rstudio: 2022.07.1+554 -> 2023.09.0+463

Updates rstudio to current version, fixes plotting and enables quarto
and markdown rendering.
Visual mode for markdown editing is still not functional.

 * Remove unneeded patch
 * Eliminate false quarto version warning
 * Fix pandoc and quarto paths
 * Adjust patch name to reflect purpose
 * Remove panmirror for now
 * Update quartoSrc

Co-authored-by: Justin Bedő <cu@cua0.org>
Also contributed: b-rodrigues and kupac

pkgs/applications/editors/rstudio/default.nix

@@ -16,13 +16,13 @@
 , qtsensors
 , qtwebengine
 , qtwebchannel
+, quarto
 , libuuid
 , hunspellDicts
 , unzip
 , ant
 , jdk
 , gnumake
-, makeWrapper
 , pandoc
 , llvmPackages
 , yaml-cpp
@@ -40,39 +40,39 @@
 
 let
   pname = "RStudio";
-  version = "2022.07.1+554";
-  RSTUDIO_VERSION_MAJOR  = "2022";
-  RSTUDIO_VERSION_MINOR  = "07";
-  RSTUDIO_VERSION_PATCH  = "1";
-  RSTUDIO_VERSION_SUFFIX = "+554";
+  version =
+  "${RSTUDIO_VERSION_MAJOR}.${RSTUDIO_VERSION_MINOR}.${RSTUDIO_VERSION_PATCH}${RSTUDIO_VERSION_SUFFIX}";
+  RSTUDIO_VERSION_MAJOR  = "2023";
+  RSTUDIO_VERSION_MINOR  = "09";
+  RSTUDIO_VERSION_PATCH  = "0";
+  RSTUDIO_VERSION_SUFFIX = "+463";
 
   src = fetchFromGitHub {
     owner = "rstudio";
     repo = "rstudio";
     rev = "v${version}";
-    sha256 = "0rmdqxizxqg2vgr3lv066cjmlpjrxjlgi0m97wbh6iyhkfm2rrj1";
+    hash = "sha256-FwNuU2rbE3GEhuwphvZISUMhvSZJ6FjjaZ1oQ9F8NWc=";
   };
 
   mathJaxSrc = fetchurl {
     url = "https://s3.amazonaws.com/rstudio-buildtools/mathjax-27.zip";
-    sha256 = "sha256-xWy6psTOA8H8uusrXqPDEtL7diajYCVHcMvLiPsgQXY=";
+    hash = "sha256-xWy6psTOA8H8uusrXqPDEtL7diajYCVHcMvLiPsgQXY=";
   };
 
   rsconnectSrc = fetchFromGitHub {
     owner = "rstudio";
     repo = "rsconnect";
-    rev = "e287b586e7da03105de3faa8774c63f08984eb3c";
-    sha256 = "sha256-ULyWdSgGPSAwMt0t4QPuzeUE6Bo6IJh+5BMgW1bFN+Y=";
+    rev = "5175a927a41acfd9a21d9fdecb705ea3292109f2";
+    hash = "sha256-c1fFcN6KAfxXv8bv4WnIqQKg1wcNP2AywhEmIbyzaBA=";
   };
 
-  panmirrorModules = mkYarnModules rec {
-    inherit pname version;
-    packageJSON = ./package.json;
-    yarnLock = "${src}/src/gwt/panmirror/src/editor/yarn.lock";
-    offlineCache = fetchYarnDeps {
-      inherit yarnLock;
-      hash = "sha256-v05Up6VMlYlvgUYQVYo+YfpcsMohliNfMgyjq6QymCI=";
-    };
+  # Ideally, rev should match the rstudio release name.
+  # e.g. release/rstudio-mountain-hydrangea
+  quartoSrc = fetchFromGitHub {
+    owner = "quarto-dev";
+    repo = "quarto";
+    rev = "bb264a572c6331d46abcf087748c021d815c55d7";
+    hash = "sha256-lZnZvioztbBWWa6H177X6rRrrgACx2gMjVFDgNup93g=";
   };
 
