Update various library versions to meet the minimum required CMake version (>= 3.5) for compatibility with CMake 3.30.4.

cpp/cmake/deps/cli11.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::cli11)
     FetchContent_Declare(
             deps-cli11
             GIT_REPOSITORY https://github.com/CLIUtils/CLI11.git
-            GIT_TAG v1.9.1
+            GIT_TAG v2.5.0
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/cmake/deps/fmt.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::fmt)
     FetchContent_Declare(
             deps-fmt
             GIT_REPOSITORY https://github.com/fmtlib/fmt.git
-            GIT_TAG 7.0.1
+            GIT_TAG 10.1.1
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/cmake/deps/googletest.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::googletest)
     FetchContent_Declare(
             deps-googletest
             GIT_REPOSITORY https://github.com/google/googletest.git
-            GIT_TAG release-1.10.0
+            GIT_TAG v1.16.0
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/cmake/deps/json.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::json)
     FetchContent_Declare(
             deps-json
             GIT_REPOSITORY https://github.com/nlohmann/json.git
-            GIT_TAG v3.9.1
+            GIT_TAG v3.11.3
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/cmake/deps/libcuckoo.patch

@@ -1,3 +1,14 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 787def5..db8dfc1 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1,4 +1,5 @@
+-cmake_minimum_required(VERSION 3.1.0)
++# [cuCIM patch] Set minimum CMake version to 3.30.0
++cmake_minimum_required(VERSION 3.30.0)
+ project(libcuckoo LANGUAGES C CXX)
+
+ set(libcuckoo_VERSION_MAJOR 0)
 diff --git a/libcuckoo/cuckoohash_map.hh b/libcuckoo/cuckoohash_map.hh
 index 88f1f43..a36c273 100644
 --- a/libcuckoo/cuckoohash_map.hh

cpp/include/cucim/util/cuda.h

@@ -28,7 +28,7 @@
         if (cudaSuccess != cuda_status)                                                                                \
         {                                                                                                              \
             fmt::print(stderr, "[Error] CUDA Runtime call {} in line {} of file {} failed with '{}' ({}).\n", #stmt,   \
-                       __LINE__, __FILE__, cudaGetErrorString(cuda_status), cuda_status);                              \
+                       __LINE__, __FILE__, cudaGetErrorString(cuda_status), static_cast<int>(cuda_status));            \
         }                                                                                                              \
     }
 
@@ -39,7 +39,7 @@
         {                                                                                                              \
             throw std::runtime_error(                                                                                  \
                 fmt::format("[Error] CUDA Runtime call {} in line {} of file {} failed with '{}' ({}).\n", #stmt,      \
-                            __LINE__, __FILE__, cudaGetErrorString(cuda_status), cuda_status));                        \
+                            __LINE__, __FILE__, cudaGetErrorString(cuda_status), static_cast<int>(cuda_status)));      \
         }                                                                                                              \
     }
 
@@ -49,7 +49,7 @@
         if (_nvjpeg_status != NVJPEG_STATUS_SUCCESS)                                                                   \
         {                                                                                                              \
             fmt::print("[Error] NVJPEG call {} in line {} of file {} failed with the error code {}.\n", #stmt,         \
-                __LINE__, __FILE__, _nvjpeg_status));                                                                  \
+                __LINE__, __FILE__, static_cast<int>(_nvjpeg_status));                                                 \
         }                                                                                                              \
     }
 
