How to prevent FetchContent to patch source packages again?

ClausKlein · August 21, 2026, 8:54am

I have this code and it works fine to fetch a boost archive and apply needed patches. I also builds fine with my cmake workflow preset.

# ---- Add Boost source tar archive via FetchContent ----
include(FetchContent)
set(BOOST_PATCH_DIR "${CMAKE_CURRENT_SOURCE_DIR}/patches/${BOOST_VERSION}")
set(BOOST_PATCHES "${BOOST_PATCH_DIR}/TheBigBoost.patch")

FetchContent_Declare(
    Boost
    URL ${BOOST_URL}
    URL_HASH SHA256=${BOOST_URL_SHA256}
    DOWNLOAD_EXTRACT_TIMESTAMP ON
    PATCH_COMMAND git apply -p0 ${BOOST_PATCHES}
    SYSTEM
    ${EXCLUDE_FROM_ALL}
)

FetchContent_MakeAvailable(Boost)
set(BOOST_SOURCE ${Boost_SOURCE_DIR})
message(STATUS "Boost_SOURCE_DIR=${Boost_SOURCE_DIR}")

# TODO(CK): should be a function instead use of BOOST_SOURCE and BOOST_VERSION
include(cmake/CheckBoostVersion.cmake)
message(STATUS "Boost found: ${BOOST_VERSION} ${BOOST_SOURCE}")

# ...

But if I run `cmake -L .` in binary directory, or if I touch my `CMakeLists.txt` and run `ninja`, this happens:

root@06bf603b8cf4:/src/build/Release# cmake -L .
-- CXXFLAGS=-stdlib=libc++ -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=0
'clang++' '-print-file-name=libc++.modules.json'
-- CMAKE_CXX_STDLIB_MODULES_JSON=/usr/lib/x86_64-linux-gnu/libc++.modules.json
-- CMAKE_CXX_STDLIB_MODULES_JSON=/usr/lib/x86_64-linux-gnu/libc++.modules.json
CMake Warning (uninitialized) at CMakeLists.txt:184 (if):
  uninitialized variable 'CPM_SOURCE_CACHE'


error: patch failed: build/Release/_deps/boost-src/tools/cmake/include/BoostInstall.cmake:337
error: build/Release/_deps/boost-src/tools/cmake/include/BoostInstall.cmake: patch does not apply
error: patch failed: build/Release/_deps/boost-src/tools/cmake/include/BoostRoot.cmake:123
error: build/Release/_deps/boost-src/tools/cmake/include/BoostRoot.cmake: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/serialization/CMakeLists.txt:6
error: build/Release/_deps/boost-src/libs/serialization/CMakeLists.txt: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/any/CMakeLists.txt:2
error: build/Release/_deps/boost-src/libs/any/CMakeLists.txt: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/conversion/CMakeLists.txt:4
error: build/Release/_deps/boost-src/libs/conversion/CMakeLists.txt: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/dll/CMakeLists.txt:5
error: build/Release/_deps/boost-src/libs/dll/CMakeLists.txt: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/lexical_cast/CMakeLists.txt:3
error: build/Release/_deps/boost-src/libs/lexical_cast/CMakeLists.txt: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/pfr/CMakeLists.txt:4
error: build/Release/_deps/boost-src/libs/pfr/CMakeLists.txt: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/type_index/CMakeLists.txt:4
error: build/Release/_deps/boost-src/libs/type_index/CMakeLists.txt: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/lexical_cast/include/boost/lexical_cast/detail/lcast_precision.hpp:10
error: build/Release/_deps/boost-src/libs/lexical_cast/include/boost/lexical_cast/detail/lcast_precision.hpp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/lexical_cast/include/boost/lexical_cast/detail/lcast_unsigned_converters.hpp:20
error: build/Release/_deps/boost-src/libs/lexical_cast/include/boost/lexical_cast/detail/lcast_unsigned_converters.hpp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/pfr/include/boost/pfr/detail/io.hpp:51
error: build/Release/_deps/boost-src/libs/pfr/include/boost/pfr/detail/io.hpp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/stacktrace/CMakeLists.txt:3
error: build/Release/_deps/boost-src/libs/stacktrace/CMakeLists.txt: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/stacktrace/test/test.cpp:276
error: build/Release/_deps/boost-src/libs/stacktrace/test/test.cpp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/libbacktrace_impls.hpp:35
error: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/libbacktrace_impls.hpp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/addr_base.hpp:15
error: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/addr_base.hpp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/frame_unwind.ipp:50
error: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/frame_unwind.ipp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/addr2line_impls.hpp:164
error: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/addr2line_impls.hpp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/frame_msvc.ipp:402
error: build/Release/_deps/boost-src/libs/stacktrace/include/boost/stacktrace/detail/frame_msvc.ipp: patch does not apply
error: patch failed: build/Release/_deps/boost-src/libs/stacktrace/modules/boost_stacktrace_dump.cppm:15
error: build/Release/_deps/boost-src/libs/stacktrace/modules/boost_stacktrace_dump.cppm: patch does not apply
CMake Error at build/Release/CMakeFiles/fc-tmp/boost/patch.cmake:7 (execute_process):
  execute_process last command failed
Call Stack (most recent call first):
  /root/.local/share/pipx/venvs/cmake/lib/python3.12/site-packages/cmake/data/share/cmake-4.4/Modules/FetchContent.cmake:1766 (include)
  /root/.local/share/pipx/venvs/cmake/lib/python3.12/site-packages/cmake/data/share/cmake-4.4/Modules/FetchContent.cmake:1729 (__FetchContent_doStepDirect)
  /root/.local/share/pipx/venvs/cmake/lib/python3.12/site-packages/cmake/data/share/cmake-4.4/Modules/FetchContent.cmake:1620 (__FetchContent_populateDirect)
  /root/.local/share/pipx/venvs/cmake/lib/python3.12/site-packages/cmake/data/share/cmake-4.4/Modules/FetchContent.cmake:2160:EVAL:2 (__FetchContent_doPopulation)
  /root/.local/share/pipx/venvs/cmake/lib/python3.12/site-packages/cmake/data/share/cmake-4.4/Modules/FetchContent.cmake:2160 (cmake_language)
  /root/.local/share/pipx/venvs/cmake/lib/python3.12/site-packages/cmake/data/share/cmake-4.4/Modules/FetchContent.cmake:2401 (__FetchContent_Populate)
  CMakeLists.txt:223 (FetchContent_MakeAvailable)


