Merge pull request #139887 from Artturin/rstudiobump

2025-02-21 19:44:09 +00:00 · 2021-10-15 08:35:40 +03:00 · 2021-10-15 08:35:40 +03:00 · db56940ea8
commit db56940ea8
parent 2138b27b18 a2fa069103
12 changed files with 8604 additions and 168 deletions
--- a/pkgs/applications/editors/rstudio/clang-location.patch
+++ b/pkgs/applications/editors/rstudio/clang-location.patch
@ -1,25 +1,61 @@
-diff --git i/src/cpp/core/libclang/LibClang.cpp w/src/cpp/core/libclang/LibClang.cpp
-index ec12a3a1ff..8c81b633ae 100644
--- i/src/cpp/core/libclang/LibClang.cpp
-+++ w/src/cpp/core/libclang/LibClang.cpp
-@@ -54,7 +54,7 @@ std::vector<std::string> defaultCompileArgs(LibraryVersion version)
+diff --git a/src/cpp/core/libclang/LibClang.cpp b/src/cpp/core/libclang/LibClang.cpp
+index 1186f3a..58e8cc7 100644
+--- a/src/cpp/core/libclang/LibClang.cpp
+++ b/src/cpp/core/libclang/LibClang.cpp
+@@ -58,7 +58,7 @@ std::vector<std::string> defaultCompileArgs(LibraryVersion version)
 
    // we need to add in the associated libclang headers as
    // they are not discovered / used by default during compilation
-   FilePath llvmPath = s_libraryPath.parent().parent();
+-   FilePath llvmPath = s_libraryPath.getParent().getParent();
 +   FilePath llvmPath("@libclang@");
    boost::format fmt("%1%/lib/clang/%2%/include");
-    fmt % llvmPath.absolutePath() % version.asString();
+    fmt % llvmPath.getAbsolutePath() % version.asString();
    std::string includePath = fmt.str();
-@@ -77,10 +77,7 @@ std::vector<std::string> systemClangVersions()
- #elif defined(__unix__)
-    // default set of versions
-    clangVersions = {
+@@ -70,46 +70,7 @@ std::vector<std::string> defaultCompileArgs(LibraryVersion version)
+ 
+ std::vector<std::string> systemClangVersions()
+ {
+-   std::vector<std::string> clangVersions;
+-   
+-#if defined(__APPLE__)
+-   // NOTE: the version of libclang.dylib bundled with Xcode
+-   // doesn't seem to work well when loaded as a library
+-   // (there seems to be extra orchestration required to get
+-   // include paths set up; easier to just depend on command
+-   // line tools since we request their installation in other
+-   // contexts as well)
+-   clangVersions = {
+-      "/Library/Developer/CommandLineTools/usr/lib/libclang.dylib"
+-   };
+-#elif defined(__unix__)
+-   // default set of versions
+-   clangVersions = {
 -      "/usr/lib/libclang.so",
 -      "/usr/lib/llvm/libclang.so",
 -      "/usr/lib64/libclang.so",
 -      "/usr/lib64/llvm/libclang.so",
-+      "@libclang.so@"
-    };
-    
-    // iterate through the set of available 'llvm' directories
+-   };
+-   
+-   // iterate through the set of available 'llvm' directories
+-   for (const char* prefix : {"/usr/lib", "/usr/lib64"})
+-   {
+-      FilePath prefixPath(prefix);
+-      if (!prefixPath.exists())
+-         continue;
+-      
+-      std::vector<FilePath> directories;
+-      Error error = prefixPath.getChildren(directories);
+-      if (error)
+-         LOG_ERROR(error);
+-
+-      // generate a path for each 'llvm' directory
+-      for (const FilePath& path : directories)
+-         if (path.getFilename().find("llvm") == 0)
+-            clangVersions.push_back(path.completePath("lib/libclang.so.1").getAbsolutePath());
+-   }
+-#endif
+-   
+   std::vector<std::string> clangVersions = { "@libclang.so@" };
+    return clangVersions;
+ }
+
--- a/pkgs/applications/editors/rstudio/default.nix
+++ b/pkgs/applications/editors/rstudio/default.nix
@ -1,141 +1,209 @@
-{ lib, mkDerivation, fetchurl, fetchpatch, fetchFromGitHub, makeDesktopItem, cmake, boost, zlib
-, openssl, R, qtbase, qtxmlpatterns, qtsensors, qtwebengine, qtwebchannel
-, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper, pandoc
+{ lib
+, mkDerivation
+, fetchurl
+, fetchpatch
+, fetchFromGitHub
+, makeDesktopItem
+, copyDesktopItems
+, cmake
+, boost
+, zlib
+, openssl
+, R
+, qtbase
+, qtxmlpatterns
+, qtsensors
+, qtwebengine
+, qtwebchannel
+, libuuid
+, hunspellDicts
+, unzip
+, ant
+, jdk
+, gnumake
+, makeWrapper
+, pandoc
 , llvmPackages
+, libyamlcpp
+, soci
+, postgresql
+, nodejs
+, mkYarnModules
+, qmake
 }:

-with lib;
 let
-  verMajor = "1";
-  verMinor = "2";
-  verPatch = "5042";
-  version = "${verMajor}.${verMinor}.${verPatch}";
-  ginVer = "2.1.2";
-  gwtVer = "2.8.1";
-in
-mkDerivation rec {
  pname = "RStudio";
-  inherit version;
-
-  nativeBuildInputs = [ cmake unzip ant jdk makeWrapper pandoc ];
-
-  buildInputs = [ boost zlib openssl R qtbase qtxmlpatterns qtsensors
-                  qtwebengine qtwebchannel libuuid ];
+  version = "1.4.1717";
+  RSTUDIO_VERSION_MAJOR = lib.versions.major version;
+  RSTUDIO_VERSION_MINOR = lib.versions.minor version;
+  RSTUDIO_VERSION_PATCH = lib.versions.patch version;

  src = fetchFromGitHub {
    owner = "rstudio";
    repo = "rstudio";
-    rev = "v${version}";
-    sha256 = "1n67fa357v51j3z1ma8v2ydfsx3y8n10k2svmfcf4mdzsi8w0kc5";
+    rev = version;
+    sha256 = "sha256-9c1bNsf8kJjpcZ2cMV/pPNtXQkFOntX29a1cdnXpllE=";
  };

-  # Hack RStudio to only use the input R and provided libclang.
-  patches = [ ./r-location.patch ./clang-location.patch
-              (fetchpatch {
-                # Fetch a patch to ensure Rstudio compiles against R
-                # 4.0.0, should be removed next 1.2.X Rstudio update
-                # or possibly 1.3.X
-                url = "https://github.com/rstudio/rstudio/commit/3fb2397c2f208bb8ace0bbaf269481ccb96b5b20.patch";
-                sha256 = "0qpgjy6aash0fc0xbns42cwpj3nsw49nkbzwyq8az01xwg81g0f3";
-              })
-            ];
-  postPatch = ''
-    substituteInPlace src/cpp/core/r_util/REnvironmentPosix.cpp --replace '@R@' ${R}
-    substituteInPlace src/cpp/core/libclang/LibClang.cpp \
-      --replace '@libclang@' ${llvmPackages.libclang.lib} \
-      --replace '@libclang.so@' ${llvmPackages.libclang.lib}/lib/libclang.so
-  '';
-
-  ginSrc = fetchurl {
-    url = "https://s3.amazonaws.com/rstudio-buildtools/gin-${ginVer}.zip";
-    sha256 = "16jzmljravpz6p2rxa87k5f7ir8vs7ya75lnfybfajzmci0p13mr";
-  };
-
-  gwtSrc = fetchurl {
-    url = "https://s3.amazonaws.com/rstudio-buildtools/gwt-${gwtVer}.zip";
-    sha256 = "19x000m3jwnkqgi6ic81lkzyjvvxcfacw2j0vcfcaknvvagzhyhb";
-  };
-
-  hunspellDictionaries = filter isDerivation (unique (attrValues hunspellDicts));
-  # These dicts contain identically-named dict files, so we only keep the
-  # -large versions in case of clashes
-  largeDicts = filter (d: hasInfix "-large-wordlist" d) hunspellDictionaries;
-  otherDicts = filter (d: !(hasAttr "dictFileName" d &&
-                            elem d.dictFileName (map (d: d.dictFileName) largeDicts))) hunspellDictionaries;
-  dictionaries = largeDicts ++ otherDicts;
-
  mathJaxSrc = fetchurl {
-    url = "https://s3.amazonaws.com/rstudio-buildtools/mathjax-26.zip";
-    sha256 = "0wbcqb9rbfqqvvhqr1pbqax75wp8ydqdyhp91fbqfqp26xzjv6lk";
+    url = "https://s3.amazonaws.com/rstudio-buildtools/mathjax-27.zip";
+    sha256 = "sha256-xWy6psTOA8H8uusrXqPDEtL7diajYCVHcMvLiPsgQXY=";
  };