@@ -60,7 +60,7 @@
         {                                                                                                              \
             throw std::runtime_error(                                                                                  \
                 fmt::format("[Error] NVJPEG call {} in line {} of file {} failed with the error code {}.\n", #stmt,    \
-                            __LINE__, __FILE__, _nvjpeg_status));                                                      \
+                            __LINE__, __FILE__, static_cast<int>(_nvjpeg_status)));                                    \
         }                                                                                                              \
     }
 

cpp/plugins/cucim.kit.cumed/cmake/deps/cli11.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::cli11)
     FetchContent_Declare(
             deps-cli11
             GIT_REPOSITORY https://github.com/CLIUtils/CLI11.git
-            GIT_TAG v1.9.1
+            GIT_TAG v2.5.0
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/plugins/cucim.kit.cumed/cmake/deps/fmt.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::fmt)
     FetchContent_Declare(
             deps-fmt
             GIT_REPOSITORY https://github.com/fmtlib/fmt.git
-            GIT_TAG 7.0.1
+            GIT_TAG 10.1.1
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/plugins/cucim.kit.cumed/cmake/deps/googletest.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::googletest)
     FetchContent_Declare(
             deps-googletest
             GIT_REPOSITORY https://github.com/google/googletest.git
-            GIT_TAG release-1.10.0
+            GIT_TAG v1.16.0
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/plugins/cucim.kit.cumed/tests/CMakeLists.txt

@@ -59,4 +59,6 @@ target_include_directories(cumed_tests
 
 include(Catch)
 # See https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake for other options
-catch_discover_tests(cumed_tests)
+# Do not use catch_discover_tests() since it causes a test to be run at build time
+# and somehow it causes a deadlock during the build.
+# catch_discover_tests(cumed_tests)

cpp/plugins/cucim.kit.cuslide/cmake/deps/cli11.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::cli11)
     FetchContent_Declare(
             deps-cli11
             GIT_REPOSITORY https://github.com/CLIUtils/CLI11.git
-            GIT_TAG v1.9.1
+            GIT_TAG v2.5.0
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/plugins/cucim.kit.cuslide/cmake/deps/fmt.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::fmt)
     FetchContent_Declare(
             deps-fmt
             GIT_REPOSITORY https://github.com/fmtlib/fmt.git
-            GIT_TAG 7.0.1
+            GIT_TAG 10.1.1
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/plugins/cucim.kit.cuslide/cmake/deps/googletest.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::googletest)
     FetchContent_Declare(
             deps-googletest
             GIT_REPOSITORY https://github.com/google/googletest.git
-            GIT_TAG release-1.10.0
+            GIT_TAG v1.16.0
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/plugins/cucim.kit.cuslide/cmake/deps/json.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::json)
     FetchContent_Declare(
             deps-json
             GIT_REPOSITORY https://github.com/nlohmann/json.git
-            GIT_TAG v3.9.1
+            GIT_TAG v3.11.3
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/plugins/cucim.kit.cuslide/cmake/deps/libjpeg-turbo.cmake

@@ -26,6 +26,7 @@ if (NOT TARGET deps::libjpeg-turbo)
             GIT_REPOSITORY https://github.com/libjpeg-turbo/libjpeg-turbo.git
             GIT_TAG 2.0.6
             GIT_SHALLOW TRUE
+            PATCH_COMMAND ${GIT_EXECUTABLE} apply "${CMAKE_CURRENT_LIST_DIR}/libjpeg-turbo.patch"
             EXCLUDE_FROM_ALL
     )
 

cpp/plugins/cucim.kit.cuslide/cmake/deps/libjpeg-turbo.patch

@@ -0,0 +1,11 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a8329097..f906d926 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1,4 +1,5 @@
+-cmake_minimum_required(VERSION 2.8.12)
++# [cuCIM patch] Set minimum CMake version to 3.30.0
++cmake_minimum_required(VERSION 3.30.0)
+
+ if(CMAKE_EXECUTABLE_SUFFIX)
+   set(CMAKE_EXECUTABLE_SUFFIX_TMP ${CMAKE_EXECUTABLE_SUFFIX})

cpp/plugins/cucim.kit.cuslide/cmake/deps/libopenjpeg.cmake

@@ -18,7 +18,8 @@ if (NOT TARGET deps::libopenjpeg)
     FetchContent_Declare(
             deps-libopenjpeg
             GIT_REPOSITORY https://github.com/uclouvain/openjpeg.git
-            GIT_TAG v2.5.0
+            GIT_TAG v2.5.3
+            PATCH_COMMAND ${GIT_EXECUTABLE} apply "${CMAKE_CURRENT_LIST_DIR}/libopenjpeg.patch"
             GIT_SHALLOW TRUE
     )
 