   description = "Set of integrated tools for the R language";
@@ -86,7 +86,6 @@ in
       unzip
       ant
       jdk
-      makeWrapper
       pandoc
       nodejs
     ] ++ lib.optionals (!server) [
@@ -102,6 +101,7 @@ in
       yaml-cpp
       soci
       postgresql
+      quarto
     ] ++ (if server then [
       sqlite.dev
       pam
@@ -119,7 +119,7 @@ in
       "-DRSTUDIO_USE_SYSTEM_SOCI=ON"
       "-DRSTUDIO_USE_SYSTEM_BOOST=ON"
       "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON"
-      "-DQUARTO_ENABLED=FALSE"
+      "-DQUARTO_ENABLED=TRUE"
       "-DPANDOC_VERSION=${pandoc.version}"
       "-DCMAKE_INSTALL_PREFIX=${placeholder "out"}/lib/rstudio"
     ] ++ lib.optionals (!server) [
@@ -133,8 +133,7 @@ in
       ./use-system-node.patch
       ./fix-resources-path.patch
       ./pandoc-nix-path.patch
-      ./remove-quarto-from-generator.patch
-      ./do-not-install-pandoc.patch
+      ./use-system-quarto.patch
     ];
 
     postPatch = ''
@@ -144,16 +143,20 @@ in
         --replace 'SOCI_LIBRARY_DIR "/usr/lib"' 'SOCI_LIBRARY_DIR "${soci}/lib"'
 
       substituteInPlace src/gwt/build.xml \
-        --replace '@node@' ${nodejs}
+        --replace '@node@' ${nodejs} \
+        --replace './lib/quarto' ${quartoSrc}
 
       substituteInPlace src/cpp/core/libclang/LibClang.cpp \
         --replace '@libclang@' ${llvmPackages.libclang.lib} \
         --replace '@libclang.so@' ${llvmPackages.libclang.lib}/lib/libclang.so
 
-      substituteInPlace src/cpp/session/include/session/SessionConstants.hpp \
-        --replace '@pandoc@' ${pandoc}/bin/pandoc
+      substituteInPlace src/cpp/session/CMakeLists.txt \
+        --replace '@pandoc@' ${pandoc} \
+        --replace '@quarto@' ${quarto}
 
-      sed '1i#include <set>' -i src/cpp/core/include/core/Thread.hpp
+      substituteInPlace src/cpp/session/include/session/SessionConstants.hpp \
+        --replace '@pandoc@' ${pandoc}/bin \
+        --replace '@quarto@' ${quarto}
     '';
 
     hunspellDictionaries = with lib; filter isDerivation (unique (attrValues hunspellDicts));
@@ -181,8 +184,6 @@ in
 
       cp -r ${rsconnectSrc} dependencies/rsconnect
       ( cd dependencies && ${R}/bin/R CMD build -d --no-build-vignettes rsconnect )
-
-      cp -r "${panmirrorModules}" src/gwt/panmirror/src/editor/node_modules
     '';
 
     postInstall = ''
@@ -206,14 +207,14 @@ in
       rm -r $out/lib/rstudio/{INSTALL,COPYING,NOTICE,README.md,SOURCE,VERSION}
     '';
 
-    meta = with lib; {
+    meta = {
       broken = (stdenv.isLinux && stdenv.isAarch64);
       inherit description;
       homepage = "https://www.rstudio.com/";
-      license = licenses.agpl3Only;
-      maintainers = with maintainers; [ ciil cfhammill ];
+      license = lib.licenses.agpl3Only;
+      maintainers = with lib.maintainers; [ ciil cfhammill ];
       mainProgram = "rstudio" + lib.optionalString server "-server";
-      platforms = platforms.linux;
+      platforms = lib.platforms.linux;
     };
 
     passthru = {

pkgs/applications/editors/rstudio/do-not-install-pandoc.patch

@@ -1,13 +0,0 @@
---- a/src/cpp/session/CMakeLists.txt
-+++ b/src/cpp/session/CMakeLists.txt
-@@ -60,8 +60,7 @@
- 
- # validate our dependencies exist
- foreach(VAR RSTUDIO_DEPENDENCIES_DICTIONARIES_DIR
--            RSTUDIO_DEPENDENCIES_MATHJAX_DIR
--            RSTUDIO_DEPENDENCIES_PANDOC_DIR)
-+            RSTUDIO_DEPENDENCIES_MATHJAX_DIR)
- 
-    # validate existence
-    if(NOT EXISTS "${${VAR}}")
-

