Fix bioconda wrapper types and R conda package load failure

- Pass SWIGWORDSIZE64 to the Python and Java SWIG runs on Linux for ALL
  SWIG versions, not only >= 4.4. Bioconda pins swig <4.3 and its
  conda-forge swig 4.2.1 build resolves int64_t to 'long long' through
  Sim.i's stdint.i include, reproducing the original vector<long long>
  vs vector<long> compile failure. With the flag the typedef says
  'long', which is correct on Linux whether a given SWIG build resolves
  the typedef or keeps int64_t literal. R keeps the >= 4.4 gate
  (TTTRLIB_SWIG_INT64_FLAG_R): SWIG 4.2's R backend breaks literal
  'long long' returns under the define, and the R module never includes
  stdint.i in the first place.
- Build tttrlibStatic without LTO. R CMD INSTALL links the static
  archive outside our CMake build; with slim LTO bitcode members the
  consumer drops vague-linkage symbols and the R package failed to load
  with undefined 'typeinfo for TTTRRange'. Same class of fix as the
  bundled libtiff archive.

Author: tpeulen

CMakeLists.txt

@@ -316,6 +316,13 @@ IF(BUILD_LIBRARY)
   # cmake needs unique target name, thus place shared in front of project
   ADD_LIBRARY(${PROJECT_NAME}Shared SHARED ${SRC_files})
   ADD_LIBRARY(${PROJECT_NAME}Static STATIC ${SRC_files})
+  IF(NOT MSVC)
+    # The static archive is consumed outside this build (e.g. R CMD INSTALL
+    # links it into the R package). If it holds slim LTO bitcode, an ar/linker
+    # without the LTO plugin drops vague-linkage symbols (typeinfo/vtables,
+    # e.g. _ZTI9TTTRRange) and the consumer fails at load. Archive real code.
+    TARGET_COMPILE_OPTIONS(${PROJECT_NAME}Static PRIVATE -fno-lto)
+  ENDIF()
 
   # Link libraries (Boost removed - using C++17 standard library)
 

ext/CMakeLists.txt

@@ -15,17 +15,23 @@ MESSAGE(STATUS "SWIG_VERSION: ${SWIG_VERSION}")
 INCLUDE(${SWIG_USE_FILE})
 INCLUDE_DIRECTORIES(.)
 
-# glibc on LP64 Linux defines int64_t as 'long', but SWIG >= 4.4 eagerly
-# resolves the stdint.i typedefs and picks 'long long' unless SWIGWORDSIZE64
-# is defined. Without this flag the generated wrappers mix
+# glibc on LP64 Linux defines int64_t as 'long', but SWIG's stdint.i (pulled
+# in by Sim.i) typedefs it to 'long long' unless SWIGWORDSIZE64 is defined,
+# and depending on the SWIG build the generated Python wrappers then mix
 # std::vector<long long> with the library's std::vector<long> and do not
-# compile on Linux. Only define it for SWIG >= 4.4: older SWIG keeps int64_t
-# literal in generated code (so the flag is unnecessary), and SWIG 4.2's R
-# backend mishandles 'long long' returns under SWIGWORDSIZE64 (the C side
-# returns a native vector while the R proxy expects an external pointer).
-IF(UNIX AND NOT APPLE AND CMAKE_SIZEOF_VOID_P EQUAL 8 AND NOT SWIG_VERSION VERSION_LESS "4.4")
+# compile (seen with conda-forge swig 4.2.1 and 4.4.1). With the flag the
+# typedef says 'long', which is correct on Linux whether SWIG resolves it or
+# keeps int64_t literal, so pass it unconditionally for the Python and Java
+# modules. The R module is the exception: it never includes stdint.i, and
+# SWIG 4.2's R backend mishandles 'long long' returns under SWIGWORDSIZE64
+# (the C side returns a native vector while the R proxy expects an external
+# pointer), so R only gets the flag for SWIG >= 4.4 where it is verified fine.
+IF(UNIX AND NOT APPLE AND CMAKE_SIZEOF_VOID_P EQUAL 8)
     SET(TTTRLIB_SWIG_INT64_FLAG "-DSWIGWORDSIZE64")
     LIST(APPEND CMAKE_SWIG_FLAGS ${TTTRLIB_SWIG_INT64_FLAG})
+    IF(NOT SWIG_VERSION VERSION_LESS "4.4")
+        SET(TTTRLIB_SWIG_INT64_FLAG_R "-DSWIGWORDSIZE64")
+    ENDIF()
 ENDIF()
 
 IF(BUILD_PYTHON_INTERFACE)
@@ -212,7 +218,7 @@ IF(BUILD_R_INTERFACE)
             SWIG_MODULE_NAME tttrlib)
 
     # r/tttrlib.i re-includes the shared fragments that live in ext/python.
-    SET(CMAKE_SWIG_FLAGS -I${CMAKE_CURRENT_SOURCE_DIR}/python ${TTTRLIB_SWIG_INT64_FLAG})
+    SET(CMAKE_SWIG_FLAGS -I${CMAKE_CURRENT_SOURCE_DIR}/python ${TTTRLIB_SWIG_INT64_FLAG_R})
 
     # Rerun SWIG when any shared fragment, the R module, or the R array library changes.
     file(GLOB R_SWIG_DEPS