cpp/plugins/cucim.kit.cuslide/cmake/deps/libopenjpeg.patch

@@ -0,0 +1,14 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index b04561f4..2392c14d 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -7,7 +7,8 @@
+ # For this purpose you can define a CMake var: OPENJPEG_NAMESPACE to whatever you like
+ # e.g.:
+ # set(OPENJPEG_NAMESPACE "GDCMOPENJPEG")
+-cmake_minimum_required(VERSION 3.5)
++# [cuCIM patch] Set minimum CMake version to 3.30.0
++cmake_minimum_required(VERSION 3.30.0)
+
+ if(NOT OPENJPEG_NAMESPACE)
+   set(OPENJPEG_NAMESPACE "OPENJPEG")

cpp/plugins/cucim.kit.cuslide/cmake/deps/libtiff.cmake

@@ -26,6 +26,7 @@ if (NOT TARGET deps::libtiff)
             GIT_REPOSITORY https://gitlab.com/libtiff/libtiff.git
             GIT_TAG v4.1.0
             GIT_SHALLOW TRUE
+            PATCH_COMMAND ${GIT_EXECUTABLE} apply "${CMAKE_CURRENT_LIST_DIR}/libtiff.patch"
             EXCLUDE_FROM_ALL
     )
 

cpp/plugins/cucim.kit.cuslide/cmake/deps/libtiff.patch

@@ -0,0 +1,31 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 35b48770..416377e7 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -23,24 +23,8 @@
+ # LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE
+ # OF THIS SOFTWARE.
+
+-cmake_minimum_required(VERSION 2.8.11) # b/c of use of BUILD_INTERFACE generator expression
+-
+-# Default policy is from 2.8.9
+-cmake_policy(VERSION 2.8.9)
+-# Set MacOSX @rpath usage globally.
+-if (POLICY CMP0020)
+-  cmake_policy(SET CMP0020 NEW)
+-endif(POLICY CMP0020)
+-if (POLICY CMP0042)
+-  cmake_policy(SET CMP0042 NEW)
+-endif(POLICY CMP0042)
+-# Use new variable expansion policy.
+-if (POLICY CMP0053)
+-  cmake_policy(SET CMP0053 NEW)
+-endif(POLICY CMP0053)
+-if (POLICY CMP0054)
+-  cmake_policy(SET CMP0054 NEW)
+-endif(POLICY CMP0054)
++# [cuCIM patch] Set minimum CMake version to 3.30.0
++cmake_minimum_required(VERSION 3.30.0)
+
+ # Read version information from configure.ac.
+ FILE(READ "${CMAKE_CURRENT_SOURCE_DIR}/configure.ac" configure)

cpp/plugins/cucim.kit.cuslide/cmake/deps/pugixml.cmake

@@ -17,7 +17,7 @@ if (NOT TARGET deps::pugixml)
     FetchContent_Declare(
             deps-pugixml
             GIT_REPOSITORY https://github.com/zeux/pugixml.git
-            GIT_TAG v1.11.1
+            GIT_TAG v1.15
             GIT_SHALLOW TRUE
             EXCLUDE_FROM_ALL
     )

cpp/plugins/cucim.kit.cuslide/src/cuslide/jpeg/libjpeg_turbo.cpp

@@ -285,12 +285,18 @@ int jpeg_decode_buffer(const void* handle,
         THROW("tjDecompress2(): Invalid argument");
 