pkgs/applications/editors/rstudio/package.json

@@ -1,85 +0,0 @@
-{
-  "name": "panmirror",
-  "version": "0.1.0",
-  "private": true,
-  "license": "agpl-3.0",
-  "dependencies": {
-    "@types/ace": "^0.0.43",
-    "@types/clipboard": "^2.0.7",
-    "@types/diff-match-patch": "^1.0.32",
-    "@types/js-yaml": "^4.0.3",
-    "@types/lodash.debounce": "^4.0.6",
-    "@types/lodash.orderby": "^4.6.6",
-    "@types/lodash.uniqby": "^4.7.6",
-    "@types/orderedmap": "^1.0.0",
-    "@types/pinyin": "^2.10.0",
-    "@types/prosemirror-commands": "^1.0.4",
-    "@types/prosemirror-dropcursor": "^1.0.3",
-    "@types/prosemirror-gapcursor": "^1.0.4",
-    "@types/prosemirror-history": "^1.0.3",
-    "@types/prosemirror-inputrules": "^1.0.4",
-    "@types/prosemirror-keymap": "^1.0.4",
-    "@types/prosemirror-schema-list": "^1.0.3",
-    "@types/prosemirror-tables": "^0.9.1",
-    "@types/react": "^17.0.20",
-    "@types/react-dom": "^17.0.9",
-    "@types/react-window": "^1.8.5",
-    "@types/transliteration": "^1.6.6",
-    "@types/zenscroll": "^4.0.1",
-    "biblatex-csl-converter": "^2.0.2",
-    "clipboard": "^2.0.8",
-    "diff-match-patch": "^1.0.5",
-    "fuse.js": "^6.4.6",
-    "js-yaml": "^4.1.0",
-    "lodash.debounce": "^4.0.8",
-    "lodash.orderby": "^4.6.0",
-    "lodash.uniqby": "^4.7.0",
-    "orderedmap": "^1.0.0",
-    "pinyin": "^2.10.2",
-    "prosemirror-changeset": "^2.1.2",
-    "prosemirror-commands": "^1.1.10",
-    "prosemirror-dev-tools": "^2.1.1",
-    "prosemirror-dropcursor": "^1.3.5",
-    "prosemirror-gapcursor": "^1.1.5",
-    "prosemirror-history": "^1.2.0",
-    "prosemirror-inputrules": "^1.1.3",
-    "prosemirror-keymap": "^1.1.4",
-    "prosemirror-model": "^1.14.3",
-    "prosemirror-schema-list": "^1.1.5",
-    "prosemirror-state": "^1.3.4",
-    "prosemirror-tables": "^1.1.1",
-    "prosemirror-transform": "^1.3.2",
-    "prosemirror-utils": "^0.9.6",
-    "prosemirror-view": "^1.20.1",
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2",
-    "react-window": "^1.8.6",
-    "sentence-splitter": "^3.2.2",
-    "thenby": "^1.3.3",
-    "tlite": "^0.1.9",
-    "transliteration": "^2.2.0",
-    "typescript": "3.8.3",
-    "zenscroll": "^4.0.2"
-  },
-  "scripts": {
-    "format": "prettier --write \"src/**/*.ts\" \"src/**/*.tsx\"",
-    "lint": "tslint -c tslint.json 'src/**/*.{ts,tsx}'",
-    "watch": "tsc --watch --noEmit --project './tsconfig.json'",
-    "generate-symbols": "ts-node tools/generate-symbols.ts"
-  },
-  "devDependencies": {
-    "@types/node": "^14.0.4",
-    "@types/unzip": "^0.1.1",
-    "fast-xml-parser": "^3.17.1",
-    "fuse-box": "^3.7.1",
-    "prettier": "^1.18.2",
-    "terser": "^4.6.2",
-    "ts-node": "^8.10.2",
-    "tslint": "^5.20.0",
-    "tslint-config-prettier": "^1.18.0",
-    "tslint-react": "^5.0.0",
-    "typescript-tslint-plugin": "^0.5.5",
-    "uglify-js": "^3.7.4",
-    "unzip": "^0.1.11"
-  }
-}

pkgs/applications/editors/rstudio/pandoc-nix-path.patch

@@ -1,11 +1,18 @@
 --- a/src/cpp/session/include/session/SessionConstants.hpp
 +++ b/src/cpp/session/include/session/SessionConstants.hpp
-@@ -140,7 +140,7 @@
+@@ -142,13 +142,13 @@
+ #define kSessionTmpDir             "rstudio-rsession"
+ 
  #ifdef QUARTO_ENABLED
- # define kDefaultPandocPath        "bin/quarto/bin"
- #else
--# define kDefaultPandocPath        "bin/pandoc"
+-# define kDefaultPandocPath        "bin/quarto/bin/tools"
 +# define kDefaultPandocPath        "@pandoc@"
+ #else
+ # define kDefaultPandocPath        "bin/pandoc"
  #endif
  
