jasp-desktop: 0.19.1 -> 0.19.3 (#410351)

pkgs/by-name/ja/jasp-desktop/cmake.patch

@@ -1,5 +1,5 @@
 diff --git a/Tools/CMake/Libraries.cmake b/Tools/CMake/Libraries.cmake
-index cc4681a..f484013 100644
+index a95ef78..6ee84cd 100644
 --- a/Tools/CMake/Libraries.cmake
 +++ b/Tools/CMake/Libraries.cmake
 @@ -67,7 +67,7 @@ if((NOT LibArchive_FOUND) AND (NOT WIN32))
@@ -11,36 +11,67 @@ index cc4681a..f484013 100644
  find_package(
    Boost 1.78 REQUIRED
    COMPONENTS filesystem
-@@ -178,10 +178,10 @@ if(LINUX)
-     set(LIBREADSTAT_INCLUDE_DIRS /app/include)
-     set(LIBREADSTAT_LIBRARY_DIRS /app/lib)
-   else()
--    set(LIBREADSTAT_INCLUDE_DIRS /usr/local/include /usr/include)
-+    set(LIBREADSTAT_INCLUDE_DIRS @readstat@/include /usr/include)
-     # The last two library paths handle the two most common multiarch cases.
-     # Other multiarch-compliant paths may come up but should be rare.
--    set(LIBREADSTAT_LIBRARY_DIRS /usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu /usr/lib/aarch64-linux-gnu)
-+    set(LIBREADSTAT_LIBRARY_DIRS @readstat@/lib /usr/lib /usr/lib/x86_64-linux-gnu /usr/lib/aarch64-linux-gnu)
+@@ -185,7 +185,7 @@ if(LINUX)
    endif()
  
    message(CHECK_START "Looking for libreadstat.so")
+-  find_file(LIBREADSTAT_LIBRARIES libreadstat.so
++  find_library(LIBREADSTAT_LIBRARIES libreadstat.so
+             HINTS ${LIBREADSTAT_LIBRARY_DIRS} REQUIRED)
+ 
+   if(EXISTS ${LIBREADSTAT_LIBRARIES})
 diff --git a/Tools/CMake/Programs.cmake b/Tools/CMake/Programs.cmake
-index dbd089d..ef6857a 100644
+index bfdc8dc..af5ac03 100644
 --- a/Tools/CMake/Programs.cmake
 +++ b/Tools/CMake/Programs.cmake
-@@ -39,6 +39,7 @@ endif()
+@@ -38,8 +38,9 @@ if(NOT WIN32)
+ endif()
  
  # ------ Linux Tools/Programs
- 
-+#[[
- if(LINUX)
+-
+-if(LINUX)
++# We don't need to check for any dependencies that are used to build R packages
++# since we build them separately
++if(false)
  
    message(CHECK_START "Looking for 'gfortran'")
-@@ -81,6 +82,7 @@ if(LINUX)
-   endif()
+   find_program(
+diff --git a/Tools/CMake/R.cmake b/Tools/CMake/R.cmake
+index 9ae27d4..64fd96a 100644
+--- a/Tools/CMake/R.cmake
++++ b/Tools/CMake/R.cmake
+@@ -841,11 +841,6 @@ message(STATUS "R_CPP_INCLUDES_LIBRARY = ${R_CPP_INCLUDES_LIBRARY}")
+ configure_file(${PROJECT_SOURCE_DIR}/Modules/setup_renv.R.in
+                 ${SCRIPT_DIRECTORY}/setup_renv.R @ONLY)
  
- endif()
-+]]#
+-execute_process(
+-  COMMAND_ECHO STDOUT
+-  #ERROR_QUIET OUTPUT_QUIET
+-  WORKING_DIRECTORY ${R_HOME_PATH}
+-  COMMAND ${R_EXECUTABLE} --slave --no-restore --no-save --file=${SCRIPT_DIRECTORY}/setup_renv.R)
  
