rstudio: rstudio-server: Update to 2025.05.1+513.

* patches/rstudio-server-panmirror.patch: Delete file.
* patches/rstudio-server-install.patch: Update to changes in 2025.05.1+513.
* guix-science/packages/rstudio-node.scm: Replace file with newly
generated contents.
* guix-science/packages/rstudio.scm
(js-panmirror): Update to 0.1.0.
(gsl-lite-for-rstudio, rapidjson-for-rstudio, hunspell-for-rstudio,
yaml-cpp-for-rstudio): New variables.
(rstudio-server): Update to 2025.05.1+513.
[source]: Remove rstudio-server-panmirror.patch.
[arguments]: Disable copilot support; add phase
'find-hunspell-and-rapidjson; update phase 'patch-paths to patch
search for system libraries; add phase 'patch-rapidjson.
[native-inputs]: Add libexpected and pkg-config.
[inputs]: Replace boost-1.83 with boost-1.88; replace yaml-cpp with
yaml-cpp-for-rstudio; add fmt-11, gsl-lite-for-rstudio,
hunspell-for-rstudio, rapidjson-for-rstudio, and websocketpp-next.

2 files changed, 136 insertions, 49 deletions

diff --git a/patches/rstudio-server-install.patch b/patches/rstudio-server-install.patch
index 56b8616..89bdee4 100644
--- a/patches/rstudio-server-install.patch
+++ b/patches/rstudio-server-install.patch
@@ -1,16 +1,49 @@
 Avoid copying all of mathjax, pandoc, and node to the output.
+Avoid building copies of existing libraries.  Link with Guix-provided libraries instead.
 
 --- a/src/cpp/session/CMakeLists.txt
 +++ b/src/cpp/session/CMakeLists.txt
-@@ -688,7 +688,4 @@
+@@ -469,18 +469,6 @@
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/../../../NOTICE
+                ${CMAKE_CURRENT_SOURCE_DIR}/resources COPYONLY)
+ 
+-# configure custom panmirror script into the resources directory
+-#
+-# On Linux and Windows builders, found in the tools directory, on Mac and dev
+-# environments found in the source tree.
+-set(RSTUDIO_PANMIRROR_SCRIPT ${CMAKE_CURRENT_SOURCE_DIR}/../../gwt/lib/quarto/packages/editor-server/src/resources/md-writer.lua)
+-if(NOT EXISTS "${RSTUDIO_PANMIRROR_SCRIPT}")
+-   set(RSTUDIO_PANMIRROR_SCRIPT ${RSTUDIO_TOOLS_ROOT}/../src/gwt/lib/quarto/packages/editor-server/src/resources/md-writer.lua)
+-endif()
+-file(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/resources/panmirror-scripts)
+-configure_file(${RSTUDIO_PANMIRROR_SCRIPT}
+-               ${CMAKE_CURRENT_SOURCE_DIR}/resources/panmirror-scripts/ COPYONLY)
+-
+ # set include directories
+ include_directories(
+    include
+@@ -682,9 +670,6 @@
+    # notice
+    install(FILES "resources/NOTICE"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+-   # panmirror scripts
+-   install(DIRECTORY "resources/panmirror-scripts"
+-           DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+    # citation
+    configure_file("resources/CITATION.in"
+@@ -721,10 +706,6 @@
+    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DICTIONARIES_DIR}"
+            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
  
 -   # install mathjax for local html preview
 -   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_MATHJAX_DIR}"
 -           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
- 
+-
     # install quarto (or pandoc if quarto disabled)
     if(QUARTO_ENABLED)
-@@ -722,9 +722,6 @@
+       # install some quarto folders into Resources, as needed
+@@ -742,9 +723,6 @@
                 EXCLUDE)
        endif()
     else()
@@ -19,20 +52,105 @@ Avoid copying all of mathjax, pandoc, and node to the output.
 -              USE_SOURCE_PERMISSIONS)
     endif()
  