- #define kDefaultQuartoPath         "bin/quarto"
+ #define kDefaultNodePath           "bin/node"
+-#define kDefaultQuartoPath         "bin/quarto"
++#define kDefaultQuartoPath         "@quarto@"
+ #define kDefaultRsclangPath        "bin/rsclang"
+ 
+ #ifdef _WIN32

pkgs/applications/editors/rstudio/remove-quarto-from-generator.patch

@@ -1,32 +0,0 @@
---- a/src/cpp/session/CMakeLists.txt
-+++ b/src/cpp/session/CMakeLists.txt
-@@ -43,12 +43,6 @@
-       set(RSTUDIO_DEPENDENCIES_MATHJAX_DIR "${RSTUDIO_DEPENDENCIES_DIR}/mathjax-27")
-    endif()
- 
--   if(EXISTS "${RSTUDIO_TOOLS_ROOT}/quarto")
--      set(RSTUDIO_DEPENDENCIES_QUARTO_DIR "${RSTUDIO_TOOLS_ROOT}/quarto")
--   else()
--      set(RSTUDIO_DEPENDENCIES_QUARTO_DIR "${RSTUDIO_DEPENDENCIES_DIR}/quarto")
--   endif()
--
- endif()
- 
- 
-@@ -67,14 +61,7 @@
- # validate our dependencies exist
- foreach(VAR RSTUDIO_DEPENDENCIES_DICTIONARIES_DIR
-             RSTUDIO_DEPENDENCIES_MATHJAX_DIR
--            RSTUDIO_DEPENDENCIES_PANDOC_DIR
--            RSTUDIO_DEPENDENCIES_QUARTO_DIR)
--
-- 
--   # skip quarto if not enabled
--   if("${VAR}" STREQUAL "RSTUDIO_DEPENDENCIES_QUARTO_DIR" AND NOT QUARTO_ENABLED)
--      continue()
--   endif()
-+            RSTUDIO_DEPENDENCIES_PANDOC_DIR)
- 
-    # validate existence
-    if(NOT EXISTS "${${VAR}}")
-

pkgs/applications/editors/rstudio/use-system-node.patch

@@ -1,29 +1,60 @@
+diff --git a/src/gwt/build.xml b/src/gwt/build.xml
+index 83e9433..f1ee63d 100644
 --- a/src/gwt/build.xml
 +++ b/src/gwt/build.xml
-@@ -83,24 +83,7 @@
-       <echo>Concatenated acesupport files to 'acesupport.js'</echo>
-    </target>
- 
--   <!-- panmirror typescript library -->
--   <!-- ensure version matches RSTUDIO_NODE_VERSION -->
--   <property name="node.version" value="16.14.0"/>
--   <property name="node.dir" value="../../dependencies/common/node/${node.version}"/>
--   <condition property="node.bin" value="../../../${node.dir}/bin/node">
+@@ -87,29 +87,7 @@
+    <!-- ensure version matches RSTUDIO_NODE_VERSION -->
+    <property name="node.version" value="16.14.0"/>
+    <property name="node.dir" value="../../dependencies/common/node/${node.version}"/>
+-   <!-- use yarn from system but will prefer yarn from dependencies if available -->
+-   <condition property="yarn.bin" value="yarn">
 -     <not>
 -        <os family="windows" />
 -     </not>
 -   </condition>
--   <condition property="node.bin" value="${node.dir}/node.exe">
+-   <available
+-      property="yarn.bin"
+-      value="${node.dir}/bin/yarn"
+-      file="${node.dir}/bin/yarn"/>
+-   <condition property="yarn.bin" value="${node.dir}/node_modules/yarn/bin/yarn.cmd">
 -     <os family="windows" />
 -   </condition>
--
--   <!-- use node from /opt/rstudio-tools if installed (typical for Docker) -->
+-   <!-- use yarn from /opt/rstudio-tools if installed (typical for Docker) -->
 -   <available
--      property="node.bin"
--      value="/opt/rstudio-tools/dependencies/common/node/${node.version}/bin/node"
--      file="/opt/rstudio-tools/dependencies/common/node/${node.version}/bin/node"/>
-+    <property name="node.bin" value="@node@/bin/node"/>
+-      property="yarn.bin"
+-      value="/opt/rstudio-tools/dependencies/common/node/${node.version}/bin/yarn"
+-      file="/opt/rstudio-tools/dependencies/common/node/${node.version}/bin/yarn"/>
+-   <!-- use yarn from c:/rstudio-tools if installed (typical for Docker on Windows) -->
+-   <available
+-      property="yarn.bin"
+-      value="c:\rstudio-tools\dependencies\common\node\${node.version}\node_modules\yarn\bin\yarn.cmd"
+-      file="c:\rstudio-tools\dependencies\common\node\${node.version}\node_modules\yarn\bin\yarn.cmd"/>
++   <property name="node.bin" value="@node@/bin/node"/>
  