- # ----------------------
+ if(APPLE)
+   # Patch renv
+@@ -867,11 +862,6 @@ endif()
+ configure_file(${PROJECT_SOURCE_DIR}/Modules/setup_rcpp_rinside.R.in
+                 ${SCRIPT_DIRECTORY}/setup_rcpp_rinside.R @ONLY)
+ 
+-execute_process(
+-  COMMAND_ECHO STDOUT
+-  #ERROR_QUIET OUTPUT_QUIET
+-  WORKING_DIRECTORY ${R_HOME_PATH}
+-  COMMAND ${R_EXECUTABLE} --slave --no-restore --no-save --file=${SCRIPT_DIRECTORY}/setup_rcpp_rinside.R)
+ 
+ if(APPLE)
+   # Patch RInside and RCpp
+@@ -892,8 +882,8 @@ endif()
+ 
+ include(FindRPackagePath)
+ 
+-find_package_path(RCPP_PATH       ${R_CPP_INCLUDES_LIBRARY} "Rcpp")
+-find_package_path(RINSIDE_PATH    ${R_CPP_INCLUDES_LIBRARY} "RInside")
++find_package_path(RCPP_PATH       ${R_LIBRARY_PATH} "Rcpp")
++find_package_path(RINSIDE_PATH    ${R_LIBRARY_PATH} "RInside")
+ 
+ set(RENV_PATH "${RENV_LIBRARY}/renv")
  

pkgs/by-name/ja/jasp-desktop/modules.nix

@@ -165,6 +165,12 @@ let
       src = jasp-src;
       sourceRoot = "${jasp-src.name}/Modules/${name}";
       propagatedBuildInputs = deps;
+
+      # some packages have a .Rprofile that tries to activate renv
+      # we disable this by removing .Rprofile
+      postPatch = ''
+        rm -f .Rprofile
+      '';
     };
 in
 {
@@ -229,6 +235,20 @@ in
       jaspGraphs
       jaspSem
     ];
+    jaspBFF = buildJaspModule "jaspBFF" [
+      BFF
+      jaspBase
+      jaspGraphs
+    ];
+    jaspBfpack = buildJaspModule "jaspBfpack" [
+      BFpack
+      bain
+      ggplot2
+      stringr
+      coda
+      jaspBase
+      jaspGraphs
+    ];
     jaspBsts = buildJaspModule "jaspBsts" [
       Boom
       bsts
@@ -305,6 +325,7 @@ in
       conting'
       multibridge
       ggplot2
+      interp
       jaspBase
       jaspGraphs
       plyr
@@ -353,6 +374,8 @@ in
       ggforce
       tidyr
       igraph
+      HDInterval
+      metafor
     ];
     jaspMachineLearning = buildJaspModule "jaspMachineLearning" [
       kknn
@@ -375,6 +398,7 @@ in
       jaspBase
       jaspGraphs
       MASS
+      mclust
       mvnormalTest
       neuralnet
       network
@@ -385,6 +409,7 @@ in
       ROCR
       Rtsne
       signal
+      VGAM
     ];
     jaspMetaAnalysis = buildJaspModule "jaspMetaAnalysis" [
       dplyr
@@ -406,6 +431,12 @@ in
       metamisc
       ggmcmc
       pema
+      clubSandwich
+      CompQuadForm
+      sp
+      dfoptim
+      nleqslv
+      patchwork
     ];
     jaspMixedModels = buildJaspModule "jaspMixedModels" [
       afex
@@ -459,6 +490,8 @@ in
       BART
       EBMAforecast
       imputeTS
+      scoringRules
+      scoringutils
     ];
     jaspProcess = buildJaspModule "jaspProcess" [
       blavaan
@@ -543,6 +576,7 @@ in
       lme4
       MASS
       psych
+      mirt
     ];
     jaspRobustTTests = buildJaspModule "jaspRobustTTests" [
       RoBTT
@@ -553,16 +587,17 @@ in
     jaspSem = buildJaspModule "jaspSem" [
       forcats
       ggplot2
-      jaspBase
-      jaspGraphs
       lavaan
       cSEM
       reshape2
+      jaspBase
+      jaspGraphs
       semPlot
       semTools
       stringr
       tibble
       tidyr
+      SEMsens
     ];
     jaspSummaryStatistics = buildJaspModule "jaspSummaryStatistics" [
       BayesFactor
@@ -579,7 +614,7 @@ in
     ];
     jaspSurvival = buildJaspModule "jaspSurvival" [
       survival
-      survminer
+      ggsurvfit
       jaspBase
       jaspGraphs
     ];
@@ -593,6 +628,12 @@ in
       plotrix
       plyr
     ];
+    jaspTestModule = buildJaspModule "jaspTestModule" [
+      jaspBase
+      jaspGraphs
+      svglite
+      stringi
+    ];
     jaspTimeSeries = buildJaspModule "jaspTimeSeries" [
       jaspBase
       jaspGraphs

