I'm seeing the same issue. If I choose "no" at the patch reverse step, the build fails because the patch fails to apply. If I choose "yes", then the patch is reversed and the library is no longer patched the way I need. It might be good to set a cache variable tracking each patch that has been applied and then skipping that patch on subsequent passes.

For anyone else who finds this, here's my workaround:

if (NOT TRACKTION_ENGINE_PATCHED) 
  set(TRACKTION_ENGINE_PATCHED TRUE CACHE INTERNAL "Whether to apply patches to Tracktion Engine")
  CPMAddPackage(
    NAME TracktionEngine
    GITHUB_REPOSITORY Tracktion/tracktion_engine
    VERSION 3.0
    SOURCE_DIR ${DEPS_DIR}/tracktion_engine
    # Prevent Tracktion Engine from compiling its examples.
    PATCHES "${CMAKE_CURRENT_SOURCE_DIR}/cmake/tracktion_engine.patch"
  )
else()
  CPMAddPackage(
    NAME TracktionEngine
    GITHUB_REPOSITORY Tracktion/tracktion_engine
    VERSION 3.0
    SOURCE_DIR ${DEPS_DIR}/tracktion_engine
  )
endif()

Have the same issue. Hope this gets fixed soon!

The workaround works only when no CPM caching is used. Otherwise probably it needs to do something more reliable, like checking whether it was just freshly downloaded or not.

Hmmm...it seems to work for me with CPM caching on (unless I'm misunderstanding what CPM caching does). In my project, I've set set(CPM_SOURCE_CACHE "${CMAKE_CURRENT_SOURCE_DIR}/deps"). On the first run, it downloads the package, applies my patch and sets my custom CMake cache variable. On subsequent runs, CPM doesn't re-download the package or apply the patch and my app builds as expected. Its possible for my custom CMake cache variable to get out of sync with the file system if the dependency cache is deleted but that CMake variable is not removed. I use a clean script to ensure both get removed.

My work around is definitely less than ideal but should work; though I may be misunderstanding something.

Could something like this be considered for a fix?

diff --git a/CMake/Modules/CPM.cmake b/CMake/Modules/CPM.cmake
index e3b1bfbda3..7ee7e5798a 100644
--- a/CMake/Modules/CPM.cmake
+++ b/CMake/Modules/CPM.cmake
@@ -765,8 +765,6 @@ function(CPMAddPackage)
     set(CPM_FETCHCONTENT_BASE_DIR ${CMAKE_BINARY_DIR}/_deps)
   endif()
 
-  cpm_add_patches(${CPM_ARGS_PATCHES})
-
   if(DEFINED CPM_ARGS_DOWNLOAD_COMMAND)
     list(APPEND CPM_ARGS_UNPARSED_ARGUMENTS DOWNLOAD_COMMAND ${CPM_ARGS_DOWNLOAD_COMMAND})
   elseif(DEFINED CPM_ARGS_SOURCE_DIR)
@@ -819,14 +817,9 @@ function(CPMAddPackage)
       )
       cpm_get_fetch_properties("${CPM_ARGS_NAME}")
 
-      if(DEFINED CPM_ARGS_GIT_TAG AND NOT (PATCH_COMMAND IN_LIST CPM_ARGS_UNPARSED_ARGUMENTS))
-        # warn if cache has been changed since checkout
-        cpm_check_git_working_dir_is_clean(${download_directory} ${CPM_ARGS_GIT_TAG} IS_CLEAN)
-        if(NOT ${IS_CLEAN})
-          message(
-            WARNING "${CPM_INDENT} Cache for ${CPM_ARGS_NAME} (${download_directory}) is dirty"
-          )
-        endif()
+      # Only apply patches if the source directory doesn't exist, meaning it's a fresh checkout
+      if(NOT EXISTS "${${CPM_ARGS_NAME}_SOURCE_DIR}")
+        cpm_add_patches(${CPM_ARGS_PATCHES})
       endif()
 
       cpm_add_subdirectory(

The following does NOT work reliably, instead the fix by @BohdanBuinich should be used.

I changed some code in CPM which fixes this issue for me. The main idea is checking first if the patch is reversible which (hopefully) is only the case if the patch had been applied previously. Command is taken from here: https://stackoverflow.com/questions/48167884/check-if-git-apply-was-already-applied

I also use git apply instead of the legacy (?) patch CLI

function(cpm_add_patches)
    (...)
    # Convert to absolute path for use with patch file command.
    get_filename_component(PATCH_FILE "${PATCH_FILE}" ABSOLUTE)

    execute_process(COMMAND "${GIT_EXECUTABLE}" "apply" "--reverse" "--check" "-p1" "${PATCH_FILE}"
        RESULT_VARIABLE apply_reverse
    )

    if (NOT apply_reverse EQUAL 0) # if a reverse patch would NOT be succesful
        # The first patch entry must be preceded by "PATCH_COMMAND" while the following items are
        # preceded by "&&".
        if(first_item)
          set(first_item False)
          list(APPEND temp_list "PATCH_COMMAND")
        else()
          list(APPEND temp_list "&&")
        endif()
        # Add the patch command to the list
        list(APPEND temp_list "${GIT_EXECUTABLE}" "apply" "-p1" "${PATCH_FILE}")
    endif()
    (...)

Any update? 😥