  rsconnectSrc = fetchFromGitHub {
    owner = "rstudio";
    repo = "rsconnect";
-    rev = "984745d8";
-    sha256 = "037z0y32k1gdda192y5qn5hi7wp8wyap44mkjlklrgcqkmlcylb9";
+    rev = "f5854bb71464f6e3017da9855f058fe3d5b32efd";
+    sha256 = "sha256-ULyWdSgGPSAwMt0t4QPuzeUE6Bo6IJh+5BMgW1bFN+Y=";
  };

-  preConfigure =
-    ''
-      export RSTUDIO_VERSION_MAJOR=${verMajor}
-      export RSTUDIO_VERSION_MINOR=${verMinor}
-      export RSTUDIO_VERSION_PATCH=${verPatch}
-
-      GWT_LIB_DIR=src/gwt/lib
-
-      mkdir -p $GWT_LIB_DIR/gin/${ginVer}
-      unzip ${ginSrc} -d $GWT_LIB_DIR/gin/${ginVer}
-
-      unzip ${gwtSrc}
-      mkdir -p $GWT_LIB_DIR/gwt
-      mv gwt-${gwtVer} $GWT_LIB_DIR/gwt/${gwtVer}
-
-      mkdir dependencies/common/dictionaries
-      for dict in ${builtins.concatStringsSep " " dictionaries}; do
-        for i in "$dict/share/hunspell/"*; do
-          ln -sv $i dependencies/common/dictionaries/
-        done
-      done
-
-      unzip ${mathJaxSrc} -d dependencies/common/mathjax-26
-
-      mkdir -p dependencies/common/pandoc
-      cp ${pandoc}/bin/pandoc dependencies/common/pandoc/
-
-      cp -r ${rsconnectSrc} dependencies/common/rsconnect
-      pushd dependencies/common
-      ${R}/bin/R CMD build -d --no-build-vignettes rsconnect
-      popd
-    '';
-
-  cmakeFlags = [ "-DRSTUDIO_TARGET=Desktop" "-DQT_QMAKE_EXECUTABLE=$NIX_QT5_TMP/bin/qmake" ];
-
-  desktopItem = makeDesktopItem {
-    name = "${pname}-${version}";
-    exec = "rstudio %F";
-    icon = "rstudio";
-    desktopName = "RStudio";
-    genericName = "IDE";
-    comment = meta.description;
-    categories = "Development;";
-    mimeType = "text/x-r-source;text/x-r;text/x-R;text/x-r-doc;text/x-r-sweave;text/x-r-markdown;text/x-r-html;text/x-r-presentation;application/x-r-data;application/x-r-project;text/x-r-history;text/x-r-profile;text/x-tex;text/x-markdown;text/html;text/css;text/javascript;text/x-chdr;text/x-csrc;text/x-c++hdr;text/x-c++src;";
+  panmirrorModules = mkYarnModules {
+    inherit pname version;
+    packageJSON = ./package.json;
+    yarnLock =  ./yarn.lock;
+    yarnNix = ./yarndeps.nix;
  };