-    <property name="panmirror.dir" value="./panmirror/src/editor"/>
+    <property name="panmirror.dir" value="./lib/quarto/apps/panmirror"/>
     <property name="panmirror.build.dir" value="./www/js/panmirror"/>
-
+@@ -126,21 +104,11 @@
+       file="c:\rstudio-tools\src\gwt\lib\quarto\apps\panmirror"/>
+ 
+    <target name="panmirror" description="Compile panmirror library">
+-      <echo message="yarn location: ${yarn.bin}"/>
+-      <echo message="panmirror location: ${panmirror.dir}"/>
+       <mkdir dir="${panmirror.build.dir}"/>
+-      <exec executable="${yarn.bin}" dir="${panmirror.dir}" resolveexecutable="true" failonerror="true">
+-         <arg value="install"/>
+-         <arg value="--network-timeout"/>
+-         <arg value="240000"/>
+-      </exec>
+-      <exec executable="${yarn.bin}" dir="${panmirror.dir}" resolveexecutable="true" failonerror="true">
+-         <arg value="build"/>
+-         <env key="PANMIRROR_OUTDIR" value="dist-rstudio"/>
++      <exec executable="${node.bin}" dir="${panmirror.dir}" spawn="${panmirror.spawn}">
++         <arg value="fuse"/>
++         <arg value="${panmirror.target}"/>
+       </exec>
+-      <copy todir="${panmirror.build.dir}">
+-         <fileset dir="${panmirror.dir}/dist-rstudio"/>
+-      </copy>
+    </target>
+ 
+    <target name="javac" description="Compile java source">

pkgs/applications/editors/rstudio/use-system-quarto.patch

@@ -0,0 +1,46 @@
+--- a/src/cpp/session/CMakeLists.txt
++++ b/src/cpp/session/CMakeLists.txt
+@@ -36,18 +36,14 @@
+    else()
+       set(RSTUDIO_DEPENDENCIES_DICTIONARIES_DIR "${RSTUDIO_DEPENDENCIES_DIR}/dictionaries")
+    endif()
+-   
++
+    if(EXISTS "${RSTUDIO_TOOLS_ROOT}/mathjax-27")
+       set(RSTUDIO_DEPENDENCIES_MATHJAX_DIR "${RSTUDIO_TOOLS_ROOT}/mathjax-27")
+    else()
+       set(RSTUDIO_DEPENDENCIES_MATHJAX_DIR "${RSTUDIO_DEPENDENCIES_DIR}/mathjax-27")
+    endif()
+ 
+-   if(EXISTS "${RSTUDIO_TOOLS_ROOT}/quarto")
+-      set(RSTUDIO_DEPENDENCIES_QUARTO_DIR "${RSTUDIO_TOOLS_ROOT}/quarto")
+-   else()
+-      set(RSTUDIO_DEPENDENCIES_QUARTO_DIR "${RSTUDIO_DEPENDENCIES_DIR}/quarto")
+-   endif()
++   set(RSTUDIO_DEPENDENCIES_QUARTO_DIR "@quarto@")
+ 
+ endif()
+ 
+@@ -56,7 +52,7 @@
+ # - by default, we use quarto + quarto's bundled pandoc
+ # - if quarto is not enabled, use pandoc fallback
+ if(QUARTO_ENABLED)
+-   set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "${RSTUDIO_DEPENDENCIES_QUARTO_DIR}/bin/tools")
++   set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "@pandoc@/bin")
+ elseif(EXISTS "${RSTUDIO_TOOLS_ROOT}/pandoc/${PANDOC_VERSION}")
+    set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "${RSTUDIO_TOOLS_ROOT}/pandoc/${PANDOC_VERSION}")
+ else()
+@@ -66,11 +62,9 @@
+ 
+ # validate our dependencies exist
+ foreach(VAR RSTUDIO_DEPENDENCIES_DICTIONARIES_DIR
+-            RSTUDIO_DEPENDENCIES_MATHJAX_DIR
+-            RSTUDIO_DEPENDENCIES_PANDOC_DIR
+-            RSTUDIO_DEPENDENCIES_QUARTO_DIR)
++            RSTUDIO_DEPENDENCIES_MATHJAX_DIR)
++
+ 
+- 
+    # skip quarto if not enabled
+    if("${VAR}" STREQUAL "RSTUDIO_DEPENDENCIES_QUARTO_DIR" AND NOT QUARTO_ENABLED)
+       continue()