Merge pull request #124 from symengine/fix/cran-issue

fix cran check issues and bump version
symengine · Feb 24, 2024 · c573238 · c573238
2 parents dc87644 + 0f5fe3e
commit c573238
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: symengine
 Title: Interface to the 'SymEngine' Library
-Version: 0.2.2
+Version: 0.2.4
 Authors@R: c(person("Jialin", "Ma", email="marlin@inventati.org", role = c("cre", "aut")),
              person("Isuru", "Fernando", email="isuruf@gmail.com", role = c("aut")),
              person("Xin", "Chen", email="xinchen.tju@gmail.com", role = c("aut")))
@@ -39,7 +39,7 @@ License: GPL (>= 2)
 Copyright: The R package bundles the 'SymEngine' library source and its subcomponents
     under 'src/upstream' directory. See file COPYRIGHTS for retained copyright notices
     as a relicensing and redistribution requirement.
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Collate: 
     'RcppExports.R'
     'basic-getinfo.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,6 +4,8 @@ S3method(as.function,BasicOrVecBasic)
 S3method(as.matrix,DenseMatrix)
 S3method(cbind,SymEngineDataType)
 S3method(rbind,SymEngineDataType)
+S3method(rep,Basic)
+S3method(rep,VecBasic)
 S3method(unique,VecBasic)
 export(Basic)
 export(Constant)

diff --git a/R/vector.R b/R/vector.R
@@ -79,27 +79,16 @@ setMethod("length", "VecBasic",
 )
 
 #' @rdname vecbasic-bindings
-setMethod("rep", c(x = "VecBasic"),
-    function(x, ...)
-        s4binding_subset(x, rep(seq_len(length(x)), ...), get_basic = FALSE)
-)
+#' @export
+rep.VecBasic <- function(x, ...) {
+    s4binding_subset(x, rep(seq_len(length(x)), ...), get_basic = FALSE)
+}
+
 #' @rdname vecbasic-bindings
-setMethod("rep", c(x = "Basic"),
-    function(x, ...)
-        s4binding_subset(x, rep(1L, ...), get_basic = FALSE)
-)
-setMethod("rep_len", c(x = "VecBasic"),
-    function(x, length.out) rep(x, length.out = length.out)
-)
-setMethod("rep_len", c(x = "Basic"),
-    function(x, length.out) rep(x, length.out = length.out)
-)
-setMethod("rep.int", c(x = "VecBasic"),
-    function(x, times)      rep(x, times = times)
-)
-setMethod("rep.int", c(x = "Basic"),
-    function(x, times)      rep(x, times = times)
-)
+#' @export
+rep.Basic <- function(x, ...) {
+    s4binding_subset(x, rep(1L, ...), get_basic = FALSE)
+}
 
 #' @rdname vecbasic-bindings
 #' @export

diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,6 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/symengine/symengine.R/workflows/R-CMD-check/badge.svg)](https://github.com/symengine/symengine.R/actions)
-[![Travis-CI Build Status](https://travis-ci.org/symengine/symengine.R.svg?branch=master)](https://travis-ci.org/symengine/symengine.R)
 [![AppVeyor Build status](https://ci.appveyor.com/api/projects/status/rr0tdh8ykvs04qg2?svg=true)](https://ci.appveyor.com/project/symengine/symengine-r)
 <!-- badges: end -->
 

diff --git a/README.md b/README.md
@@ -6,8 +6,6 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/symengine/symengine.R/workflows/R-CMD-check/badge.svg)](https://github.com/symengine/symengine.R/actions)
-[![Travis-CI Build
-Status](https://travis-ci.org/symengine/symengine.R.svg?branch=master)](https://travis-ci.org/symengine/symengine.R)
 [![AppVeyor Build
 status](https://ci.appveyor.com/api/projects/status/rr0tdh8ykvs04qg2?svg=true)](https://ci.appveyor.com/project/symengine/symengine-r)
 <!-- badges: end -->

diff --git a/configure b/configure
@@ -61,14 +61,18 @@ if test -z "$R_CXX"; then
     echo >&2 "could not detect C++ compiler with R CMD config"
 fi
 