-  qtWrapperArgs = [ "--suffix PATH : ${gnumake}/bin" ];
+in
+mkDerivation rec {
+  inherit pname version src RSTUDIO_VERSION_MAJOR RSTUDIO_VERSION_MINOR RSTUDIO_VERSION_PATCH;

-  postInstall = ''
-      mkdir $out/share
-      cp -r ${desktopItem}/share/applications $out/share
-      mkdir $out/share/icons
-      ln $out/rstudio.png $out/share/icons
+  nativeBuildInputs = [
+    cmake
+    unzip
+    ant
+    jdk
+    makeWrapper
+    pandoc
+    nodejs
+    copyDesktopItems
+  ];
+
+  buildInputs = [
+    boost
+    zlib
+    openssl
+    R
+    qtbase
+    qtxmlpatterns
+    qtsensors
+    qtwebengine
+    qtwebchannel
+    libuuid
+    libyamlcpp
+    soci
+    postgresql
+  ];
+
+  cmakeFlags = [
+    "-DRSTUDIO_TARGET=Desktop"
+    "-DCMAKE_BUILD_TYPE=Release"
+    "-DQT_QMAKE_EXECUTABLE=${qmake}/bin/qmake"
+    "-DRSTUDIO_USE_SYSTEM_SOCI=ON"
+    "-DRSTUDIO_USE_SYSTEM_BOOST=ON"
+    "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON"
+    "-DPANDOC_VERSION=${pandoc.version}"
+    "-DCMAKE_INSTALL_PREFIX=${placeholder "out"}/lib/rstudio"
+  ];
+
+  # Hack RStudio to only use the input R and provided libclang.
+  patches = [
+    ./r-location.patch
+    ./clang-location.patch
+    # postFetch doesn't work with this | error: unexpected end-of-file
+    # replacing /usr/bin/node is done in postPatch
+    # https://src.fedoraproject.org/rpms/rstudio/tree/rawhide
+    (fetchpatch {
+      name = "system-node.patch";
+      url = "https://src.fedoraproject.org/rpms/rstudio/raw/5bda2e290c9e72305582f2011040938d3e356906/f/0004-use-system-node.patch";
+      sha256 = "sha256-P1Y07RB/ceFNa749nyBUWSE41eiiZgt43zVcmahvfZM=";
+    })
+  ];
+
+  postPatch = ''
+    substituteInPlace src/cpp/core/r_util/REnvironmentPosix.cpp --replace '@R@' ${R}
+
+    substituteInPlace src/cpp/CMakeLists.txt \
+      --replace 'SOCI_LIBRARY_DIR "/usr/lib"' 'SOCI_LIBRARY_DIR "${soci}/lib"'
+
+    substituteInPlace src/gwt/build.xml \
+      --replace '/usr/bin/node' '${nodejs}/bin/node'
+
+    substituteInPlace src/cpp/core/libclang/LibClang.cpp \
+      --replace '@libclang@' ${llvmPackages.libclang.lib} \
+      --replace '@libclang.so@' ${llvmPackages.libclang.lib}/lib/libclang.so
+
+      substituteInPlace src/cpp/session/include/session/SessionConstants.hpp \
+        --replace "bin/pandoc" "${pandoc}/bin/pandoc"
  '';

