galaaz 2.1.1 → 2.1.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## 2.1.3
+
+### Fixed
+
+- Gatekeeper builds on **R 4.5+/4.6** (Omarchy): replace removed `Rf_findVar` with
+  `R_getVarEx` (fallback to `Rf_findVar` on older R).
+
+## 2.1.2
+
+### Fixed
+
+- CRAN installs (`galaaz setup` / `galaaz add`) use a writable user library
+  (`R_LIBS_USER`, default `~/.local/lib/R/library`) so Omarchy/Arch no longer fail
+  with `lib = "/usr/lib/R/library" is not writable`.
+- Gatekeeper `ext/new_bridge` Makefile uses `R CMD config --ldflags` instead of
+  hardcoded `-L$(R_HOME)/lib -lR` (breaks when `RHOME` is `/usr/lib64/R`).
+- `galaaz setup` marks profile `core` on success.
+
+### Notes
+
+- Omarchy dogfood: `script/omarchy/install-galaaz.sh` installs latest from RubyGems
+  (optional pin: `GALAAZ_GEM_VERSION=x.y.z`). Re-copy into `~/.local/bin/omarchy-install-galaaz`
+  after updating the script.
+
 ## 2.1.1
 
 ### Added

data/ext/new_bridge/Makefile

@@ -1,21 +1,21 @@
 # Makefile for Galaaz Gatekeeper shared library
 # Usage: make clean all
 
-# R configuration
+# Prefer `R` / `Rscript` on PATH (Omarchy/Arch: RHOME may be /usr/lib64/R).
 R_HOME := $(shell R RHOME)
-R_CPPFLAGS := $(shell $(R_HOME)/bin/R CMD config --cppflags)
-R_LIBS := $(shell $(R_HOME)/bin/R CMD config --ldflags)
+R_CPPFLAGS := $(shell R CMD config --cppflags)
+# Full linker flags from R (do NOT hardcode -L$(R_HOME)/lib — wrong on some Arch layouts).
+R_LDFLAGS := $(shell R CMD config --ldflags)
 
-# Rcpp configuration
-RCPP_INCLUDE := $(shell $(R_HOME)/bin/Rscript -e "cat(system.file('include', package='Rcpp'))")
+# Rcpp configuration (needs R_LIBS_USER for user-library installs)
+RCPP_INCLUDE := $(shell Rscript -e "cat(system.file('include', package='Rcpp'))")
 RCPP_CPPFLAGS := -I$(RCPP_INCLUDE)
 
 # Compiler settings
-CXX := $(shell $(R_HOME)/bin/R CMD config CXX)
-CXXFLAGS := $(shell $(R_HOME)/bin/R CMD config CXXFLAGS)
+CXX := $(shell R CMD config CXX)
+CXXFLAGS := $(shell R CMD config CXXFLAGS)
 CPPFLAGS := $(R_CPPFLAGS) $(RCPP_CPPFLAGS) -I.
-# Core R library only (avoid system libs that may not be present)
-LDFLAGS := -L$(R_HOME)/lib -lR -Wl,-rpath,$(R_HOME)/lib
+LDFLAGS := $(R_LDFLAGS) -Wl,-rpath,$(R_HOME)/lib
 
 # Target library
 TARGET := galaaz_gatekeeper.so
@@ -34,7 +34,7 @@ $(TARGET): $(OBJ)
 
 check: $(TARGET)
 	@echo "Checking library..."
-	@$(R_HOME)/bin/Rscript -e "dyn.load('$(TARGET)'); cat('Library loads successfully\n')"
+	@Rscript -e "dyn.load('$(TARGET)'); cat('Library loads successfully\n')"
 
 clean:
 	rm -f $(OBJ) $(TARGET)

data/ext/new_bridge/galaaz_gatekeeper_phase1.cpp

@@ -45,6 +45,7 @@
 // -----------------------------------------------------------------------------
 
 #include <Rcpp.h>
+#include <Rversion.h>
 #include <arpa/inet.h>
 #include <chrono>
 #include <cstdint>
@@ -61,6 +62,15 @@
 #include <unistd.h>
 #include <vector>
 
+// R 4.5+: Rf_findVar is no longer a public API entry (hidden in R 4.6).
+// R_getVarEx(sym, rho, inherits, ifnotfound) is the supported replacement.
+static inline SEXP galaaz_find_var(SEXP sym, SEXP env) {
+#if defined(R_VERSION) && R_VERSION >= R_Version(4, 5, 0)
+  return R_getVarEx(sym, env, TRUE, R_UnboundValue);
+#else
+  return Rf_findVar(sym, env);
+#endif
+}
 // Active bridge socket used by main loop and callback path.
 static int g_bridge_fd = -1;
 // Instance id of the currently serviced REQ; reused by callback CALL messages.
@@ -848,7 +858,7 @@ EvalResult eval_unbox_walk_cmd(const std::string& cmd, const Rcpp::Environment&
   }
 
   SEXP sym = Rf_install(handle.c_str());
-  SEXP root = Rf_findVar(sym, env);
+  SEXP root = galaaz_find_var(sym, env);
   if (root == R_UnboundValue) return {false, payload_error("unbox_walk unknown handle")};
 
   std::vector<std::pair<SEXP, int>> stack;
@@ -1001,7 +1011,7 @@ EvalResult eval_unbox_materialize_cmd(const std::string& cmd, const Rcpp::Enviro
   }
 
