sci-mathematics/rstudio: Bump to 1.3.959

Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Mark Wright <gienah@gentoo.org>

6 files changed, 578 insertions, 0 deletions

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch
new file mode 100644
index 000000000000..dc35d0ce0083
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch
@@ -0,0 +1,106 @@
+From 71b1a935762efd24a79de193662450de5a89f67e Mon Sep 17 00:00:00 2001
+From: Jonathan McPherson <jonathan@rstudio.com>
+Date: Tue, 14 Jan 2020 12:53:20 -0800
+Subject: [PATCH] use R_NoSave over R_Slave for R 4.0+
+
+---
+ src/cpp/r/CMakeLists.txt             | 12 ++++++++++++
+ src/cpp/r/config.h.in                |  8 +++++++-
+ src/cpp/r/session/REmbeddedPosix.cpp | 20 ++++++++++++++------
+ 3 files changed, 33 insertions(+), 7 deletions(-)
+
+diff --git a/src/cpp/r/CMakeLists.txt b/src/cpp/r/CMakeLists.txt
+index 6984ae309c..29784b8b67 100644
+--- a/src/cpp/r/CMakeLists.txt
++++ b/src/cpp/r/CMakeLists.txt
+@@ -15,6 +15,18 @@
+ 
+ project (R)
+ 
++# find the version of R in play
++find_package(LibR REQUIRED)
++execute_process(
++    COMMAND "${LIBR_EXECUTABLE}" "--vanilla" "--slave" "-e" "cat(as.character(getRversion()))"
++    OUTPUT_VARIABLE LIBR_VERSION)
++
++# parse and save the R version to a variable
++string(REPLACE "." ";" R_VERSION_LIST "${LIBR_VERSION}")
++list(GET R_VERSION_LIST 0 R_VERSION_MAJOR)
++list(GET R_VERSION_LIST 1 R_VERSION_MINOR)
++list(GET R_VERSION_LIST 2 R_VERSION_PATCH)
++
+ # include files
+ file(GLOB_RECURSE R_HEADER_FILES "*.h*")
+ 
+diff --git a/src/cpp/r/config.h.in b/src/cpp/r/config.h.in
+index 6ba67c8e09..00bc8b6191 100644
+--- a/src/cpp/r/config.h.in
++++ b/src/cpp/r/config.h.in
+@@ -1,7 +1,7 @@
+ /*
+  * config.h.in
+  *
+- * Copyright (C) 2009-12 by RStudio, PBC
++ * Copyright (C) 2009-20 by RStudio, Inc.
+  *
+  * Unless you have received this program directly from RStudio pursuant
+  * to the terms of a commercial license agreement with RStudio, then
+@@ -16,4 +16,10 @@
+ 
+ #cmakedefine PANGO_CAIRO_FOUND
+ 
++// Important: These variables represent the version of R found during
++// compile/link time, NOT the version of R present at runtime.
++#define R_VERSION_MAJOR ${R_VERSION_MAJOR}
++#define R_VERSION_MINOR ${R_VERSION_MINOR}
++#define R_VERSION_PATCH ${R_VERSION_PATCH}
++
+ 
+diff --git a/src/cpp/r/session/REmbeddedPosix.cpp b/src/cpp/r/session/REmbeddedPosix.cpp
+index ac71b94522..73e2e2ce7f 100644
+--- a/src/cpp/r/session/REmbeddedPosix.cpp
++++ b/src/cpp/r/session/REmbeddedPosix.cpp
+@@ -1,7 +1,7 @@
+ /*
+  * REmbeddedPosix.cpp
+  *
+- * Copyright (C) 2009-19 by RStudio, PBC
++ * Copyright (C) 2009-20 by RStudio, Inc.