-- Configuring incomplete, errors occurred!
-- Cache values
BOOST_BEAST_BUILD_EXAMPLES:BOOL=OFF
BOOST_BEAST_BUILD_FUZZERS:BOOL=OFF
BOOST_BEAST_BUILD_TESTS:BOOL=OFF
BOOST_BEAST_WARNINGS_AS_ERRORS:BOOL=OFF
BOOST_BUILD_ALL:BOOL=ON
BOOST_BUILD_TESTING:BOOL=TRUE
BOOST_CONTAINER_HEADER_ONLY:BOOL=TRUE
BOOST_CONTEXT_ABI:STRING=sysv
BOOST_CONTEXT_ARCHITECTURE:STRING=x86_64
BOOST_CONTEXT_ASM_SUFFIX:STRING=.S
BOOST_CONTEXT_ASSEMBLER:STRING=gas
BOOST_CONTEXT_BINARY_FORMAT:STRING=elf
BOOST_CONTEXT_IMPLEMENTATION:STRING=fcontext
BOOST_FILESYSTEM_DISABLE_ARC4RANDOM:BOOL=OFF
BOOST_FILESYSTEM_DISABLE_BCRYPT:BOOL=OFF
BOOST_FILESYSTEM_DISABLE_COPY_FILE_RANGE:BOOL=OFF
BOOST_FILESYSTEM_DISABLE_GETRANDOM:BOOL=OFF
BOOST_FILESYSTEM_DISABLE_SENDFILE:BOOL=OFF
BOOST_FILESYSTEM_DISABLE_STATX:BOOL=OFF
BOOST_FILESYSTEM_EMSCRIPTEN_USE_WASI:BOOL=OFF
BOOST_FILESYSTEM_NO_DEPRECATED:BOOL=OFF
BOOST_HEAP_BUILD_TESTS:BOOL=OFF
BOOST_HEAP_USE_FILE_SET:BOOL=OFF
BOOST_LOCKFREE_BUILD_TESTS:BOOL=OFF
BOOST_LOCKFREE_TESTS_STRESSTEST:BOOL=OFF
BOOST_LOCKFREE_USE_FILE_SET:BOOL=OFF
BOOST_MATH_BUILD_WITH_LEGACY_FUNCTIONS:BOOL=OFF
BOOST_MSM_BUILD_MRDOCS:BOOL=OFF
BOOST_MSM_TEST_NLOHMANN_JSON:BOOL=OFF
BOOST_OPENMETHOD_BUILD_EXAMPLES:BOOL=OFF
BOOST_OPENMETHOD_BUILD_TESTS:BOOL=OFF
BOOST_OPENMETHOD_MRDOCS_BUILD:BOOL=OFF
BOOST_OPENMETHOD_WARNINGS_AS_ERRORS:BOOL=OFF
BOOST_PROCESS_USE_STD_FS:BOOL=TRUE
BOOST_RANDOM_ENABLE_RANDOM_DEVICE:BOOL=ON
BOOST_REGEX_STANDALONE:BOOL=OFF
BOOST_SRC_DIR:STRING=/src/build/Release/_deps/boost-src/libs/beast/../..
BOOST_STACKTRACE_ENABLE_ADDR2LINE:BOOL=ON
BOOST_STACKTRACE_ENABLE_BACKTRACE:BOOL=OFF
BOOST_STACKTRACE_ENABLE_BASIC:BOOL=ON