-    # install embedded packages
-
---- a/src/cpp/session/CMakeLists.txt
-+++ b/src/cpp/session/CMakeLists.txt
-@@ -712,12 +712,6 @@
-            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+    # install Copilot Language Server
+--- a/src/cpp/ext/CMakeLists.txt
++++ b/src/cpp/ext/CMakeLists.txt
+@@ -228,30 +228,3 @@
+    websocketpp  WEBSOCKETPP
+    yaml-cpp     YAML_CPP
+    zlib         ZLIB)
+-
+-# Create rapidjson target.
+-add_library(rstudio-rapidjson INTERFACE EXCLUDE_FROM_ALL)
+-target_compile_definitions(rstudio-rapidjson INTERFACE "-DRAPIDJSON_NO_SIZETYPEDEFINE")
+-target_include_directories(rstudio-rapidjson INTERFACE "${RAPIDJSON_SOURCE_DIR}/include")
+-
+-
+-# Create websocketpp target.
+-add_library(rstudio-websocketpp INTERFACE EXCLUDE_FROM_ALL)
+-target_include_directories(rstudio-websocketpp INTERFACE "${WEBSOCKETPP_SOURCE_DIR}")
+-
+-
+-# Create hunspell target.
+-file(GLOB HUNSPELL_HEADER_FILES "${HUNSPELL_SOURCE_DIR}/src/hunspell/*.h*")
+-file(GLOB HUNSPELL_SOURCE_FILES "${HUNSPELL_SOURCE_DIR}/src/hunspell/*.c*")
+-add_library(rstudio-hunspell STATIC ${HUNSPELL_SOURCE_FILES} ${HUNSPELL_HEADER_FILES})
+-set_target_properties(rstudio-hunspell PROPERTIES LINKER_LANGUAGE CXX)
+-target_include_directories(rstudio-hunspell SYSTEM AFTER INTERFACE "${HUNSPELL_SOURCE_DIR}/src")
+-target_compile_definitions(rstudio-hunspell PUBLIC HUNSPELL_STATIC=1)
+-
+-if(WIN32)
+-   target_include_directories(rstudio-hunspell SYSTEM AFTER PRIVATE "${HUNSPELL_PREFIX_DIR}/msvc")
+-   target_compile_options(rstudio-hunspell PRIVATE /wd4244 /wd4267)
+-   target_compile_options(rstudio-hunspell INTERFACE /wd4996)
+-else()
+-   target_compile_options(rstudio-hunspell PRIVATE -Wno-deprecated-declarations -Wno-sign-compare -Wno-unused-but-set-variable)
+-endif()
+--- a/src/cpp/shared_core/CMakeLists.txt
++++ b/src/cpp/shared_core/CMakeLists.txt
+@@ -46,6 +46,8 @@
+ set (SHARED_INCLUDE_DIRS
+    include
+    ${BOOST_INCLUDEDIR}
++   ${rapidjson_INCLUDE_DIRS}
++   ${gsl_lite_INCLUDE_DIRS}
+    ${EXT_SOURCE_DIR})
  
+ # UNIX specific
+@@ -93,7 +94,7 @@
+    ${Boost_LIBRARIES}
+    ${SHARED_CORE_SYSTEM_LIBS}
+-   gsl::gsl-lite-v1
++   ${gsl_lite_LIBRARIES}
+-   rstudio-rapidjson)
++   ${rapidjson_LIBRARIES})
  