+  *
+  * Unless you have received this program directly from RStudio pursuant
+  * to the terms of a commercial license agreement with RStudio, then
+@@ -38,6 +38,8 @@ extern "C" void (*ptr_R_ProcessEvents)(void);
+ extern "C"  typedef void (*ptr_QuartzCocoa_SetupEventLoop)(int, unsigned long);
+ #endif
+ 
++#include "config.h"
++
+ extern int R_running_as_main_program;  // from unix/system.c
+ 
+ using namespace rstudio::core;
+@@ -103,14 +105,20 @@ void runEmbeddedR(const core::FilePath& /*rHome*/,    // ignored on posix
+    //
+    structRstart rp;
+    Rstart Rp = &rp;
+-   R_DefParams(Rp) ;
+-   Rp->R_Slave = FALSE ;
++   R_DefParams(Rp);
++#if R_VERSION_MAJOR > 3
++   // R 4.0 and above use --no-echo to suppress output
++   Rp->R_NoEcho = FALSE;
++#else
++   // R 3.x and below use --slave
++   Rp->R_Slave = FALSE;
++#endif
+    Rp->R_Quiet = quiet ? TRUE : FALSE;
+-   Rp->R_Interactive = TRUE ;
+-   Rp->SaveAction = defaultSaveAction ;
++   Rp->R_Interactive = TRUE;
++   Rp->SaveAction = defaultSaveAction;
+    Rp->RestoreAction = SA_NORESTORE; // handled within initialize()
+    Rp->LoadInitFile = loadInitFile ? TRUE : FALSE;
+-   R_SetParams(Rp) ;
++   R_SetParams(Rp);
+ 
+    // redirect console
+    R_Interactive = TRUE; // should have also been set by call to Rf_initialize_R
diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch
new file mode 100644
index 000000000000..0f6af4ef7f12
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch
@@ -0,0 +1,184 @@
+--- rstudio-1.3.959-orig/src/cpp/session/SessionClientInit.cpp	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/SessionClientInit.cpp	2020-05-24 17:21:56.960469575 +1000
+@@ -91,13 +91,13 @@
+       boost::shared_ptr<http::Cookie>* pCookie)
+ {
+    // extract the base URL
+-   json::JsonRpcRequest request;
++   core::json::JsonRpcRequest request;
+    Error error = parseJsonRpcRequest(ptrConnection->request().body(), &request);
+    if (error)
+       return error;
+    std::string baseURL;
+ 
+-   error = json::readParams(request.params, &baseURL);
++   error = core::json::readParams(request.params, &baseURL);
+    if (error)
+       return error;
+ 
+@@ -143,7 +143,7 @@
+    if (options.programMode() == kSessionProgramModeServer && 
+        !core::http::validateCSRFHeaders(ptrConnection->request()))
+    {
+-      ptrConnection->sendJsonRpcError(Error(json::errc::Unauthorized, ERROR_LOCATION));
++      ptrConnection->sendJsonRpcError(Error(core::json::errc::Unauthorized, ERROR_LOCATION));
+       return;
+    }
+ 
+@@ -173,12 +173,12 @@
+    }
+ 
+    // prepare session info 
+-   json::Object sessionInfo ;
++   core::json::Object sessionInfo ;
+    sessionInfo["clientId"] = clientId;
+    sessionInfo["mode"] = options.programMode();
+ 
+    // build initialization options for client
+-   json::Object initOptions;
++   core::json::Object initOptions;
+    initOptions["restore_workspace"] = options.rRestoreWorkspace();
+    initOptions["run_rprofile"] = options.rRunRprofile();
+    sessionInfo["init_options"] = initOptions;
+@@ -194,8 +194,8 @@
+    }
+ 
+    // temp dir
+-   FilePath tempDir = rstudio::r::session::utils::tempDir();
+-   Error error = tempDir.ensureDirectory();
++   core::FilePath tempDir = rstudio::r::session::utils::tempDir();
++   core::Error error = tempDir.ensureDirectory();
+    if (error)
+       LOG_ERROR(error);
+    sessionInfo["temp_dir"] = tempDir.getAbsolutePath();
+@@ -213,12 +213,12 @@
+    sessionInfo["prompt"] = rstudio::r::options::getOption<std::string>("prompt");
+ 
+    // client state
+-   json::Object clientStateObject;
++   core::json::Object clientStateObject;
+    rstudio::r::session::clientState().currentState(&clientStateObject);
+    sessionInfo["client_state"] = clientStateObject;
+    
