[check,libsbml] Update, port fixes

ports/check/linkage.patch

@@ -0,0 +1,20 @@
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 4a02dbe..3e147e4 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -188,7 +188,14 @@ target_include_directories(checkShared
+ )
+
+ if(NOT THIS_IS_SUBPROJECT)
+-  install(TARGETS check checkShared
++  if(BUILD_SHARED_LIBS)
++    set(lib checkShared)
++    set_target_properties(check PROPERTIES EXCLUDE_FROM_ALL 1)
++  else()
++    set(lib check)
++    set_target_properties(checkShared PROPERTIES EXCLUDE_FROM_ALL 1)
++  endif()
++  install(TARGETS ${lib}
+     EXPORT check-targets
+     ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+     LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/manual-link

ports/check/portfile.cmake

@@ -4,33 +4,33 @@ vcpkg_from_github(
     REF 11970a7e112dfe243a2e68773f014687df2900e8 # 0.15.2
     SHA512 210c9617fa1c1ce16bef983b0e6cb587b1774c3f7ce27a53ca7799642dc7a14be8de567d69dc0e57845684c6f7991d772c73654f63c8755afda3b37a35c7156e
     HEAD_REF master
-    PATCHES fix-lib-path.patch
+    PATCHES
+        fix-lib-path.patch
+        linkage.patch
 )
 
 vcpkg_cmake_configure(
     SOURCE_PATH "${SOURCE_PATH}"
     OPTIONS
-        -DCHECK_ENABLE_TESTS=OFF
         -DBUILD_TESTING=OFF
         -DCHECK_ENABLE_GCOV=OFF
-        -DENABLE_MEMORY_LEAKING_TESTS=OFF
+        -DCHECK_ENABLE_TESTS=OFF
         -DCHECK_ENABLE_TIMEOUT_TESTS=OFF
+        -DENABLE_MEMORY_LEAKING_TESTS=OFF
+        -DINSTALL_CHECKMK=OFF
 )
 
 vcpkg_cmake_install()
-
-vcpkg_cmake_config_fixup(CONFIG_PATH lib/cmake/check)
-
 vcpkg_copy_pdbs()
+vcpkg_cmake_config_fixup(CONFIG_PATH lib/cmake/check)
+vcpkg_fixup_pkgconfig()
 
-if(VCPKG_LIBRARY_LINKAGE STREQUAL static)
-    file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/bin" "${CURRENT_PACKAGES_DIR}/debug/bin")
+if(VCPKG_LIBRARY_LINKAGE STREQUAL "dynamic" AND VCPKG_TARGET_IS_WINDOWS)
+    vcpkg_replace_string("${CURRENT_PACKAGES_DIR}/include/check.h" "#define CK_DLL_EXP" "#define CK_DLL_EXP __declspec(dllimport)")
 endif()
 
-# cleanup
 file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/include" "${CURRENT_PACKAGES_DIR}/debug/share")
 file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/share/man")
 
-vcpkg_fixup_pkgconfig()
-
-file(INSTALL "${SOURCE_PATH}/COPYING.LESSER" DESTINATION "${CURRENT_PACKAGES_DIR}/share/${PORT}" RENAME copyright)
+file(COPY "${CURRENT_PORT_DIR}/usage" DESTINATION "${CURRENT_PACKAGES_DIR}/share/${PORT}")
+vcpkg_install_copyright(FILE_LIST "${SOURCE_PATH}/COPYING.LESSER")

ports/check/usage

@@ -0,0 +1,4 @@
+check provides CMake targets:
+
+  find_package(check CONFIG REQUIRED)
+  target_link_libraries(main PRIVATE $<IF:$<TARGET_EXISTS:Check::check>,Check::check,Check::checkShared>)

ports/check/vcpkg.json

@@ -1,7 +1,7 @@
 {
   "name": "check",
   "version": "0.15.2",
-  "port-version": 4,
+  "port-version": 5,
   "description": "A unit testing framework for C",
   "homepage": "https://github.com/libcheck/check",
   "license": "LGPL-2.1-only",