-echo == setting cmake environment variables
+echo == setting environment variables for cmake
+
+CC="$R_CC"                             ; echo setting CC="$CC"             ; export CC
+CXX="$R_CXX"                           ; echo setting CXX="$CXX"           ; export CXX
+
+echo == translating to cmake variables
+
+CMAKE_C_FLAGS="$R_CFLAGS $R_CPICFLAGS"                                                                           ; echo setting CMAKE_C_FLAGS="$CMAKE_C_FLAGS"          
+CMAKE_CXX_FLAGS="$R_CXXFLAGS $R_CXXPICFLAGS"                                                                     ; echo setting CMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS"      
+CMAKE_INCLUDE_PATH=`"${R_HOME}/bin/Rscript" ./tools/translate_to_cmake_flags.R CMAKE_INCLUDE_PATH "$R_CPPFLAGS"` ; echo setting CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH"
+CMAKE_LIBRARY_PATH=`"${R_HOME}/bin/Rscript" ./tools/translate_to_cmake_flags.R CMAKE_LIBRARY_PATH "$R_LDFLAGS"`  ; echo setting CMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH"
 
-CMAKE_C_COMPILER="$R_CC"                                                                                                       ; echo setting CMAKE_C_COMPILER="$CMAKE_C_COMPILER"                   ; export CMAKE_C_COMPILER="$CMAKE_C_COMPILER"
-CMAKE_C_FLAGS="$R_CFLAGS $R_CPICFLAGS"                                                                                         ; echo setting CMAKE_C_FLAGS="$CMAKE_C_FLAGS"                         ; export CMAKE_C_FLAGS="$CMAKE_C_FLAGS"
-CMAKE_CXX_COMPILER="$R_CXX"                                                                                                    ; echo setting CMAKE_CXX_COMPILER="$CMAKE_CXX_COMPILER"               ; export CMAKE_CXX_COMPILER="$CMAKE_CXX_COMPILER"
-CMAKE_CXX_FLAGS="$R_CXXFLAGS $R_CXXPICFLAGS"                                                                                   ; echo setting CMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS"                     ; export CMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS"
-CMAKE_INCLUDE_PATH=`"${R_HOME}/bin/Rscript" ./tools/translate_to_cmake_flags.R CMAKE_INCLUDE_PATH "$R_CPPFLAGS"`               ; echo setting CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH"               ; export CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH"
-CMAKE_LIBRARY_PATH=`"${R_HOME}/bin/Rscript" ./tools/translate_to_cmake_flags.R CMAKE_LIBRARY_PATH "$R_LDFLAGS"`                ; echo setting CMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH"               ; export CMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH"
 
 ## Use ./tools/SYMENGINE_BUNDLED file as indicator so that
 ## this won't run on CRAN machine.
@@ -101,11 +105,18 @@ if [ -z "$SymEngine_DIR" ]; then
 
     PKG_DIR=`pwd`
     cd src/upstream
+
+    set -x
 
     $CMAKE_BIN \
         -DCMAKE_AR=$AR \
         -DCMAKE_RANLIB=$RANLIB \
         \
+        -DCMAKE_C_FLAGS="$CMAKE_C_FLAGS" \
+        -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \
+        -DCMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH" \
+        -DCMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH" \
+        \
         -DCMAKE_BUILD_TYPE=Release \
         -DWITH_BFD=no \
         -DWITH_SYMENGINE_ASSERT=no \
@@ -129,6 +140,8 @@ if [ -z "$SymEngine_DIR" ]; then
     if [ $? -ne 0 ]; then
         exit 1
     fi
+
+    set +x
 
     cd $PKG_DIR
 

diff --git a/configure.win b/configure.win
@@ -61,14 +61,18 @@ if test -z "$R_CXX"; then
     echo >&2 "could not detect C++ compiler with R CMD config"
 fi
 
