sci-mathematics/rstudio: Bump to 1.2.5033, use acct rstudio-server

Thanks to John Dough for reporting the version bump bug #702140.

Thanks to toralf for reporting bug #693662.  The egit_clean: command not found
is fixed by inherit vcs-clean.

The QA: other
The ebuild is installing to one or more unexpected paths:

  /usr/extras

is fixed with the sed under this comment:
# install themes in /etc/rstudio/extra/sthemes instead of /usr/extra/themes

The: One or more CMake variables were not used by the project:
  QT_QMAKE_EXECUTABLE
  RSTUDIO_INSTALL_FREEDESKTOP

is fixed by only setting these variables if use !dedicated.

Thanks to Alessandro Barbieri reporting bug #696944, the dependencies are
unbundled in rstudio 1.2.5033.ebuild, and some needless dependencies are
removed.

Closes: https://bugs.gentoo.org/show_bug.cgi?id=702140
Closes: https://bugs.gentoo.org/show_bug.cgi?id=693662
Closes: https://bugs.gentoo.org/show_bug.cgi?id=696944
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Mark Wright <gienah@gentoo.org>

3 files changed, 233 insertions, 0 deletions

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.5033-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.2.5033-pandoc.patch
new file mode 100644
index 000000000000..b4f611063e17
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.5033-pandoc.patch
@@ -0,0 +1,32 @@
+--- rstudio-1.2.5033-orig/src/cpp/session/CMakeLists.txt	2019-12-04 17:22:17.000000000 +1100
++++ rstudio-1.2.5033/src/cpp/session/CMakeLists.txt	2020-01-07 12:29:20.174304185 +1100
+@@ -25,9 +25,6 @@
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
+   message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+ 
+ # we often install embedded versions of these packages but don't do so currently
+ 
+@@ -490,19 +487,6 @@
+    install(DIRECTORY "resources/connections"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install pandoc
+-   if(WIN32)
+-      set(PANDOC_VERSION "2.7.2" CACHE INTERNAL "Pandoc version")
+-   else()
+-      set(PANDOC_VERSION "2.3.1" CACHE INTERNAL "Pandoc version")
+-   endif()
+-
+-   set(PANDOC_BIN "${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  ${RSTUDIO_INSTALL_BIN}/pandoc)
+-
+    # install rmarkdown package
+    # file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
+    # install(FILES ${RMARKDOWN_PACKAGE}
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.5033-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.2.5033-paths.patch
new file mode 100644
index 000000000000..aa6a9b23fdec
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.5033-paths.patch
@@ -0,0 +1,118 @@
+--- rstudio-1.2.5033-orig/CMakeGlobals.txt	2019-12-04 17:22:17.000000000 +1100
++++ rstudio-1.2.5033/CMakeGlobals.txt	2020-01-07 12:20:19.115307754 +1100
+@@ -175,7 +175,7 @@
+    else()
+      set(RSTUDIO_INSTALL_BIN bin)
+    endif()
+-   set(RSTUDIO_INSTALL_SUPPORTING .)
++   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
+ endif()
+ 
+ # if the install prefix is /usr/local then tweak as appropriate
+--- rstudio-1.2.5033-orig/src/cpp/server/CMakeLists.txt	2019-12-04 17:22:17.000000000 +1100
++++ rstudio-1.2.5033/src/cpp/server/CMakeLists.txt	2020-01-07 12:17:32.736309024 +1100
+@@ -194,7 +194,7 @@
+    configure_file(${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")
+@@ -202,7 +202,7 @@
+    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")
+@@ -210,13 +210,13 @@
+    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")
+@@ -224,12 +224,12 @@
+    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-1.2.5033-orig/src/cpp/server/ServerOptions.cpp	2019-12-04 17:22:17.000000000 +1100
++++ rstudio-1.2.5033/src/cpp/server/ServerOptions.cpp	2020-01-07 12:17:32.773309023 +1100
+@@ -389,8 +389,8 @@
+ 
+    // convert relative paths by completing from the system installation
+    // path (this allows us to be relocatable)
+-   resolvePath(resourcePath, &wwwLocalPath_);
+-   resolvePath(resourcePath, &wwwSymbolMapsPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
+    resolvePath(binaryPath, &authPamHelperPath_);
+    resolvePath(binaryPath, &rsessionPath_);
+    resolvePath(binaryPath, &rldpathPath_);
+--- rstudio-1.2.5033-orig/src/cpp/session/SessionOptions.cpp	2019-12-04 17:22:17.000000000 +1100
++++ rstudio-1.2.5033/src/cpp/session/SessionOptions.cpp	2020-01-07 12:17:32.774309023 +1100
+@@ -53,7 +53,7 @@
+ 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";
+ 
+@@ -571,14 +571,14 @@
+    }
+    
+    // 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_.childPath(DISTRO_SHARE), &rResourcesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &agreementFilePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &coreRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &modulesRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionLibraryPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
+    resolvePostbackPath(resourcePath_, &rpostbackPath_);
+ #ifdef _WIN32
+    resolvePath(resourcePath_, &consoleIoPath_);
+@@ -611,7 +611,7 @@
+    }
+    winptyPath_ = pty.complete(completion).absolutePath();
+ #endif // _WIN32
+-   resolvePath(resourcePath_, &hunspellDictionariesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
+    resolvePath(resourcePath_, &mathjaxPath_);
+    resolvePath(resourcePath_, &libclangHeadersPath_);
+    resolvePandocPath(resourcePath_, &pandocPath_);
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.5033-prefs.patch b/sci-mathematics/rstudio/files/rstudio-1.2.5033-prefs.patch
new file mode 100644
index 000000000000..034eba37a8b9
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.5033-prefs.patch
@@ -0,0 +1,83 @@
+--- rstudio-1.2.5033-orig/src/gwt/build.xml	2019-12-04 17:22:17.000000000 +1100
++++ rstudio-1.2.5033/src/gwt/build.xml	2020-01-10 18:35:29.913030923 +1100
+@@ -28,17 +28,35 @@
+             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/2.8.1"/>
++   <property name="gwt.sdk" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/gwt-2.8/lib"/>
++
++   <!-- 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="${src.dir}/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
++   <property environment="env"/>
+ 
+    <path id="project.class.path">
+      <pathelement location="${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="${gin.sdk}" includes="*.jar"/>
+    </path>
+ 
+    <path id="test.class.path">
+@@ -112,8 +130,10 @@
+             <pathelement location="${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="${www.dir}"/>
+          <arg value="-localWorkers"/>
+@@ -154,6 +174,7 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-style"/>
+          <arg value="PRETTY"/>
+@@ -176,6 +197,7 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-style"/>
+          <arg value="PRETTY"/>
+@@ -202,6 +224,7 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+       	<arg value="-src"/>
+       	<arg value = "src"/>
+@@ -237,6 +260,7 @@
+             <pathelement location="${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"/>