ports/libsbml/dependencies.diff

@@ -0,0 +1,133 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a8af3a4..3926b68 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -421,8 +421,9 @@ set(LIBSBML_XML_LIBRARY_LIBS)
+ if(WITH_EXPAT)
+
+     if(NOT TARGET EXPAT::EXPAT)
+-    find_package(EXPAT REQUIRED)
+     endif()
++    find_package(EXPAT NAMES expat REQUIRED)
++    set(EXPAT_LIBRARY expat::expat)
+
+     add_definitions( -DUSE_EXPAT )
+     list(APPEND SWIG_EXTRA_ARGS -DUSE_EXPAT)
+@@ -443,7 +444,8 @@ endif(WITH_EXPAT)
+ set(USE_LIBXML OFF)
+ if(WITH_LIBXML)
+
+-  find_package(LIBXML REQUIRED)
++  find_package(LIBXML NAMES LibXml2 REQUIRED)
++  set(LIBXML_LIBRARY LibXml2::LibXml2)
+
+   add_definitions( -DUSE_LIBXML )
+   list(APPEND SWIG_EXTRA_ARGS -DUSE_LIBXML)
+@@ -495,7 +497,9 @@ endif()
+ option(WITH_BZIP2    "Enable the use of bzip2 compression."  ${BZIP_INITIAL_VALUE})
+ set(USE_BZ2 OFF)
+ if(WITH_BZIP2)
+-  find_package(BZ2 REQUIRED)
++  if(NOT TARGET BZ2::BZ2)
++  endif()
++  find_package(BZip2 REQUIRED)
+   set(USE_BZ2 ON)
+   add_definitions( -DUSE_BZ2 )
+   list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
+@@ -521,6 +525,9 @@ Separate multiple directories using semicolons." )
+ # Locate zlib
+ #
+
++if(WITH_ZLIB)
++    find_package(ZLIB REQUIRED)
++endif()
+ set(ZLIB_INITIAL_VALUE)
+ if (NOT LIBZ_LIBRARY)
+ find_library(LIBZ_LIBRARY
+@@ -614,7 +621,6 @@ valid. It should contain the file zlib.h, but it does not.")
+ endif(WITH_ZLIB)
+
+ # install find scripts only for used dependencies
+-install(FILES ${LIBSBML_FIND_MODULES} DESTINATION share/cmake/Modules)
+
+ ###############################################################################
+ #
+@@ -671,7 +677,12 @@ if(WITH_CHECK)
+
+   enable_testing()
+
+-  find_package(CHECK REQUIRED)
++  find_package(CHECK NAMES check REQUIRED)
++  if(BUILD_SHARED_LIBS)
++    add_library(CHECK::CHECK ALIAS Check::checkShared)
++  else()
++    add_library(CHECK::CHECK ALIAS Check::check)
++  endif()
+
+   if (UNIX)
+       # setup valgrind
+@@ -1005,17 +1016,18 @@ install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
+ #
+
+ set (PRIVATE_LIBS "-lstdc++ -lm")
++set (PRIVATE_REQUIRES "")
+ if (WITH_ZLIB)
+-set (PRIVATE_LIBS "${LIBZ_LIBRARY} ${PRIVATE_LIBS}")
++    string(APPEND PRIVATE_REQUIRES " zlib")
+ endif()
+ if (WITH_BZIP2)
+-set (PRIVATE_LIBS "${LIBBZ_LIBRARY} ${PRIVATE_LIBS}")
++    string(APPEND PRIVATE_REQUIRES " bzip2")
+ endif()
+ if (WITH_LIBXML)
+-set (PRIVATE_LIBS "${LIBXML_LIBRARY} ${PRIVATE_LIBS}")
++    string(APPEND PRIVATE_REQUIRES " libxml-2.0")
+ endif()
+ if (WITH_EXPAT)
+-set (PRIVATE_LIBS "${LIBEXPAT_LIBRARY} ${PRIVATE_LIBS}")
++    string(APPEND PRIVATE_REQUIRES " expat")
+ endif()
+ if (WITH_XERCES)
+ set (PRIVATE_LIBS "${XERCES_LIBRARY} ${PRIVATE_LIBS}")
+@@ -1037,9 +1049,7 @@ if (WITH_XERCES)
+ file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Conflicts: xerces-c = 2.6.0\n")
+ endif()
+
+-if (WITH_LIBXML)
+-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Requires.private: libxml-2.0 >= 2.6.22\n")
+-endif()
++file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Requires.private: ${PRIVATE_REQUIRES}\n")
+
+ if (UNIX OR MINGW)
+ install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc"
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 79301a6..0957d29 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -311,7 +311,7 @@ if(WITH_BZIP2)
+         sbml/compress/bzfstream.h
+         sbml/compress/bzfstream.cpp
+         )
+-  set(LIBSBML_LIBS ${LIBSBML_LIBS} BZ2::BZ2)
++  set(LIBSBML_LIBS ${LIBSBML_LIBS} BZip2::BZip2)
+
+ endif()
+
+@@ -405,7 +405,7 @@ if(WITH_EXPAT)
+         sbml/xml/ExpatHandler.h
+         sbml/xml/ExpatParser.h
+     )
+-    set(LIBSBML_LIBS ${LIBSBML_LIBS} EXPAT::EXPAT)
++    set(LIBSBML_LIBS ${LIBSBML_LIBS} expat::expat)
+
+ endif(WITH_EXPAT)
+
+@@ -423,7 +423,7 @@ if(WITH_LIBXML)
+         sbml/xml/LibXMLParser.h
+         sbml/xml/LibXMLTranscode.h
+     )
+-    set(LIBSBML_LIBS ${LIBSBML_LIBS} LIBXML::LIBXML)
++    set(LIBSBML_LIBS ${LIBSBML_LIBS} LibXml2::LibXml2)
+
+ endif(WITH_LIBXML)
+