-  meta = with lib;
-    { description = "Set of integrated tools for the R language";
-      homepage = "https://www.rstudio.com/";
-      license = licenses.agpl3;
-      maintainers = with maintainers; [ ciil ];
-      platforms = platforms.linux;
-    };
+  hunspellDictionaries = with lib; filter isDerivation (unique (attrValues hunspellDicts));
+  # These dicts contain identically-named dict files, so we only keep the
+  # -large versions in case of clashes
+  largeDicts = with lib; filter (d: hasInfix "-large-wordlist" d) hunspellDictionaries;
+  otherDicts = with lib; filter
+    (d: !(hasAttr "dictFileName" d &&
+      elem d.dictFileName (map (d: d.dictFileName) largeDicts)))
+    hunspellDictionaries;
+  dictionaries = largeDicts ++ otherDicts;
+
+  preConfigure = ''
+    mkdir dependencies/dictionaries
+    for dict in ${builtins.concatStringsSep " " dictionaries}; do
+      for i in "$dict/share/hunspell/"*; do
+        ln -s $i dependencies/dictionaries/
+      done
+    done
+
+    unzip -q ${mathJaxSrc} -d dependencies/mathjax-27
+
+    mkdir -p dependencies/pandoc/${pandoc.version}
+    cp ${pandoc}/bin/pandoc dependencies/pandoc/${pandoc.version}/pandoc
+
+    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 = ''
+    mkdir -p $out/share/icons $out/bin
+    ln $out/lib/rstudio/rstudio.png $out/share/icons
+
+    for f in {diagnostics,rpostback,rstudio}; do
+      ln -s $out/lib/rstudio/bin/$f $out/bin
+    done
+
+    for f in .gitignore .Rbuildignore LICENSE README; do
+      find . -name $f -delete
+    done
+    rm -r $out/lib/rstudio/{INSTALL,COPYING,NOTICE,README.md,SOURCE,VERSION}
+    rm -r $out/lib/rstudio/bin/{pandoc/pandoc,pandoc}
+  '';
+
+  qtWrapperArgs = [
+    "--suffix PATH : ${lib.makeBinPath [ gnumake ]}"
+  ];
+
+  desktopItems = [
+    (makeDesktopItem {
+      name = "${pname}";
+      exec = "rstudio %F";
+      icon = "rstudio";
+      desktopName = "RStudio";
+      genericName = "IDE";
+      comment = meta.description;
+      categories = "Development;";
+      mimeType = "text/x-r-source;text/x-r;text/x-R;text/x-r-doc;text/x-r-sweave;text/x-r-markdown;text/x-r-html;text/x-r-presentation;application/x-r-data;application/x-r-project;text/x-r-history;text/x-r-profile;text/x-tex;text/x-markdown;text/html;text/css;text/javascript;text/x-chdr;text/x-csrc;text/x-c++hdr;text/x-c++src;";
+    })
+  ];
+
+  meta = with lib; {
+    description = "Set of integrated tools for the R language";
+    homepage = "https://www.rstudio.com/";
+    license = licenses.agpl3Only;
+    maintainers = with maintainers; [ ciil ];
+    platforms = platforms.linux;
+  };
 }
--- a/pkgs/applications/editors/rstudio/package.json
+++ b/pkgs/applications/editors/rstudio/package.json
@ -0,0 +1,83 @@
+{
+  "name": "panmirror",
+  "version": "0.1.0",
+  "private": true,
+  "license": "agpl-3.0",
+  "dependencies": {
+    "@types/ace": "^0.0.43",
+    "@types/clipboard": "^2.0.1",
+    "@types/diff-match-patch": "^1.0.32",
+    "@types/js-yaml": "^3.12.3",
+    "@types/lodash.debounce": "^4.0.6",
+    "@types/lodash.uniqby": "^4.7.6",
+    "@types/orderedmap": "^1.0.0",
+    "@types/prosemirror-commands": "^1.0.3",
