl, rwork, &info);
 
@@ -106,7 +105,6 @@ void arnoldi_eigs(double _Complex *mat, int dim, int ldm, int q,
   }
 
 
-  /* call arpack like you would have, but, use zneupd_c instead of zneupd_ */
   zneupd_c(rvec, howmny, select, d, z, ldz, sigma, workev, bmat, N, which, nev,
            tol, resid, ncv, V, ldv, iparam, ipntr, workd, workl, lworkl, rwork,
            &info);