--   # install node
--   install(
--      DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/node/${RSTUDIO_INSTALLED_NODE_VERSION}-patched/"
--      DESTINATION "${RSTUDIO_INSTALL_BIN}/node"
--      USE_SOURCE_PERMISSIONS)
--
-    # install quarto (or pandoc if quarto disabled)
-    if(QUARTO_ENABLED)
-       # install some quarto folders into Resources, as needed
+ # Define executable for running unit tests
+ if (RSTUDIO_UNIT_TESTS_ENABLED)
+--- a/src/cpp/core/CMakeLists.txt
++++ b/src/cpp/core/CMakeLists.txt
+@@ -318,6 +318,10 @@
+    ${EXT_SOURCE_DIR}
+    ${CMAKE_CURRENT_BINARY_DIR}
+    ${TESTS_INCLUDE_DIR}
++   ${hunspell_INCLUDE_DIRS}
++   ${tl-expected_INCLUDE_DIRS}
++   ${gsl_lite_INCLUDE_DIRS}
++   ${websocketpp_INCLUDE_DIRS}
+ )
+ 
+ # define shared library
+@@ -327,8 +329,8 @@
+ # link dependencies
+ target_link_libraries(rstudio-core
+    rstudio-shared-core
+-   rstudio-hunspell
+-   rstudio-websocketpp
++   ${hunspell_LIBRARIES}
++   ${websocketpp_LIBRARIES}
+    ${Boost_LIBRARIES}
+    ${CRASHPAD_LIBRARIES}
+    ${SOCI_LIBRARIES}
+@@ -361,7 +363,7 @@
+       rstudio-shared-core
+       rstudio-core
+       rstudio-core-synctex
+-      rstudio-hunspell
++      ${hunspell_LIBRARIES}
+       ${Boost_LIBRARIES}
+       ${SOCI_LIBRARIES}
+       ${CORE_SYSTEM_LIBRARIES}
+--- a/src/cpp/CMakeLists.txt
++++ b/src/cpp/CMakeLists.txt
+@@ -492,5 +492,11 @@
+ 
+    find_package(OpenSSL REQUIRED)
+    include_directories(SYSTEM "${OPENSSL_INCLUDE_DIR}")
++   find_package(fmt REQUIRED)
++   find_package(gsl-lite REQUIRED)
++   find_package(tl-expected REQUIRED)
++   find_package(yaml-cpp REQUIRED)
++   find_package(hunspell REQUIRED)
++   include_directories(SYSTEM "${hunspell_INCLUDE_DIRS}")
+ 
+ endif()
diff --git a/patches/rstudio-server-panmirror.patch b/patches/rstudio-server-panmirror.patch
deleted file mode 100644
index d0c2ca0..0000000
--- a/patches/rstudio-server-panmirror.patch
+++ /dev/null
@@ -1,31 +0,0 @@
---- a/src/cpp/session/CMakeLists.txt
-+++ b/src/cpp/session/CMakeLists.txt
-@@ -456,18 +456,6 @@
- configure_file(${CMAKE_CURRENT_SOURCE_DIR}/../../../NOTICE
-                ${CMAKE_CURRENT_SOURCE_DIR}/resources COPYONLY)
- 
--# configure custom panmirror script into the resources directory
--#
--# On Linux and Windows builders, found in the tools directory, on Mac and dev
--# environments found in the source tree.
--set(RSTUDIO_PANMIRROR_SCRIPT ${CMAKE_CURRENT_SOURCE_DIR}/../../gwt/lib/quarto/packages/editor-server/src/resources/md-writer.lua)
--if(NOT EXISTS "${RSTUDIO_PANMIRROR_SCRIPT}")
--   set(RSTUDIO_PANMIRROR_SCRIPT ${RSTUDIO_TOOLS_ROOT}/../src/gwt/lib/quarto/packages/editor-server/src/resources/md-writer.lua)
--endif()
--file(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/resources/panmirror-scripts)
--configure_file(${RSTUDIO_PANMIRROR_SCRIPT}
--               ${CMAKE_CURRENT_SOURCE_DIR}/resources/panmirror-scripts/ COPYONLY)
--
- # set include directories
- include_directories(
-    include
-@@ -672,9 +660,6 @@
-    # notice
-    install(FILES "resources/NOTICE"
-            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
--   # panmirror scripts
--   install(DIRECTORY "resources/panmirror-scripts"
--           DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
- 
-    # citation
-    configure_file("resources/CITATION.in"