Fixes #5

Author: gregorgorjanc

RcppTskit/R/Class-TreeSequence.R

@@ -17,11 +17,11 @@ TreeSequence <- R6::R6Class(
     #' @param options see \code{\link{ts_load}()}
     #' @param pointer an external pointer to a tree sequence
     initialize = function(file, options = 0L, pointer = NULL) {
-      if (missing(file) & is.null(pointer)) {
+      if (missing(file) && is.null(pointer)) {
         stop("you must provide a file name or a pointer!")
       }
-      if (!missing(file) & !is.null(pointer)) {
-        stop("you must provide either a file name or a pointer!")
+      if (!missing(file) && !is.null(pointer)) {
+        stop("you must provide either a file name or a pointer, but not both!")
       }
       if (!missing(file)) {
         if (!is.character(file)) {

RcppTskit/inst/include/tskit/core.h

@@ -5,7 +5,7 @@
 #include <tskit/tskit/core.h>
 
 // Redefinition of tsk_bug_assert to avoid aborting R sessions with tskit C API
-// (following R extensions manual recommendations).
+// (see R extensions manual).
 // While tsk_bug_assert is called only in C API (atm) we provide both C and C++
 // macros for completeness.
 // TODO: Redefine TSK_BUG_ASSERT_MESSAGE or create RcppTskit version if we will
@@ -33,7 +33,7 @@
 #endif
 
 // Redefinition of tsk_trace_error to avoid writing to stderr from tskit C API
-// (following R extensions manual recommendations).
+// (see R extensions manual).
 // While tsk_trace_error is called only in C API (atm) we provide both C and C++
 // macros for completeness.
 #undef tsk_trace_error
@@ -61,4 +61,19 @@ static inline int _RcppTskit_trace_error_c(int err, int line,
 #define tsk_trace_error(err) (err)
 #endif
 
+// Discard tskit debug output to avoid using stdout, as it is not captured by R.
+// (see R extensions manual).
+#if defined(_WIN32)
+#define RCPPTSKIT_NULL_DEVICE "NUL"
+#else
+#define RCPPTSKIT_NULL_DEVICE "/dev/null"
 #endif
+
+static inline FILE *rcpptskit_default_debug_stream(void) {
+  return fopen(RCPPTSKIT_NULL_DEVICE, "w");
+}
+
+#undef TSK_DEFAULT_DEBUG_STREAM
+#define TSK_DEFAULT_DEBUG_STREAM rcpptskit_default_debug_stream()
+
+#endif // RCPPTSKIT_TSKIT_CORE_H

RcppTskit/inst/include/tskit/tskit/core.h

@@ -511,7 +511,7 @@ disallowed (use compute_mutation_times?).
 */
 #define TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME                    -510
 
-/** 
+/**
 A mutation's parent was not consistent with the topology of the tree.
  */
 #define TSK_ERR_BAD_MUTATION_PARENT                                 -511
@@ -971,6 +971,12 @@ not be freed by client code.
 */
 const char *tsk_strerror(int err);
 
+/* Redefine this macro in downstream builds if stdout is not the
+ * approriate stream to emit debug information when the TSK_DEBUG
+ * flag is passed to supporting functions (e.g. in R).
+ */
+#define TSK_DEFAULT_DEBUG_STREAM stdout
+
 #ifdef TSK_TRACE_ERRORS
 
 static inline int
@@ -981,6 +987,11 @@ _tsk_trace_error(int err, int line, const char *file)
     return err;
 }
 
+/*
+Developer note: this macro may be redefined as part of compilation for
+an R package, and should be treated as part of the documented API
+(no changes).
+*/
 #define tsk_trace_error(err) (_tsk_trace_error(err, __LINE__, __FILE__))
 #else
 #define tsk_trace_error(err) (err)
@@ -1001,6 +1012,11 @@ means compiling without NDEBUG. This macro still asserts when NDEBUG is defined.
 If you are using this macro in your own software then please set TSK_BUG_ASSERT_MESSAGE
 to point users to your issue tracker.
 */
+/*
+Developer note: this macro may redefined as part of compilation for
+an R package, and should be treated as part of the documented API
+(no changes).
+*/
 #define tsk_bug_assert(condition)                                                       \
     do {                                                                                \
         if (!(condition)) {                                                             \

RcppTskit/src/tskit/core.c

@@ -1041,7 +1041,7 @@ FILE *
 tsk_get_debug_stream(void)
 {
     if (_tsk_debug_stream == NULL) {
-        _tsk_debug_stream = stdout;
+        _tsk_debug_stream = TSK_DEFAULT_DEBUG_STREAM;
     }
     return _tsk_debug_stream;
 }