+    "@types/prosemirror-dev-tools": "^2.1.0",
+    "@types/prosemirror-dropcursor": "^1.0.0",
+    "@types/prosemirror-gapcursor": "^1.0.1",
+    "@types/prosemirror-history": "^1.0.1",
+    "@types/prosemirror-inputrules": "^1.0.3",
+    "@types/prosemirror-keymap": "^1.0.3",
+    "@types/prosemirror-model": "^1.7.2",
+    "@types/prosemirror-schema-list": "^1.0.1",
+    "@types/prosemirror-state": "^1.2.5",
+    "@types/prosemirror-tables": "^0.9.1",
+    "@types/prosemirror-transform": "^1.1.1",
+    "@types/react": "^16.9.32",
+    "@types/react-dom": "^16.9.6",
+    "@types/react-window": "^1.8.2",
+    "@types/zenscroll": "^4.0.0",
+    "biblatex-csl-converter": "^1.9.1",
+    "clipboard": "^2.0.6",
+    "diff-match-patch": "^1.0.4",
+    "fuse.js": "^6.0.4",
+    "js-yaml": "^3.13.1",
+    "lodash.debounce": "^4.0.8",
+    "lodash.uniqby": "^4.7.0",
+    "orderedmap": "^1.0.0",
+    "prosemirror-changeset": "^2.1.2",
+    "prosemirror-commands": "^1.1.4",
+    "prosemirror-dev-tools": "^2.1.1",
+    "prosemirror-dropcursor": "^1.3.2",
+    "prosemirror-gapcursor": "^1.1.5",
+    "prosemirror-history": "^1.1.3",
+    "prosemirror-inputrules": "^1.1.2",
+    "prosemirror-keymap": "^1.1.4",
+    "prosemirror-model": "^1.11.0",
+    "prosemirror-schema-list": "^1.1.4",
+    "prosemirror-state": "^1.3.3",
+    "prosemirror-tables": "^1.1.1",
+    "prosemirror-transform": "^1.2.8",
+    "prosemirror-utils": "^0.9.6",
+    "prosemirror-view": "^1.15.6",
+    "react": "^16.13.1",
+    "react-dom": "^16.13.1",
+    "react-window": "^1.8.5",
+    "sentence-splitter": "^3.2.0",
+    "thenby": "^1.3.3",
+    "tlite": "^0.1.9",
+    "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"
+  }
+}
--- a/pkgs/applications/editors/rstudio/r-location.patch
+++ b/pkgs/applications/editors/rstudio/r-location.patch
@ -1,19 +1,23 @@
-diff -ur rstudio-1.1.216-old/src/cpp/core/CMakeLists.txt rstudio-1.1.216-new/src/cpp/core/CMakeLists.txt
--- rstudio-1.1.216-old/src/cpp/core/r_util/REnvironmentPosix.cpp	2017-04-30 03:37:26.669418665 -0400
-+++ rstudio-1.1.216-new/src/cpp/core/r_util/REnvironmentPosix.cpp	2017-04-30 03:36:33.590726185 -0400
-@@ -87,10 +87,7 @@
+diff --git a/src/cpp/core/r_util/REnvironmentPosix.cpp b/src/cpp/core/r_util/REnvironmentPosix.cpp
+index dbc9a9a1..9a526a86 100644
+--- a/src/cpp/core/r_util/REnvironmentPosix.cpp
+++ b/src/cpp/core/r_util/REnvironmentPosix.cpp
+@@ -107,12 +107,9 @@ FilePath systemDefaultRScript(std::string* pErrMsg)
 {
-    // define potential paths
-    std::vector<std::string> rScriptPaths;
-   rScriptPaths.push_back("/usr/bin/R");
-   rScriptPaths.push_back("/usr/local/bin/R");
-   rScriptPaths.push_back("/opt/local/bin/R");
-   rScriptPaths.push_back("/Library/Frameworks/R.framework/Resources/bin/R");
-+   rScriptPaths.push_back("@R@/bin/R");
-    return scanForRScript(rScriptPaths, pErrMsg);
- }
+    // check fallback paths
+    std::vector<std::string> rScriptPaths = {
+-      "/usr/bin/R",
+-      "/usr/local/bin/R",
+-      "/opt/local/bin/R",
+      "@R@/bin/R"
+    #ifdef __APPLE__
+-      "/opt/homebrew/bin/R",
+-      "/Library/Frameworks/R.framework/Resources/bin/R",
+      "@R@/bin/R",
+    #endif
+    };
 