BOOST_STACKTRACE_ENABLE_FROM_EXCEPTION:BOOL=ON
BOOST_STACKTRACE_ENABLE_NOOP:BOOL=ON
BOOST_STACKTRACE_ENABLE_WINDBG:BOOL=OFF
BOOST_STACKTRACE_ENABLE_WINDBG_CACHED:BOOL=OFF
BOOST_TEST_HEADERS_ONLY:BOOL=TRUE
BOOST_THREAD_THREADAPI:STRING=pthread
BOOST_URL:STRING=https://github.com/boostorg/boost/releases/download/boost-1.92.0/boost-1.92.0-cmake.7z
BOOST_URL_BUILD_EXAMPLES:BOOL=OFF
BOOST_URL_BUILD_FUZZERS:BOOL=OFF
BOOST_URL_BUILD_TESTS:BOOL=OFF
BOOST_URL_DISABLE_THREADS:BOOL=OFF
BOOST_URL_MRDOCS_BUILD:BOOL=OFF
BOOST_URL_SHA256:STRING=158852d45a7ce23de167a3dc2e57b04490829b233f06e835d5c81a65547ef68b
BOOST_URL_WARNINGS_AS_ERRORS:BOOL=OFF
BOOST_USE_MODULES:BOOL=ON
BOOST_USE_WINAPI_VERSION:STRING=
BOOST_UUID_LINK_LIBATOMIC:BOOL=ON
BUILD_SHARED_LIBS:BOOL=TRUE
BUILD_TESTING:BOOL=OFF
BoostPrettyPrinters_GDB:FILEPATH=BoostPrettyPrinters_GDB-NOTFOUND
Boost_NOWIDE_WERROR:BOOL=ON
CCACHE_BIN:FILEPATH=/usr/bin/ccache
CMAKE_BUILD_TYPE:STRING=Release
CMAKE_CXX_COMPILER_LAUNCHER:FILEPATH=/usr/bin/ccache
CMAKE_CXX_EXTENSIONS:BOOL=FALSE
CMAKE_CXX_STANDARD_REQUIRED:BOOL=TRUE
CMAKE_CXX_STDLIB_MODULES_JSON:FILEPATH=/usr/lib/x86_64-linux-gnu/libc++.modules.json
CMAKE_C_COMPILER_LAUNCHER:FILEPATH=/usr/bin/ccache
CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE
CMAKE_INSTALL_PREFIX:PATH=/src/stagedir
CMAKE_PREFIX_PATH:STRING=/src/stagedir
CMAKE_SKIP_INSTALL_RULES:BOOL=FALSE
FETCHCONTENT_BASE_DIR:PATH=/src/build/Release/_deps
FETCHCONTENT_FULLY_DISCONNECTED:BOOL=OFF
FETCHCONTENT_QUIET:BOOL=ON
FETCHCONTENT_SOURCE_DIR_BOOST:PATH=
FETCHCONTENT_UPDATES_DISCONNECTED:BOOL=OFF
FETCHCONTENT_UPDATES_DISCONNECTED_BOOST:BOOL=OFF
root@06bf603b8cf4:/src/build/Release#