ports/libsbml/dirent.diff

@@ -0,0 +1,28 @@
+diff --git a/src/sbml/validator/test/tps/dirent.c b/src/sbml/validator/test/tps/dirent.c
+index beafc5e..48a60ca 100644
+--- a/src/sbml/validator/test/tps/dirent.c
++++ b/src/sbml/validator/test/tps/dirent.c
+@@ -1,3 +1,4 @@
++#if 0
+ /* /////////////////////////////////////////////////////////////////////////////
+  * File:    dirent.c
+  *
+@@ -239,3 +240,4 @@ struct dirent *readdir(DIR *dir)
+ }
+
+ /* ////////////////////////////////////////////////////////////////////////// */
++#endif
+diff --git a/src/sbml/validator/test/tps/dirent.h b/src/sbml/validator/test/tps/dirent.h
+index 4703aa2..8e4c29c 100644
+--- a/src/sbml/validator/test/tps/dirent.h
++++ b/src/sbml/validator/test/tps/dirent.h
+@@ -46,6 +46,9 @@
+
+ #ifndef SYNSOFT_UNIXEM_INCL_H_DIRENT
+ #define SYNSOFT_UNIXEM_INCL_H_DIRENT
++#include <dirent.h>
++#endif
++#if 0
+
+ #ifndef _SYNSOFT_DOCUMENTATION_SKIP_SECTION
+ # define SYNSOFT_UNIXEM_VER_H_DIRENT_MAJOR      2

ports/libsbml/libsbml-config.cmake

@@ -1,6 +1,6 @@
 include(CMakeFindDependencyMacro)
-find_dependency(libsbml-static CONFIG)
+find_dependency(@name@ CONFIG)
 if(NOT TARGET libsbml)
     add_library(libsbml INTERFACE IMPORTED)
-    target_link_libraries(libsbml INTERFACE libsbml-static)
+    target_link_libraries(libsbml INTERFACE $<TARGET_NAME:@name@>)
 endif()

ports/libsbml/no-docs.diff

@@ -0,0 +1,12 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 8ad678a..f856774 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1012,7 +1012,6 @@ set(DOCUMENTATION_FILES
+         VERSION.txt
+ )
+
+-install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
+
+ ###############################################################################
+ #