+    // source documents
+-   json::Array jsonDocs;
++   core::json::Array jsonDocs;
+    error = modules::source::clientInitDocuments(&jsonDocs);
+    if (error)
+       LOG_ERROR(error);
+@@ -243,7 +243,7 @@
+    if (resumed)
+    {
+       // console actions
+-      json::Object actionsObject;
++     core::json::Object actionsObject;
+       consoleActions.asJson(&actionsObject);
+       sessionInfo["console_actions"] = actionsObject;
+    }
+@@ -310,12 +310,12 @@
+    }
+    else
+    {
+-      sessionInfo["active_project_file"] = json::Value();
+-      sessionInfo["project_ui_prefs"] = json::Value();
+-      sessionInfo["project_open_docs"] = json::Value();
++      sessionInfo["active_project_file"] = core::json::Value();
++      sessionInfo["project_ui_prefs"] = core::json::Value();
++      sessionInfo["project_open_docs"] = core::json::Value();
+       sessionInfo["project_supports_sharing"] = false;
+       sessionInfo["project_owned_by_user"] = false;
+-      sessionInfo["project_user_data_directory"] = json::Value();
++      sessionInfo["project_user_data_directory"] = core::json::Value();
+    }
+ 
+    sessionInfo["system_encoding"] = std::string(::locale2charset(nullptr));
+@@ -352,20 +352,20 @@
+       sessionInfo["build_tools_bookdown_website"] =
+                               module_context::isBookdownWebsite();
+ 
+-      FilePath buildTargetDir = projects::projectContext().buildTargetPath();
++      core::FilePath buildTargetDir = projects::projectContext().buildTargetPath();
+       if (!buildTargetDir.isEmpty())
+       {
+          sessionInfo["build_target_dir"] = module_context::createAliasedPath(
+                                                                 buildTargetDir);
+-         sessionInfo["has_pkg_src"] = (type == r_util::kBuildTypePackage) &&
++         sessionInfo["has_pkg_src"] = (type == core::r_util::kBuildTypePackage) &&
+             buildTargetDir.completeChildPath("src").exists();
+          sessionInfo["has_pkg_vig"] =
+-               (type == r_util::kBuildTypePackage) &&
++               (type == core::r_util::kBuildTypePackage) &&
+                   buildTargetDir.completeChildPath("vignettes").exists();
+       }
+       else
+       {
+-         sessionInfo["build_target_dir"] = json::Value();
++         sessionInfo["build_target_dir"] = core::json::Value();
+          sessionInfo["has_pkg_src"] = false;
+          sessionInfo["has_pkg_vig"] = false;
+       }
+@@ -373,9 +373,9 @@
+    }
+    else
+    {
+-      sessionInfo["build_tools_type"] = r_util::kBuildTypeNone;
++      sessionInfo["build_tools_type"] = core::r_util::kBuildTypeNone;
+       sessionInfo["build_tools_bookdown_website"] = false;
+-      sessionInfo["build_target_dir"] = json::Value();
++      sessionInfo["build_target_dir"] = core::json::Value();
+       sessionInfo["has_pkg_src"] = false;
+       sessionInfo["has_pkg_vig"] = false;
+    }
+@@ -384,7 +384,7 @@
+    sessionInfo["presentation_commands"] = options.allowPresentationCommands();
+ 
+    sessionInfo["tutorial_api_available"] = false;
+-   sessionInfo["tutorial_api_client_origin"] = json::Value();
++   sessionInfo["tutorial_api_client_origin"] = core::json::Value();
+ 
+    sessionInfo["build_state"] = modules::build::buildStateAsJson();
+    sessionInfo["devtools_installed"] = module_context::isMinimumDevtoolsInstalled();
+@@ -395,7 +395,7 @@
+ 
+    // console history -- we do this at the end because
+    // restoreBuildRestartContext may have reset it
+-   json::Array historyArray;
++   core::json::Array historyArray;
+    rstudio::r::session::consoleHistory().asJson(&historyArray);
+    sessionInfo["console_history"] = historyArray;
+    sessionInfo["console_history_capacity"] =
+@@ -470,14 +470,14 @@
+ 
+    sessionInfo["multi_session"] = options.multiSession();