ClausKlein · August 22, 2026, 12:02pm

@craig.scott Do you have any idea how to prevent this feature?

Or is this an issue?

ClausKlein · August 22, 2026, 3:09pm

One way I found to prevent this is:

message(STATUS "Boost found: ${BOOST_VERSION} ${BOOST_SOURCE}")
# TODO(CK): one possible workaround to not call the PATCH_COMMAND while each RERUN_CMAKE
set(FETCHCONTENT_SOURCE_DIR_BOOST
    "${Boost_SOURCE_DIR}"
    CACHE PATH
    "Boost patched source DIR"
    FORCE
)

craig.scott · August 22, 2026, 10:11pm

The behavior in your original post is not what I’d expect. I suggest you try to reduce it down to an absolutely minimal reproducer. Try it with different dependencies as well. In the process of doing that, I suspect you might find something about your project that is causing, or at least related to, the observed unexpected behavior.

ClausKlein · August 23, 2026, 1:40pm

It seems a site effect of import std; usage?

First try is this, but it should be a smaller MRE, I think:

ClausKlein · August 23, 2026, 5:37pm

No, it is independent of building `CXX_MODULES`.

But when the patches touches files/project used by the top-level project, then it happens!

here is my MRE: GitHub - ClausKlein/FetchContentTest · GitHub

Aiden.Woodruff · August 26, 2026, 7:34pm

Claus, would you include the CMakeUserPresets.json file in your reproducer? It is referenced by the GNUmakefile and README.md but seems to be missing.

ClausKlein · August 26, 2026, 7:54pm

It is included under cmake subdir and should be creates as a symbolic link from gmake:

iMac:FetchContentTest clausklein$ gmake -n
ln -fs cmake/CMakeUserPresets.json CMakeUserPresets.json
cmake --preset release --fresh --log-level=VERBOSE
touch .init
ninja -C build/release build/release/compile_commands.json
if [ "X" != "Xbuild/release/compile_commands.json" ] ; then \
	ln -fs build/release/compile_commands.json compile_commands.json; \
fi
cmake --workflow --preset release
iMac:FetchContentTest clausklein$

ClausKlein · August 26, 2026, 8:02pm

It happens also without preset and makefile:

iMac:FetchContentTest clausklein$ CC=gcc-16 CXX=g++-16 cmake -S . -B build -G Ninja -D CMAKE_CXX_STANDARD=23 -D CMAKE_BUILD_TYPE=Release -D CMAKE_PREFIX_PATH="${HOME}/.local" --log-level=VERBOSE --fresh
-- The CXX compiler identification is GNU 16.2.0
-- The C compiler identification is GNU 16.2.0
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - no
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - no
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/local/bin/g++-16 - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - no
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - no
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/local/bin/gcc-16 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Executing download step for boost-cmake
-- verifying file...
       file='/Users/clausklein/cmake/FetchContentTest/build/_deps/boost-cmake-tmp/v1.92.0-rc3.tar.gz'
-- File already exists and hash match (skip download):
  file='/Users/clausklein/cmake/FetchContentTest/build/_deps/boost-cmake-tmp/v1.92.0-rc3.tar.gz'
  SHA256='bbcd4de95670755b39f874ae7efe307beef19c6b53c9736c037ebd794e10bab0'
-- extracting...
     src='/Users/clausklein/cmake/FetchContentTest/build/_deps/boost-cmake-tmp/v1.92.0-rc3.tar.gz'
     dst='/Users/clausklein/cmake/FetchContentTest/build/_deps/boost-cmake-src'
-- extracting... [tar xf]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
-- Executing update step for boost-cmake
-- Executing patch step for boost-cmake
'patch' '--backup' '--forward' '-p1' '-i' '/Users/clausklein/cmake/FetchContentTest/mypatch.patch'
patching file 'examples/regex.cpp'
CMake Warning at build/_deps/boost-cmake-src/cmake/prelude.cmake:36 (message):
  This CMake file has to be included before first project() command call!
Call Stack (most recent call first):
  build/_deps/boost-cmake-src/examples/CMakeLists.txt:3 (include)