   SEXP sym = Rf_install(handle.c_str());
-  SEXP root = Rf_findVar(sym, env);
+  SEXP root = galaaz_find_var(sym, env);
   if (root == R_UnboundValue) return {false, payload_error("unbox_materialize unknown handle")};
 
   std::vector<uint8_t> value_bytes;
@@ -1176,7 +1186,7 @@ static EvalResult eval_pull_vector_cmd(const std::string& cmd, const Rcpp::Envir
   }
 
   SEXP sym = Rf_install(handle.c_str());
-  SEXP vec = Rf_findVar(sym, env);
+  SEXP vec = galaaz_find_var(sym, env);
   if (vec == R_UnboundValue) {
     return {false, payload_error("pull_vector unknown handle")};
   }

data/lib/galaaz/cli.rb

@@ -87,8 +87,10 @@ module Galaaz
       abort_unless(ok, 'make failed building ext/new_bridge')
       so = File.join(bridge, 'galaaz_gatekeeper.so')
       abort_unless(File.file?(so), "gatekeeper missing after build: #{so}")
+      mark_profile!('core')
       puts 'galaaz setup: OK'
       puts "You can now run: galaaz doctor"
+      puts 'Omarchy menu: Install → Development → Galaaz (add-ons appear after core)'
       0
     end
 
@@ -435,10 +437,27 @@ module Galaaz
       install_cran!(['Rcpp'])
     end
 
+    # Omarchy/Arch: /usr/lib/R/library is not writable for normal users.
+    def r_lib_bootstrap
+      <<~R
+        lib <- Sys.getenv("R_LIBS_USER", unset = "")
+        if (!nzchar(lib)) {
+          lib <- file.path(Sys.getenv("HOME"), ".local", "lib", "R", "library")
+          Sys.setenv(R_LIBS_USER = lib)
+        }
+        dir.create(lib, recursive = TRUE, showWarnings = FALSE)
+        .libPaths(c(lib, .libPaths()))
+        renviron <- file.path(Sys.getenv("HOME"), ".Renviron")
+        line <- paste0("R_LIBS_USER=", lib)
+        if (!file.exists(renviron) || !any(grepl("^R_LIBS_USER=", readLines(renviron, warn = FALSE)))) {
+          cat(line, "\\n", file = renviron, append = TRUE)
+        }
+      R
+    end
+
     def r_namespace?(pkg)
-      out, status = Open3.capture2e(
-        'Rscript', '-e', "quit(status=if (requireNamespace('#{pkg}', quietly=TRUE)) 0 else 1)"
-      )
+      script = "#{r_lib_bootstrap}\nquit(status=if (requireNamespace('#{pkg}', quietly=TRUE)) 0 else 1)"
+      _out, status = Open3.capture2e('Rscript', '-e', script)
       status.success?
     rescue Errno::ENOENT
       false
@@ -447,13 +466,14 @@ module Galaaz
     def install_cran!(pkgs)
       list = pkgs.map { |p| "'#{p}'" }.join(', ')
       script = <<~R
+        #{r_lib_bootstrap}
         repos <- '#{CRAN}'
         pkgs <- c(#{list})
         inst <- rownames(installed.packages())
         need <- pkgs[!pkgs %in% inst]
         if (length(need)) {
-          message('Installing: ', paste(need, collapse=', '))
-          install.packages(need, repos = repos)
+          message('Installing into ', lib, ': ', paste(need, collapse=', '))
+          install.packages(need, lib = lib, repos = repos)
         }
         missing <- pkgs[!pkgs %in% rownames(installed.packages())]
         if (length(missing)) {
@@ -470,14 +490,15 @@ module Galaaz
 
       list = pkgs.map { |p| "'#{p}'" }.join(', ')
       script = <<~R
+        #{r_lib_bootstrap}
         repos <- '#{CRAN}'
         pkgs <- c(#{list})
         inst <- rownames(installed.packages())
         need <- pkgs[!pkgs %in% inst]
         if (length(need)) {
-          message('Installing (optional): ', paste(need, collapse=', '))
+          message('Installing (optional) into ', lib, ': ', paste(need, collapse=', '))
           tryCatch(
-            install.packages(need, repos = repos),
+            install.packages(need, lib = lib, repos = repos),
             error = function(e) message(e)
           )
         }

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "galaaz"
-$version="2.1.1"
+$version="2.1.3"

metadata

@@ -1,11 +1,10 @@
 --- !ruby/object:Gem::Specification
 name: galaaz
 version: !ruby/object:Gem::Version
-  version: 2.1.1
+  version: 2.1.3
 platform: ruby
 authors:
 - Rodrigo Botafogo
-autorequire:
 bindir: bin
 cert_chain: []
 date: 2026-09-04 00:00:00.000000000 Z
@@ -87,11 +86,11 @@ description: |
 email: rodrigo.a.botafogo@gmail.com
 executables:
 - galaaz
-- gstudio
-- gknit
 - gbookdown
-- grun
+- gknit
 - gknit-draft
+- grun
+- gstudio
 extensions: []
 extra_rdoc_files: []
 files:
@@ -485,7 +484,6 @@ metadata:
   documentation_uri: https://rbotafogo.github.io/galaaz/
   changelog_uri: https://github.com/rbotafogo/galaaz/blob/galaaz2_0/CHANGELOG.md
   yard.run: yri
-post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -500,8 +498,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.22
-signing_key:
+rubygems_version: 4.0.3
 specification_version: 4
 summary: 'R-on-Rails: tightly couple Ruby and GNU R for data science on the web'
 test_files: []