+ 
+-   json::Object rVersionsJson;
++   core::json::Object rVersionsJson;
+    rVersionsJson["r_version"] = module_context::rVersion();
+    rVersionsJson["r_version_label"] = module_context::rVersionLabel();
+    rVersionsJson["r_home_dir"] = module_context::rHomeDir();
+    sessionInfo["r_versions_info"] = rVersionsJson;
+ 
+    sessionInfo["show_user_home_page"] = options.showUserHomePage();
+-   sessionInfo["user_home_page_url"] = json::Value();
++   sessionInfo["user_home_page_url"] = core::json::Value();
+    
+    sessionInfo["r_addins"] = modules::r_addins::addinRegistryAsJson();
+    sessionInfo["package_provided_extensions"] = modules::ppe::indexer().getPayload();
+@@ -501,7 +501,7 @@
+ 
+    sessionInfo["launcher_jobs_enabled"] = modules::overlay::launcherJobsFeatureDisplayed();
+ 
+-   json::Object packageDependencies;
++   core::json::Object packageDependencies;
+    error = modules::dependency_list::getDependencyList(&packageDependencies);
+    if (error)
+       LOG_ERROR(error);
+@@ -529,7 +529,7 @@
+ 
+    // create response  (we always set kEventsPending to false so that the client
+    // won't poll for events until it is ready)
+-   json::JsonRpcResponse jsonRpcResponse;
++   core::json::JsonRpcResponse jsonRpcResponse;
+    jsonRpcResponse.setField(kEventsPending, "false");
+    jsonRpcResponse.setResult(sessionInfo);
+ 
diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch
new file mode 100644
index 000000000000..d8718dda9b18
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch
@@ -0,0 +1,42 @@
+--- rstudio-1.3.959-orig/src/cpp/session/CMakeLists.txt	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/CMakeLists.txt	2020-05-24 18:54:40.444955162 +1000
+@@ -22,12 +22,6 @@
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries")
+   message(FATAL_ERROR "Dictionaries not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27")
+-  message(FATAL_ERROR "Mathjax 2.7 not found (re-run install-dependencies script to install)")
+-endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+ 
+ # verify embedded packages are available
+ foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})
+@@ -500,10 +494,6 @@
+    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries"
+            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+ 
+-   # install mathjax for local html preview
+-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27"
+-           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+-
+    # icons for database connections
+    install(DIRECTORY "resources/connections"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+@@ -516,15 +506,6 @@
+    install(DIRECTORY "resources/dependencies"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install pandoc
+-   set(PANDOC_VERSION "2.7.3" CACHE INTERNAL "Pandoc version")
+-
+-   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/${PANDOC_VERSION}")
+-   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
+-   install(FILES ${PANDOC_FILES}
+-           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+-           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
+-
+    # install embedded packages
+    foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})
+       file(GLOB PKG_FILES "${RSTUDIO_DEPENDENCIES_DIR}/common/${PKG}*.tar.gz")
diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch
new file mode 100644
index 000000000000..175d52f7149a
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch
@@ -0,0 +1,118 @@
+--- rstudio-1.3.959-orig/CMakeGlobals.txt	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/CMakeGlobals.txt	2020-05-25 19:30:10.711859714 +1000
+@@ -181,7 +181,7 @@
+    else()
+      set(RSTUDIO_INSTALL_BIN bin)
+    endif()
+-   set(RSTUDIO_INSTALL_SUPPORTING .)