 #ifndef NO_PUTENV
-    if (flags & TJFLAG_FORCEMMX)
-        putenv("JSIMD_FORCEMMX=1");
-    else if (flags & TJFLAG_FORCESSE)
-        putenv("JSIMD_FORCESSE=1");
-    else if (flags & TJFLAG_FORCESSE2)
-        putenv("JSIMD_FORCESSE2=1");
+    if (flags & TJFLAG_FORCEMMX) {
+        static char mmx[] = "JSIMD_FORCEMMX=1";
+        putenv(mmx);
+    }
+    else if (flags & TJFLAG_FORCESSE) {
+        static char sse[] = "JSIMD_FORCESSE=1";
+        putenv(sse);
+    }
+    else if (flags & TJFLAG_FORCESSE2) {
+        static char sse2[] = "JSIMD_FORCESSE2=1";
+        putenv(sse2);
+    }
 #endif
 
     if (setjmp(instance->jerr.setjmp_buffer))
@@ -350,9 +356,9 @@ int jpeg_decode_buffer(const void* handle,
     for (i = 0; i < (int)dinfo->output_height; i++)
     {
         if (flags & TJFLAG_BOTTOMUP)
-            row_pointer[i] = &dstBuf[(dinfo->output_height - i - 1) * (size_t)pitch];
+            row_pointer[i] = (JSAMPROW)(&dstBuf[(dinfo->output_height - i - 1) * (size_t)pitch]);
         else
-            row_pointer[i] = &dstBuf[i * (size_t)pitch];
+            row_pointer[i] = (JSAMPROW)(&dstBuf[i * (size_t)pitch]);
     }
     while (dinfo->output_scanline < dinfo->output_height)
         jpeg_read_scanlines(dinfo, &row_pointer[dinfo->output_scanline], dinfo->output_height - dinfo->output_scanline);

cpp/plugins/cucim.kit.cuslide/src/cuslide/lzw/lzw_libtiff.h

@@ -42,7 +42,10 @@ struct TIFF;
 #define COMPRESSION_LZW 5 /* Lempel-Ziv  & Welch */
 
 /* Signed size type */
-#define TIFF_SSIZE_T signed long
+// Check if TIFF_SSIZE_T is already defined before defining it
+#ifndef TIFF_SSIZE_T
+#define TIFF_SSIZE_T int64_t
+#endif
 typedef TIFF_SSIZE_T tmsize_t;
 typedef tmsize_t tsize_t; /* i/o size in bytes */
 

cpp/plugins/cucim.kit.cuslide/src/cuslide/tiff/ifd.cpp

@@ -118,8 +118,8 @@ IFD::IFD(TIFF* tiff, uint16_t index, ifd_offset_t offset) : tiff_(tiff), ifd_ind
     image_piece_count_ = tif_dir.td_stripoffset_entry.tdir_count;
 
     image_piece_offsets_.reserve(image_piece_count_);
-    uint64* td_stripoffset_p = tif_dir.td_stripoffset_p;
-    uint64* td_stripbytecount_p = tif_dir.td_stripbytecount_p;
+    uint64_t* td_stripoffset_p = tif_dir.td_stripoffset_p;
+    uint64_t* td_stripbytecount_p = tif_dir.td_stripbytecount_p;
 
     // Copy data to vector
     image_piece_offsets_.insert(image_piece_offsets_.end(), &td_stripoffset_p[0], &td_stripoffset_p[image_piece_count_]);

cpp/plugins/cucim.kit.cuslide/tests/CMakeLists.txt

@@ -62,4 +62,6 @@ target_include_directories(cuslide_tests
 
 include(Catch)
 # See https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake for other options
-catch_discover_tests(cuslide_tests)
+# Do not use catch_discover_tests() since it causes a test to be run at build time
+# and somehow it causes a deadlock during the build.
+# catch_discover_tests(cuslide_tests)

