diff --git a/builtins/cfitsio/CMakeLists.txt b/builtins/cfitsio/CMakeLists.txt
index f179721885b27..d098a1d57d38b 100644
--- a/builtins/cfitsio/CMakeLists.txt
+++ b/builtins/cfitsio/CMakeLists.txt
@@ -24,6 +24,8 @@ endif()
 # flag required only on Windows, on old alma paltforms it make troubles
 if(WIN32)
   set(patch_args --ignore-whitespace)
+  # delete the source directory to make sure there is no conflict with the git apply command
+  execute_process(COMMAND ${CMAKE_COMMAND} -E remove_directory ${CFITSIO_PREFIX})
 endif()
 
 ExternalProject_Add(
@@ -48,7 +50,7 @@ ExternalProject_Add(
                 ${CMAKE_CURRENT_SOURCE_DIR}/no-fortran-wrapper.diff
   BUILD_COMMAND ${CMAKE_COMMAND} --build . ${CFITSIO_BUILD_COMMAND_FLAGS}
   INSTALL_COMMAND ${CMAKE_COMMAND} --build . ${CFITSIO_BUILD_COMMAND_FLAGS} --target install
-  LOG_DOWNLOAD 1 LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
+  LOG_PATCH 1 LOG_DOWNLOAD 1 LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
   BUILD_BYPRODUCTS ${CFITSIO_LIBRARIES}
   TIMEOUT 600
 )
diff --git a/builtins/gl2ps/CMakeLists.txt b/builtins/gl2ps/CMakeLists.txt
index 5ab968966276b..66bbd95d6d82b 100644
--- a/builtins/gl2ps/CMakeLists.txt
+++ b/builtins/gl2ps/CMakeLists.txt
@@ -27,6 +27,8 @@ endif()
 # flag required only on Windows, on old alma paltforms it make troubles
 if(WIN32)
   set(patch_args --ignore-whitespace)
+  # delete the source directory to make sure there is no conflict with the git apply command
+  execute_process(COMMAND ${CMAKE_COMMAND} -E remove_directory ${ROOT_GL2PS_PREFIX})
 endif()
 
 ExternalProject_Add(
@@ -46,11 +48,7 @@ ExternalProject_Add(
              -DBUILD_SHARED_LIBS=OFF
   BUILD_COMMAND ${CMAKE_COMMAND} --build . ${ROOT_GL2PS_BUILD_COMMAND_FLAGS}
   INSTALL_COMMAND ${CMAKE_COMMAND} --build . ${ROOT_GL2PS_BUILD_COMMAND_FLAGS} --target install
-  LOG_DOWNLOAD 1
-  LOG_CONFIGURE 1
-  LOG_BUILD 1
-  LOG_INSTALL 1
-  LOG_OUTPUT_ON_FAILURE 1
+  LOG_PATCH 1 LOG_DOWNLOAD 1 LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
   BUILD_BYPRODUCTS ${ROOT_GL2PS_LIBRARY}
   TIMEOUT 600)
 
diff --git a/builtins/libgif/CMakeLists.txt b/builtins/libgif/CMakeLists.txt
index 48a2ed37254b3..4ffc9accb4b60 100644
--- a/builtins/libgif/CMakeLists.txt
+++ b/builtins/libgif/CMakeLists.txt
@@ -26,6 +26,8 @@ endif()
 # flag required only on Windows, on old alma paltforms it make troubles
 if(WIN32)
   set(patch_args --ignore-whitespace)
+  # delete the source directory to make sure there is no conflict with the git apply command
+  execute_process(COMMAND ${CMAKE_COMMAND} -E remove_directory ${ROOT_LIBGIF_PREFIX})
 endif()
 
 ExternalProject_Add(
@@ -43,7 +45,7 @@ ExternalProject_Add(
     -DCMAKE_C_VISIBILITY_PRESET=hidden
     BUILD_COMMAND ${CMAKE_COMMAND} --build . ${ROOT_LIBGIF_BUILD_COMMAND_FLAGS}
     INSTALL_COMMAND ${CMAKE_COMMAND} --build . ${ROOT_LIBGIF_BUILD_COMMAND_FLAGS} --target install
-    LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
+    LOG_PATCH 1 LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
     BUILD_BYPRODUCTS ${ROOT_LIBGIF_LIBRARY}
     TIMEOUT 600
 )