++   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
+ endif()
+ 
+ # if the install prefix is /usr/local then tweak as appropriate
+--- rstudio-1.3.959-orig/src/cpp/server/CMakeLists.txt	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/server/CMakeLists.txt	2020-05-25 19:30:10.711859714 +1000
+@@ -190,7 +190,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
+ 
+    # install configured redhat init.d script
+    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
+@@ -198,7 +198,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
+ 
+    # install configured suse init.d script
+    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
+@@ -206,13 +206,13 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_SUSE_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
+ 
+    # install pam profile
+    set(RSERVER_PAM_DIR "extras/pam")
+    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
+-           DESTINATION ${RSERVER_PAM_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
+ 
+    # install configured upstart profile
+    set(RSERVER_UPSTART_DIR "extras/upstart")
+@@ -220,12 +220,12 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+ 
+     # install configured systemd profile
+    set(RSERVER_SYSTEMD_DIR "extras/systemd")
+--- rstudio-1.3.959-orig/src/cpp/server/ServerOptions.cpp	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/server/ServerOptions.cpp	2020-05-25 19:34:19.377675880 +1000
+@@ -442,8 +442,8 @@
+ 
+    // convert relative paths by completing from the system installation
+    // path (this allows us to be relocatable)
+-   resolvePath(resourcePath, &wwwLocalPath_);
+-   resolvePath(resourcePath, &wwwSymbolMapsPath_);
++   resolvePath(resourcePath.completeChildPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath.completeChildPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
+    resolvePath(binaryPath, &authPamHelperPath_);
+    resolvePath(binaryPath, &rsessionPath_);
+    resolvePath(binaryPath, &rldpathPath_);
+--- rstudio-1.3.959-orig/src/cpp/session/SessionOptions.cpp	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/SessionOptions.cpp	2020-05-25 19:33:58.318606745 +1000
+@@ -52,7 +52,7 @@
+ namespace session {  
+ 
+ namespace {
+-const char* const kDefaultPandocPath = "bin/pandoc";
++const char* const kDefaultPandocPath = "bin";
+ const char* const kDefaultPostbackPath = "bin/postback/rpostback";
+ const char* const kDefaultRsclangPath = "bin/rsclang";
+ 
+@@ -586,14 +586,14 @@
+    }
+    
+    // convert relative paths by completing from the app resource path
+-   resolvePath(resourcePath_, &rResourcesPath_);
+-   resolvePath(resourcePath_, &agreementFilePath_);
+-   resolvePath(resourcePath_, &wwwLocalPath_);
+-   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
+-   resolvePath(resourcePath_, &coreRSourcePath_);
+-   resolvePath(resourcePath_, &modulesRSourcePath_);
+-   resolvePath(resourcePath_, &sessionLibraryPath_);
+-   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &rResourcesPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &agreementFilePath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &coreRSourcePath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &modulesRSourcePath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &sessionLibraryPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
+    resolvePostbackPath(resourcePath_, &rpostbackPath_);
+ #ifdef _WIN32
+    resolvePath(resourcePath_, &consoleIoPath_);
+@@ -626,7 +626,7 @@
+    }
+    winptyPath_ = pty.completePath(completion).getAbsolutePath();
+ #endif // _WIN32
+-   resolvePath(resourcePath_, &hunspellDictionariesPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &hunspellDictionariesPath_);
+    resolvePath(resourcePath_, &mathjaxPath_);
+    resolvePath(resourcePath_, &libclangHeadersPath_);
+    resolvePandocPath(resourcePath_, &pandocPath_);
diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch
new file mode 100644
index 000000000000..4f9613947694
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch
@@ -0,0 +1,68 @@
+--- rstudio-1.3.959-orig/src/gwt/build.xml	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/gwt/build.xml	2020-05-25 17:38:28.911881424 +1000
+@@ -28,19 +28,37 @@
+             classname="com.google.javascript.jscomp.ant.CompileTask"
+             classpath="${tools.dir}/compiler/compiler.jar"/>
+ 
++   <!-- Configure path to aopalliance -->
++   <property name="aopalliance.sdk" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/aopalliance-1/lib"/>
++
++   <!-- Configure path to javax-inject -->
++   <property name="javax.inject" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/javax-inject/lib"/>