-@@ -226,8 +223,7 @@
+@@ -225,8 +222,7 @@ FilePath systemDefaultRScript(std::string* pErrMsg)
       // scan in standard locations as a fallback
       std::string scanErrMsg;
       std::vector<std::string> rScriptPaths;
@ -21,5 +25,6 @@ diff -ur rstudio-1.1.216-old/src/cpp/core/CMakeLists.txt rstudio-1.1.216-new/src
 -      rScriptPaths.push_back("/usr/bin/R");
 +      rScriptPaths.push_back("@R@/bin/R");
       FilePath scriptPath = scanForRScript(rScriptPaths, &scanErrMsg);
-       if (scriptPath.empty())
+       if (scriptPath.isEmpty())
       {
+
--- a/pkgs/applications/editors/rstudio/yarn.lock
+++ b/pkgs/applications/editors/rstudio/yarn.lock
--- a/pkgs/applications/editors/rstudio/yarndeps.nix
+++ b/pkgs/applications/editors/rstudio/yarndeps.nix
--- a/pkgs/development/libraries/liblinphone/default.nix
+++ b/pkgs/development/libraries/liblinphone/default.nix
@ -35,6 +35,7 @@
 , python3
 , readline
 , soci
+, boost
 , speex
 , sqlite
 , lib, stdenv
@ -93,6 +94,7 @@ stdenv.mkDerivation rec {
    pango
    readline
    soci
+    boost
    speex
    sqlite
    udev
--- a/pkgs/development/libraries/libyaml-cpp/0.3.0.nix
+++ b/pkgs/development/libraries/libyaml-cpp/0.3.0.nix
@ -0,0 +1,32 @@
+{ lib, stdenv, fetchFromGitHub, cmake }:
+
+stdenv.mkDerivation rec {
+  pname = "libyaml-cpp";
+  version = "0.3.0";
+
+  src = fetchFromGitHub {
+    owner = "jbeder";
+    repo = "yaml-cpp";
+    rev = "release-${version}";
+    sha256 = "sha256-pmgcULTXhl83+Wc8ZsGebnJ1t0XybHhUEJxDnEZE5x8=";
+  };
+
+  # implement https://github.com/jbeder/yaml-cpp/commit/52a1378e48e15d42a0b755af7146394c6eff998c
+  postPatch = ''
+    substituteInPlace CMakeLists.txt \
+      --replace 'option(YAML_BUILD_SHARED_LIBS "Build Shared Libraries" OFF)' \
+                'option(YAML_BUILD_SHARED_LIBS "Build yaml-cpp shared library" ''${BUILD_SHARED_LIBS})'
+  '';
+
+  nativeBuildInputs = [ cmake ];
+
+  cmakeFlags = [ "-DBUILD_SHARED_LIBS=ON" "-DYAML_CPP_BUILD_TESTS=OFF" ];
+
+  meta = with lib; {
+    inherit (src.meta) homepage;
+    description = "A YAML parser and emitter for C++";
+    license = licenses.mit;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ andir ];
+  };
+}
--- a/pkgs/development/libraries/libyaml-cpp/default.nix
+++ b/pkgs/development/libraries/libyaml-cpp/default.nix
@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, cmake }:
+{ lib, stdenv, fetchFromGitHub, cmake, fetchpatch }:

 stdenv.mkDerivation rec {
  pname = "libyaml-cpp";
@ -11,12 +11,14 @@ stdenv.mkDerivation rec {
    sha256 = "sha256-2tFWccifn0c2lU/U1WNg2FHrBohjx8CXMllPJCevaNk=";
  };

-  # implement https://github.com/jbeder/yaml-cpp/commit/52a1378e48e15d42a0b755af7146394c6eff998c
-  postPatch = ''
-    substituteInPlace CMakeLists.txt \
-      --replace 'option(YAML_BUILD_SHARED_LIBS "Build Shared Libraries" OFF)' \
-                'option(YAML_BUILD_SHARED_LIBS "Build yaml-cpp shared library" ''${BUILD_SHARED_LIBS})'
-  '';
+  patches = [
+    # https://github.com/jbeder/yaml-cpp/issues/774
+    # https://github.com/jbeder/yaml-cpp/pull/1037
+    (fetchpatch {
+      url = "https://github.com/jbeder/yaml-cpp/commit/4f48727b365962e31451cd91027bd797bc7d2ee7.patch";
+      sha256 = "sha256-jarZAh7NgwL3xXzxijDiAQmC/EC2WYfNMkYHEIQBPhM=";
+    })
+  ];

  nativeBuildInputs = [ cmake ];

--- a/pkgs/development/libraries/lime/default.nix
+++ b/pkgs/development/libraries/lime/default.nix
@ -5,6 +5,7 @@
 , lib
 , soci
 , sqlite
+, boost
 , stdenv
 }:

@ -21,7 +22,7 @@ stdenv.mkDerivation rec {
    sha256 = "sha256-11vvvA+pud/eOyYsbRKVvGfiyhwdhNPfRQSfaquUro8=";
  };

-  buildInputs = [ bctoolbox soci belle-sip sqlite ];
+  buildInputs = [ bctoolbox soci belle-sip sqlite boost ];
  nativeBuildInputs = [ cmake ];

  # Do not build static libraries
--- a/pkgs/development/libraries/soci/default.nix
+++ b/pkgs/development/libraries/soci/default.nix
@ -1,25 +1,31 @@
 { cmake
 , fetchFromGitHub
 , sqlite
+, postgresql
+, boost
 , lib, stdenv
 }:

 stdenv.mkDerivation rec {
  pname = "soci";
-  version = "4.0.1";
+  version = "4.0.2";

  src = fetchFromGitHub {
    owner = "SOCI";
    repo = pname;
-    rev = version;
-    sha256 = "sha256-d4GtxDaB+yGfyCnbvnLRUYcrPSMkUF7Opu6+SZd8opM=";
+    rev = "v${version}";
+    sha256 = "sha256-NE0ApbX8HG2VAQ9cg9+kX3kJQ4PR1XvWL9BlT8NphmE=";
  };

  # Do not build static libraries
  cmakeFlags = [ "-DSOCI_STATIC=OFF" "-DCMAKE_CXX_STANDARD=11" ];

  nativeBuildInputs = [ cmake ];
-  buildInputs = [ sqlite ];
+  buildInputs = [
+    sqlite
+    postgresql
+    boost
+  ];

  meta = with lib; {
    description = "Database access library for C++";
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -18167,17 +18167,12 @@ with pkgs;

  libyamlcpp = callPackage ../development/libraries/libyaml-cpp { };

+  libyamlcpp_0_3 = callPackage ../development/libraries/libyaml-cpp/0.3.0.nix { };
+
  libcyaml = callPackage ../development/libraries/libcyaml { };

  rang = callPackage ../development/libraries/rang { };

-  libyamlcpp_0_3 = pkgs.libyamlcpp.overrideAttrs (oldAttrs: {
-    src = pkgs.fetchurl {
-      url = "https://github.com/jbeder/yaml-cpp/archive/release-0.3.0.tar.gz";
-      sha256 = "12aszqw6svwlnb6nzhsbqhz3c7vnd5ahd0k6xlj05w8lm83hx3db";
-      };
-  });
-
  libykclient = callPackage ../development/libraries/libykclient { };

  libykneomgr = callPackage ../development/libraries/libykneomgr { };
@ -27493,9 +27488,7 @@ with pkgs;
  rsclock = callPackage ../applications/misc/rsclock { };

  rstudio = libsForQt5.callPackage ../applications/editors/rstudio {
-    boost = boost166;
-    llvmPackages = llvmPackages_7;
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+    jdk = jdk8;
  };

  rsync = callPackage ../applications/networking/sync/rsync (config.rsync or {});