-- Configuring done (3.2s)
-- Generating done (0.0s)
-- Build files have been written to: /Users/clausklein/cmake/FetchContentTest/build
iMac:FetchContentTest clausklein$ ninja -C build/ 
ninja: Entering directory `build/'
[0/1] Re-running CMake...
patching file 'examples/regex.cpp'
Ignoring previously applied (or reversed) patch.
1 out of 1 hunks ignored--saving rejects to 'examples/regex.cpp.rej'
CMake Error at build/CMakeFiles/fc-tmp/boost-cmake/patch.cmake:7 (execute_process):
  execute_process last command failed
Call Stack (most recent call first):
  /Users/clausklein/.local/share/cmake-4.4/Modules/FetchContent.cmake:1766 (include)
  /Users/clausklein/.local/share/cmake-4.4/Modules/FetchContent.cmake:1729 (__FetchContent_doStepDirect)
  /Users/clausklein/.local/share/cmake-4.4/Modules/FetchContent.cmake:1620 (__FetchContent_populateDirect)
  /Users/clausklein/.local/share/cmake-4.4/Modules/FetchContent.cmake:2160:EVAL:2 (__FetchContent_doPopulation)
  /Users/clausklein/.local/share/cmake-4.4/Modules/FetchContent.cmake:2160 (cmake_language)
  /Users/clausklein/.local/share/cmake-4.4/Modules/FetchContent.cmake:2401 (__FetchContent_Populate)
  CMakeLists.txt:42 (FetchContent_MakeAvailable)


-- Configuring incomplete, errors occurred!
FAILED: [code=1] build.ninja /Users/clausklein/cmake/FetchContentTest/build/cmake_install.cmake /Users/clausklein/cmake/FetchContentTest/build/_deps/boost-cmake-build/cmake_install.cmake /Users/clausklein/cmake/FetchContentTest/build/CTestTestfile.cmake /Users/clausklein/cmake/FetchContentTest/build/_deps/boost-cmake-build/CTestTestfile.cmake 
/Users/clausklein/.local/bin/cmake --regenerate-during-build -S/Users/clausklein/cmake/FetchContentTest -B/Users/clausklein/cmake/FetchContentTest/build
ninja: error: rebuilding 'build.ninja': subcommand failed
iMac:FetchContentTest clausklein$

Aiden.Woodruff · August 26, 2026, 8:41pm

I am able to reproduce by running the following steps:

cmake -B build --log-level=VERBOSE --fresh
cmake --build build
touch CMakeLists.txt
cmake --build build.

The --log-level=VERBOSE is required. This seems like a legitimate bug?

ClausKlein · August 27, 2026, 7:39am

Yes, I can confirm, it is a site effect of cmake -L build --log-level=VERBOSE

Aiden.Woodruff · August 27, 2026, 2:11pm

Claus, I opened a CMake issue here: https://gitlab.kitware.com/cmake/cmake/-/work_items/28055

ClausKlein · August 27, 2026, 7:27pm

Thanks!
It fails caused by the stamp file is NOT newer than patch file after it was called with --log-level set the first time:

function(__FetchContent_doStepDirect)
  set(noValueOptions )
  set(singleValueOptions
    SCRIPT_FILE
    STAMP_FILE
  )
  set(multiValueOptions
    DEPENDS
  )
  cmake_parse_arguments(PARSE_ARGV 0 arg
    "${noValueOptions}" "${singleValueOptions}" "${multiValueOptions}"
  )

  if(NOT EXISTS ${arg_STAMP_FILE})
    set(do_step YES)
  else()
    set(do_step NO)
    foreach(dep_file IN LISTS arg_DEPENDS arg_SCRIPT_FILE)
      if(NOT EXISTS "${arg_STAMP_FILE}" OR
        NOT EXISTS "${dep_file}" OR
        NOT "${arg_STAMP_FILE}" IS_NEWER_THAN "${dep_file}")
        set(do_step YES)
        break()
      endif()
    endforeach()
  endif()

  if(do_step)
    include(${arg_SCRIPT_FILE})
    file(TOUCH "${arg_STAMP_FILE}")
  endif()
endfunction()

ClausKlein · August 30, 2026, 5:37pm

After locking into the ExternalProject and FetchContent code, I decided to use CMAKE_MESSAGE_LOG_LEVEL instead to use --log-level command line option.

Then the log-level is consistent in each cmake preset workflow step and everything works fine.

How to prevent FetchContent to patch source packages again?

But if I run cmake -L . in binary directory, or if I touch my CMakeLists.txt and run ninja, this happens:

One way I found to prevent this is:

No, it is independent of building CXX_MODULES.

But when the patches touches files/project used by the top-level project, then it happens!

But if I run `cmake -L .` in binary directory, or if I touch my `CMakeLists.txt` and run `ninja`, this happens:

No, it is independent of building `CXX_MODULES`.