fixes for R_NO_REMAP

ahmohamed · Nov 27, 2024 · b338534 · b338534
1 parent 271cd7a
commit b338534
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Showing 8 changed files with 168 additions and 164 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -51,10 +51,10 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.4', bioc: '3.19'}
-          - { os: windows-latest, r: '4.4', bioc: '3.19'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: NetPathMiner
-Version: 1.43.0
+Version: 1.43.1
 Date: 2014 onwards
 Title: NetPathMiner for Biological Network Construction, Path Mining
     and Visualization

diff --git a/src/handlesegfault.c b/src/handlesegfault.c
@@ -6,14 +6,14 @@
 #ifndef WIN_COMPILE
 #ifdef HAVE_XML
 void segfault_KGML(int signal, siginfo_t *si, void *arg){
-	EVAL(lang2(install("registerMemoryErr"), mkString("KGML2igraph")));
-	error("Critical memory error in KGML2igraph. Please save your work and restart R.");
+	EVAL(Rf_lang2(Rf_install("registerMemoryErr"), Rf_mkString("KGML2igraph")));
+	Rf_error("Critical memory error in KGML2igraph. Please save your work and restart R.");
 }
 #endif
 #ifdef HAVE_SBML
 void segfault_SBML(int signal, siginfo_t *si, void *arg){
-	EVAL(lang2(install("registerMemoryErr"), mkString("SBML2igraph")));
-	error("Critical memory error in SBML2igraph. Please save your work and restart R.");
+	EVAL(Rf_lang2(Rf_install("registerMemoryErr"), Rf_mkString("SBML2igraph")));
+	Rf_error("Critical memory error in SBML2igraph. Please save your work and restart R.");
 }
 #endif
 #endif

diff --git a/src/hme3m.h b/src/hme3m.h
@@ -10,7 +10,7 @@
 # define FCONE
 #endif
 
-#define oops(s) { perror((s)); error("Failed to allocate memory"); }
+#define oops(s) { perror((s)); Rf_error("Failed to allocate memory"); }
 #define MALLOC(s,t) if(((s) = malloc(t)) == NULL) { oops("error: malloc() "); }
 
 void hme3m(double * y,

diff --git a/src/init.h b/src/init.h
@@ -12,6 +12,10 @@
 using namespace std;
 #endif //__cplusplus
 
+#ifndef R_NO_REMAP
+#define R_NO_REMAP
+#endif
+
 #include <R.h>
 #include <Rmath.h>
 #include <Rdefines.h>

diff --git a/src/kgml_interface.cpp b/src/kgml_interface.cpp
diff --git a/src/methods.cpp b/src/methods.cpp
@@ -175,7 +175,7 @@ SEXP expand_complexes(SEXP ATTR_LS, SEXP EL, SEXP V, SEXP EXPAND, SEXP MISSING){
 	PROTECT( PARENTS = NEW_LIST(parents.size()) );
 
 	for(size_t i=0; i<vertices.size(); i++)
-		SET_STRING_ELT(VERTICES, i, mkChar( vertices[i].c_str() ));
+		SET_STRING_ELT(VERTICES, i, Rf_mkChar( vertices[i].c_str() ));
 
 	for(size_t i=0; i<edges.size(); i++)
 		INTEGER(EDGES)[i] = edges[i]+1;
@@ -198,13 +198,13 @@ SEXP expand_complexes(SEXP ATTR_LS, SEXP EL, SEXP V, SEXP EXPAND, SEXP MISSING){
 
 	PROTECT( OUT = NEW_LIST(5));
 	PROTECT( NAMES = NEW_STRING(5));
-	SET_VECTOR_ELT(OUT, 0, VERTICES); SET_STRING_ELT(NAMES, 0, mkChar("vertices"));
-	SET_VECTOR_ELT(OUT, 1, EDGES);	SET_STRING_ELT(NAMES, 1, mkChar("edges"));
-	SET_VECTOR_ELT(OUT, 2, RECONNECT);	SET_STRING_ELT(NAMES, 2, mkChar("reconnect"));
-	SET_VECTOR_ELT(OUT, 3, PARENTS);	SET_STRING_ELT(NAMES, 3, mkChar("parents"));
-	SET_VECTOR_ELT(OUT, 4, E_PARENTS);	SET_STRING_ELT(NAMES, 4, mkChar("e.parents"));
+	SET_VECTOR_ELT(OUT, 0, VERTICES); SET_STRING_ELT(NAMES, 0, Rf_mkChar("vertices"));
+	SET_VECTOR_ELT(OUT, 1, EDGES);	SET_STRING_ELT(NAMES, 1, Rf_mkChar("edges"));
+	SET_VECTOR_ELT(OUT, 2, RECONNECT);	SET_STRING_ELT(NAMES, 2, Rf_mkChar("reconnect"));
+	SET_VECTOR_ELT(OUT, 3, PARENTS);	SET_STRING_ELT(NAMES, 3, Rf_mkChar("parents"));
+	SET_VECTOR_ELT(OUT, 4, E_PARENTS);	SET_STRING_ELT(NAMES, 4, Rf_mkChar("e.parents"));
 
-	setAttrib(OUT,R_NamesSymbol,NAMES);
+	Rf_setAttrib(OUT,R_NamesSymbol,NAMES);
 	UNPROTECT(7);
 	return(OUT);
 }