-echo == setting cmake environment variables
+echo == setting environment variables for cmake
+
+CC="$R_CC"                             ; echo setting CC="$CC"             ; export CC
+CXX="$R_CXX"                           ; echo setting CXX="$CXX"           ; export CXX
+
+echo == translating to cmake variables
+
+CMAKE_C_FLAGS="$R_CFLAGS $R_CPICFLAGS"                                                                           ; echo setting CMAKE_C_FLAGS="$CMAKE_C_FLAGS"          
+CMAKE_CXX_FLAGS="$R_CXXFLAGS $R_CXXPICFLAGS"                                                                     ; echo setting CMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS"      
+CMAKE_INCLUDE_PATH=`"${R_HOME}/bin/Rscript" ./tools/translate_to_cmake_flags.R CMAKE_INCLUDE_PATH "$R_CPPFLAGS"` ; echo setting CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH"
+CMAKE_LIBRARY_PATH=`"${R_HOME}/bin/Rscript" ./tools/translate_to_cmake_flags.R CMAKE_LIBRARY_PATH "$R_LDFLAGS"`  ; echo setting CMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH"
 
-CMAKE_C_COMPILER="$R_CC"                                                                                                       ; echo setting CMAKE_C_COMPILER="$CMAKE_C_COMPILER"                   ; export CMAKE_C_COMPILER="$CMAKE_C_COMPILER"
-CMAKE_C_FLAGS="$R_CFLAGS $R_CPICFLAGS"                                                                                         ; echo setting CMAKE_C_FLAGS="$CMAKE_C_FLAGS"                         ; export CMAKE_C_FLAGS="$CMAKE_C_FLAGS"
-CMAKE_CXX_COMPILER="$R_CXX"                                                                                                    ; echo setting CMAKE_CXX_COMPILER="$CMAKE_CXX_COMPILER"               ; export CMAKE_CXX_COMPILER="$CMAKE_CXX_COMPILER"
-CMAKE_CXX_FLAGS="$R_CXXFLAGS $R_CXXPICFLAGS"                                                                                   ; echo setting CMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS"                     ; export CMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS"
-CMAKE_INCLUDE_PATH=`"${R_HOME}/bin/Rscript" ./tools/translate_to_cmake_flags.R CMAKE_INCLUDE_PATH "$R_CPPFLAGS"`               ; echo setting CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH"               ; export CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH"
-CMAKE_LIBRARY_PATH=`"${R_HOME}/bin/Rscript" ./tools/translate_to_cmake_flags.R CMAKE_LIBRARY_PATH "$R_LDFLAGS"`                ; echo setting CMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH"               ; export CMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH"
 
 ## Use ./tools/SYMENGINE_BUNDLED file as indicator so that
 ## this won't run on CRAN machine.
@@ -101,11 +105,18 @@ if [ -z "$SymEngine_DIR" ]; then
 
     PKG_DIR=`pwd`
     cd src/upstream
+
+    set -x
 
     $CMAKE_BIN \
         -DCMAKE_AR=$AR \
         -DCMAKE_RANLIB=$RANLIB \
         \
+        -DCMAKE_C_FLAGS="$CMAKE_C_FLAGS" \
+        -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \
+        -DCMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH" \
+        -DCMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH" \
+        \
         -DCMAKE_BUILD_TYPE=Release \
         -DWITH_BFD=no \
         -DWITH_SYMENGINE_ASSERT=no \
@@ -129,6 +140,8 @@ if [ -z "$SymEngine_DIR" ]; then
     if [ $? -ne 0 ]; then
         exit 1
     fi
+
+    set +x
 
     cd $PKG_DIR
 

diff --git a/man/symengine.Rd b/man/symengine.Rd
diff --git a/man/vecbasic-bindings.Rd b/man/vecbasic-bindings.Rd
diff --git a/src/Makevars.in b/src/Makevars.in
@@ -1,6 +1,4 @@
 
-CXX_STD = CXX11
-
 PKG_LIBS = @@@PKG_LIBS@@@
 
 PKG_CPPFLAGS = @@@PKG_CPPFLAGS@@@

diff --git a/src/rbinding.cpp b/src/rbinding.cpp
@@ -26,35 +26,30 @@ static_assert(std::alignment_of<CRCPBasic>::value
 // Some cwrapper helpers ///////////
 