++
++   <!-- Configure path to validation-api -->
++   <property name="validation.api" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/validation-api-1.0/lib"/>
++   <property name="validation.api.sources" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/validation-api-1.0/sources"/>
++
+    <!-- Configure path to GWT SDK -->
+    <property name="gwt.sdk" value="${lib.dir}/gwt/gwt-rstudio-1.3"/>
++   <!-- Configure path to Google Gin -->
++   <property name="gin.sdk" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/gin-2.1/lib"/>
++
+    <property name="gwt.extra.args" value=""/>
+    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
+    <property name="ace.bin" value="${src.dir}/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
++   <property environment="env"/>
+ 
+    <!-- configure code server -->
+    <property name="bind.address" value="127.0.0.1"/>
+ 
+    <path id="project.class.path">
+      <pathelement location="${build.dir}"/>
++      <fileset dir="${aopalliance.sdk}" includes="*.jar"/>
++      <fileset dir="${javax.inject}" includes="*.jar"/>
++      <fileset dir="${validation.api}" includes="*.jar"/>
++      <fileset dir="${validation.api.sources}" includes="*.zip"/>
+       <fileset dir="${gwt.sdk}" includes="*.jar"/>
+-      <fileset dir="${lib.dir}/gin/2.1.2" includes="*.jar"/>
++      <fileset dir="${gin.sdk}" includes="*.jar"/>
+    </path>
+ 
+    <path id="test.class.path">
+@@ -114,8 +132,10 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
+          <jvmarg value="-Xmx1536M"/>
++         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
+          <arg value="-war"/>
+          <arg value="${www.dir}"/>
+          <arg value="-localWorkers"/>
+@@ -168,6 +188,7 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-style"/>
+          <arg value="PRETTY"/>
+@@ -212,6 +233,7 @@
+             <pathelement location="${test.dir}"/>
+             <pathelement location="${src.dir}"/>
+         </classpath>
++        <jvmarg value="-Duser.home=${env.T}"/>
+         <classpath refid="project.class.path"/>
+         <classpath refid="unittest.class.path"/>
+         <arg value="org.rstudio.studio.client.RStudioUnitTestSuite"/>
diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch
new file mode 100644
index 000000000000..3ced4f9afa1c
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch
@@ -0,0 +1,60 @@
+--- rstudio-1.3.959-orig/src/cpp/desktop/CMakeLists.txt	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/desktop/CMakeLists.txt	2020-05-24 17:15:47.039422975 +1000
+@@ -138,6 +138,13 @@
+ get_filename_component(QT_LIBRARY_PATH "${QT_BIN_DIR}/../lib"     ABSOLUTE CACHE)
+ get_filename_component(QT_INSTALL_PATH "${QT_BIN_DIR}/.."         ABSOLUTE CACHE)
+ 
++find_path(QTSINGLEAPPLIB_INCLUDE_DIR NAMES QtSingleApplication
++  PATH_SUFFIXES QtSolutions
++  PATHS
++  /usr/include/qt5)
++find_library(QTSINGLEAPPLIB Qt5Solutions_SingleApplication-2.6
++  libQt5Solutions_SingleApplication-2.6)
++
+ # disable clang warnings for qt sources
+ if(APPLE)
+    add_definitions(-Wno-unused-private-field
+@@ -156,7 +163,6 @@
+ 
+ set(MOC_DESKTOP_HEADER_FILES ${DESKTOP_HEADER_FILES})
+ list(REMOVE_ITEM MOC_DESKTOP_HEADER_FILES
+-  ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/qtsingleapplication/qtlockedfile.h
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopDetectRHome.hpp
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopOptions.hpp
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopRVersion.hpp
+@@ -225,8 +231,6 @@
+   DesktopSynctex.cpp
+   DesktopJobLauncherOverlay.cpp
+   RemoteDesktopSessionLauncherOverlay.cpp
+-  3rdparty/qtsingleapplication/qtsingleapplication.cpp
+-  3rdparty/qtsingleapplication/qtlocalpeer.cpp
+ )
+ 
+ if(WIN32)
+@@ -283,6 +287,7 @@
+   ${OPENSSL_INCLUDE_DIR}
+   ${CMAKE_CURRENT_SOURCE_DIR}
+   ${CMAKE_CURRENT_BINARY_DIR}
++  ${QTSINGLEAPPLIB_INCLUDE_DIR}
+   ${EXT_SOURCE_DIR}
+   ${SESSION_SOURCE_DIR}/include
+   ${TESTS_INCLUDE_DIR}
+@@ -386,6 +391,7 @@
+    # set link dependencies
+    target_link_libraries(rstudio
+       ${RSTUDIO_QTMODULES}
++      ${QTSINGLEAPPLIB}
+       ${QT_LIBRARIES}
+       ${Boost_LIBRARIES}
+       rstudio-core
+--- rstudio-1.3.959-orig/src/cpp/desktop/DesktopPosixApplication.hpp	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/desktop/DesktopPosixApplication.hpp	2020-05-24 17:13:22.050016953 +1000
+@@ -16,7 +16,7 @@
+ #ifndef DESKTOP_POSIX_APPLICATION_HPP
+ #define DESKTOP_POSIX_APPLICATION_HPP
+ 
+-#include "3rdparty/qtsingleapplication/QtSingleApplication"
++#include <QtSingleApplication>
+ 
+ #include "DesktopApplicationLaunch.hpp"
+