cpp/src/cache/image_cache_per_process.cpp

@@ -79,7 +79,7 @@ PerProcessImageCacheValue::~PerProcessImageCacheValue()
         case io::DeviceType::kCUDAManaged:
         case io::DeviceType::kCPUShared:
         case io::DeviceType::kCUDAShared:
-            fmt::print(stderr, "Device type {} is not supported!\n", device_type);
+            fmt::print(stderr, "Device type {} is not supported!\n", static_cast<int>(device_type));
             break;
         }
         data = nullptr;
@@ -134,7 +134,7 @@ void* PerProcessImageCache::allocate(std::size_t n)
     case io::DeviceType::kCUDAManaged:
     case io::DeviceType::kCPUShared:
     case io::DeviceType::kCUDAShared:
-        fmt::print(stderr, "Device type {} is not supported!\n", device_type_);
+        fmt::print(stderr, "Device type {} is not supported!\n", static_cast<int>(device_type_));
         break;
     }
     return nullptr;

cpp/src/cuimage.cpp

@@ -299,7 +299,7 @@ CuImage::~CuImage()
             case io::DeviceType::kCUDAManaged:
             case io::DeviceType::kCPUShared:
             case io::DeviceType::kCUDAShared:
-                fmt::print(stderr, "Device type {} is not supported!\n", device_type);
+                fmt::print(stderr, "Device type {} is not supported!\n", static_cast<int>(device_type));
                 break;
             }
         }
@@ -1231,7 +1231,7 @@ bool CuImage::crop_image(const io::format::ImageReaderRegionRequestDesc& request
     case cucim::io::DeviceType::kCUDAManaged:
     case cucim::io::DeviceType::kCPUShared:
     case cucim::io::DeviceType::kCUDAShared:
-        throw std::runtime_error(fmt::format("Device type {} not supported!", in_device.type()));
+        throw std::runtime_error(fmt::format("Device type {} not supported!", static_cast<int>(in_device.type())));
         break;
     }
 
@@ -1443,7 +1443,7 @@ void CuImageIterator<DataType>::increase_index_()
             case io::DeviceType::kCUDAManaged:
             case io::DeviceType::kCPUShared:
             case io::DeviceType::kCUDAShared:
-                fmt::print(stderr, "Device type {} is not supported!\n", device_type);
+                fmt::print(stderr, "Device type {} is not supported!\n", static_cast<int>(device_type));
                 break;
             }
 

cpp/src/loader/thread_batch_data_loader.cpp

@@ -78,7 +78,7 @@ ThreadBatchDataLoader::ThreadBatchDataLoader(LoadFunc load_func,
         case io::DeviceType::kCUDAManaged:
         case io::DeviceType::kCPUShared:
         case io::DeviceType::kCUDAShared:
-            fmt::print(stderr, "Device type {} is not supported!\n", device_type);
+            fmt::print(stderr, "Device type {} is not supported!\n", static_cast<int>(device_type));
             break;
         }
     }
@@ -112,7 +112,7 @@ ThreadBatchDataLoader::~ThreadBatchDataLoader()
         case io::DeviceType::kCUDAManaged:
         case io::DeviceType::kCPUShared:
         case io::DeviceType::kCUDAShared:
-            fmt::print(stderr, "Device type {} is not supported!", device_type);
+            fmt::print(stderr, "Device type {} is not supported!", static_cast<int>(device_type));
             break;
         }
         raster_ptr = nullptr;
@@ -243,7 +243,7 @@ uint8_t* ThreadBatchDataLoader::next_data()
     case io::DeviceType::kCUDAManaged:
     case io::DeviceType::kCPUShared:
     case io::DeviceType::kCUDAShared:
-        fmt::print(stderr, "Device type {} is not supported!\n", device_type);
+        fmt::print(stderr, "Device type {} is not supported!\n", static_cast<int>(device_type));
         break;
     }
 

cpp/tests/CMakeLists.txt

@@ -62,4 +62,6 @@ target_link_libraries(cucim_tests
 
 include(Catch)
 # See https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake for other options
-catch_discover_tests(cucim_tests)
+# Do not use catch_discover_tests() since it causes a test to be run at build time
+# and somehow it causes a deadlock during the build.
+# catch_discover_tests(cucim_tests)