 // Exception handling
-const char* cwrapper_exception_message(CWRAPPER_OUTPUT_TYPE id) {
+static
+void cwrapper_hold(CWRAPPER_OUTPUT_TYPE output) {
+    if (!output) return;
+
     // Refer:
     // https://github.com/symengine/symengine/blob/master/symengine/symengine_exception.h
-    switch(id) {
+    switch(output) {
     case SYMENGINE_NO_EXCEPTION:
-        return "SymEngine exception: No exception, it should not go here";
+        Rf_error("SymEngine exception: No exception, it should not go here");
     case SYMENGINE_RUNTIME_ERROR:
-        return "SymEngine exception: Runtime error";
+        Rf_error("SymEngine exception: Runtime error");
     case SYMENGINE_DIV_BY_ZERO:
-        return "SymEngine exception: Div by zero";
+        Rf_error("SymEngine exception: Div by zero");
     case SYMENGINE_NOT_IMPLEMENTED:
-        return "SymEngine exception: Not implemented SymEngine feature";
+        Rf_error("SymEngine exception: Not implemented SymEngine feature");
     case SYMENGINE_DOMAIN_ERROR:
-        return "SymEngine exception: Domain error";
+        Rf_error("SymEngine exception: Domain error");
     case SYMENGINE_PARSE_ERROR:
-        return "SymEngine exception: Parse error";
+        Rf_error("SymEngine exception: Parse error");
     default:
-        return "SymEngine exception: Unexpected SymEngine error code";
+        Rf_error("SymEngine exception: Unexpected SymEngine error code");
     }
 }
 
-static inline
-void cwrapper_hold(CWRAPPER_OUTPUT_TYPE output) {
-    if (output)
-        Rf_error(cwrapper_exception_message(output));
-    else
-        return;
-}
-
 
 using namespace Rcpp;
 
@@ -961,7 +956,7 @@ void s4DenseMat_mut_addcols(RObject A, RObject B) {
     size_t nrow_self  = dense_matrix_rows(self);
     size_t nrow_value = dense_matrix_rows(value);
     if (nrow_self != nrow_value)
-        Rf_error("Number of rows not equal (%d != %d)\n", nrow_self, nrow_value);
+        Rf_error("Number of rows not equal (%zu != %zu)\n", nrow_self, nrow_value);
     cwrapper_hold(dense_matrix_row_join(self, value));
     return;
 }
@@ -972,7 +967,7 @@ void s4DenseMat_mut_addrows(RObject A, RObject B) {
     size_t ncol_self  = dense_matrix_cols(self);
     size_t ncol_value = dense_matrix_cols(value);
     if (ncol_self != ncol_value)
-        Rf_error("Number of cols not equal (%d != %d)\n", ncol_self, ncol_value);
+        Rf_error("Number of cols not equal (%zu != %zu)\n", ncol_self, ncol_value);
     cwrapper_hold(dense_matrix_col_join(self, value));
     return;
 }

diff --git a/tools/bundle_symengine_source.sh b/tools/bundle_symengine_source.sh
@@ -17,7 +17,7 @@ fi
 PKG_DIR=`pwd`
 
 SYMENGINE_REPO="symengine/symengine"
-SYMENGINE_COMMIT=ad84b9677e814e6ac328d7127da092d4d8722afe
+SYMENGINE_COMMIT=c1fc32cf0902ecd7b1a0e5369c38dd22ad75c726
 
 echo === Bundle source from commit: $SYMENGINE_COMMIT
 

diff --git a/tools/cran_comments/cran-comments_0.2.3.md b/tools/cran_comments/cran-comments_0.2.3.md
@@ -0,0 +1,5 @@
+
+This version (0.2.3) should fix issues in CRAN check results:
+- warning on format specifies type
+- remove C++11 requirement
+- should also resolve the error (fPIC flag) in Intel test
diff --git a/tools/cran_comments/cran-comments_0.2.4.md b/tools/cran_comments/cran-comments_0.2.4.md
@@ -0,0 +1,2 @@
+
+This version (0.2.4) fixes the build error on MacOS.