pkgs/by-name/ja/jasp-desktop/package.nix

@@ -1,31 +1,34 @@
 {
   lib,
   stdenv,
+
   fetchFromGitHub,
-  fetchpatch,
+
   buildEnv,
   linkFarm,
-  replaceVars,
-  R,
-  rPackages,
+
   cmake,
   ninja,
   pkg-config,
+
   boost,
+  freexl,
   libarchive,
-  readstat,
   qt6,
+  R,
+  readstat,
+  rPackages,
 }:
 
 let
-  version = "0.19.1";
+  version = "0.19.3";
 
   src = fetchFromGitHub {
     owner = "jasp-stats";
     repo = "jasp-desktop";
-    rev = "v${version}";
-    hash = "sha256-SACGyNVxa6rFjloRQrEVtUgujEEF7WYL8Qhw6ZqLwdQ=";
+    tag = "v${version}";
     fetchSubmodules = true;
+    hash = "sha256-p489Q3jMQ7UWOCdAGskRF9KSLoRSatUwGVfj0/g4aPo=";
   };
 
   moduleSet = import ./modules.nix {
@@ -58,25 +61,19 @@ stdenv.mkDerivation {
   inherit version src;
 
   patches = [
-    # remove unused cmake deps, ensure boost is dynamically linked, patch readstat path
-    (replaceVars ./cmake.patch {
-      inherit readstat;
-    })
-
-    (fetchpatch {
-      name = "fix-qt-6.8-crash.patch";
-      url = "https://github.com/jasp-stats/jasp-desktop/commit/d96a35d262312f72081ac3f96ae8c2ae7c796b0.patch";
-      hash = "sha256-KcsFy1ImPTHwDKN5Umfoa9CbtQn7B3FNu/Srr0dEJGA=";
-    })
+    # - ensure boost is linked dynamically
+    # - fix readstat's find logic
+    # - disable some of the renv logic
+    # - dont't check for dependencies required for building modules
+    ./cmake.patch
   ];
 
   cmakeFlags = [
-    "-DGITHUB_PAT=dummy"
-    "-DGITHUB_PAT_DEF=dummy"
-    "-DINSTALL_R_FRAMEWORK=OFF"
-    "-DLINUX_LOCAL_BUILD=OFF"
-    "-DINSTALL_R_MODULES=OFF"
-    "-DCUSTOM_R_PATH=${customREnv}"
+    (lib.cmakeFeature "GITHUB_PAT" "dummy")
+    (lib.cmakeFeature "GITHUB_PAT_DEF" "dummy")
+    (lib.cmakeBool "LINUX_LOCAL_BUILD" false)
+    (lib.cmakeBool "INSTALL_R_MODULES" false)
+    (lib.cmakeFeature "CUSTOM_R_PATH" "${customREnv}")
   ];
 
   nativeBuildInputs = [
@@ -87,10 +84,12 @@ stdenv.mkDerivation {
   ];
 
   buildInputs = [
-    customREnv
     boost
+    customREnv
+    freexl
     libarchive
     readstat
+
     qt6.qtbase
     qt6.qtdeclarative
     qt6.qtwebengine
@@ -98,6 +97,7 @@ stdenv.mkDerivation {
     qt6.qt5compat
   ];
 
+  # needed so that JASPEngine can find libRInside.so
   env.NIX_LDFLAGS = "-L${rPackages.RInside}/library/RInside/lib";
 
   postInstall = ''
@@ -107,7 +107,7 @@ stdenv.mkDerivation {
     # Remove flatpak proxy script
     rm $out/bin/org.jaspstats.JASP
     substituteInPlace $out/share/applications/org.jaspstats.JASP.desktop \
-        --replace-fail "Exec=org.jaspstats.JASP" "Exec=JASP"
+      --replace-fail "Exec=org.jaspstats.JASP" "Exec=JASP"
 
     # symlink modules from the store
     ln -s ${modulesDir} $out/Modules