Merge branch 'main' into set-webr-env

Makefile

@@ -1,4 +1,4 @@
-WEBR_ROOT = $(abspath .)
+WEBR_ROOT ?= $(abspath .)
 WASM = $(WEBR_ROOT)/wasm
 HOST = $(WEBR_ROOT)/host
 TOOLS = $(WEBR_ROOT)/tools
@@ -8,53 +8,65 @@ default: webr
 # This is created at configure-time
 include $(TOOLS)/fortran.mk
 
-# Build webR and install the web app in `./dist`
 .PHONY: webr
-webr: $(EMFC) $(FORTRAN_WASM_LIB) libs
+webr: $(EMFC) $(FORTRAN_WASM_LIB) libs ## Build webR and install the web app in `./dist`
 	cd R && $(MAKE) && $(MAKE) install
 	cd src && $(MAKE)
 
-# Supporting libs for webr
 .PHONY: libs
-libs:
+libs: ## Compile supporting libs for webR
 	cd libs && $(MAKE)
 
-# Build webR in a temporary docker container
 .PHONY: docker-webr
-docker-webr:
+docker-webr: ## Build webR in a temporary Docker container
 	mkdir -p dist
 	docker build -t webr-build .
 	docker run --rm --mount type=bind,source=$(PWD),target=/app webr-build
 
 # Create a permanent docker container for building webR. Call `make`
 # from within the container to start the build.
 .PHONY: docker-container-%
-docker-container-%:
+docker-container-%: ## Build webR development Docker container using a supplied name
 	docker build -t webr-build .
 	docker run -dit --name $* --mount type=bind,source=$(PWD),target=/app webr-build bash
 
-docs: docs/build
-docs/build:
+docs: docs/build ## Build documentation and Quarto website
+docs/build: ## Build documentation and Quarto website
 	cd docs && $(MAKE) api && $(MAKE) html
 
 .PHONY: check
-check:
+check: ## Run unit tests and calculate coverage
 	cd src && $(MAKE) check
 
 .PHONY: check-pr
-check-pr:
+check-pr: ## Run additional pull request tests, linter, and calculate coverage
 	cd src && $(MAKE) lint && $(MAKE) check && $(MAKE) check-packages
 
 .PHONY: clean
-clean:
+clean: ## Remove Wasm R build
 	rm -rf $(HOST) $(WASM)/R-*
 	cd R && $(MAKE) clean
 
 .PHONY: clean-wasm
-clean-wasm: clean
+clean-wasm: clean ## Remove Wasm R build and supporting libs
 	rm -rf $(WASM)
 	cd libs && $(MAKE) clean
 
 .PHONY: distclean
-distclean: clean-wasm clean-tools
+distclean: clean-wasm clean-tools ## Remove Wasm R build, supporting libs, build tools, and webR distribution
 	rm -rf dist
+
+.PHONY: help
+help:  ## Show help messages for make targets
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(firstword $(MAKEFILE_LIST)) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[32m%-18s\033[0m %s\n", $$1, $$2}'
+
+.PHONY: debug
+debug: ## Print all variables for debugging
+	@printf "\033[32m%-18s\033[0m %s\n" "WEBR_ROOT" "$(WEBR_ROOT)"
+	@printf "\033[32m%-18s\033[0m %s\n" "WASM" "$(WASM)"
+	@printf "\033[32m%-18s\033[0m %s\n" "HOST" "$(HOST)"
+	@printf "\033[32m%-18s\033[0m %s\n" "TOOLS" "$(TOOLS)"
+	@printf "\033[32m%-18s\033[0m %s\n" "EMFC" "$(EMFC)"
+	@printf "\033[32m%-18s\033[0m %s\n" "FORTRAN_WASM_LIB" "$(FORTRAN_WASM_LIB)"
+	@printf "\033[32m%-18s\033[0m %s\n" "PWD" "$(PWD)"
+	@printf "\033[32m%-18s\033[0m %s\n" "MAKE" "$(MAKE)"

NEWS.md

@@ -4,8 +4,14 @@
 
 * A `webR.version` property has been added, containing the current version and build information (#409).
 
+* An `RObject.class()` method has been added, returning an `RCharacter` object with the names of the classes from which the given R object inherits. This has been implemented using R's `class()` function, and so the implicit class is similarly returned when the R object has no `class` attribute.
+
 * WebR now sets the environment variable `WEBR` equal to `"1"` and `WEBR_VERSION` equal to the webR version string in the WebAssembly environment (#414).
 
+## Bug Fixes
+
+* Fix installing packages via shim with `character.only = TRUE` (#413).
+
 # webR 0.3.2
 
 ## New features

packages/webr/R/library.R

@@ -33,7 +33,9 @@ library_shim <- function(pkg, ..., show_menu = getOption("webr.show_menu")) {
       return(invisible(NULL))
     }
   }
-  base::library(package, character.only = TRUE, ...)
+  args <- list(package, character.only = TRUE, ...)
+  args <- args[!duplicated(names(args))]
+  do.call(base::library, args)
 }
 
 #' @rdname library_shim
@@ -46,5 +48,7 @@ require_shim <- function(pkg, ..., show_menu = getOption("webr.show_menu")) {
       return(invisible(NULL))
     }
   }
-  base::require(package, character.only = TRUE, ...)
+  args <- list(package, character.only = TRUE, ...)
+  args <- args[!duplicated(names(args))]
+  do.call(base::require, args)
 }

src/tests/webR/robj.test.ts

@@ -53,6 +53,40 @@ test('Get RObject type as a string', async () => {
   expect(await result.toString()).toEqual('[object RObject:null]');
 });
 
+describe('Working with R object classes', () => {
+  test('Get R object intrinsic class', async () => {
+    const numeric = await new webR.RDouble([1, 2, 3]);
+    const character = await new webR.RCharacter(['a', 'b', 'c']);
+
+    const numericClass = await numeric.class();
+    const characterClass = await character.class();
+    expect(await numericClass.toArray()).toContain("numeric");
+    expect(await characterClass.toArray()).toContain("character");
+  });
+
+  test('Get R object class vector', async () => {
+    const jsObj = { a: [1, 2, 3], b: [3, 4, 5], c: ['x', 'y', 'z'] };
+    const rObj = await new webR.RDataFrame(jsObj);
+    const classes = await rObj.class();
+    expect(await classes.toArray()).toEqual(["data.frame"]);
+  });
+
+  test('Get R object class vector from attributes', async () => {
+    const rObj = await webR.evalR('x <- 123; class(x) <- c("abc", "def"); x');
+    const classes = await rObj.class();
+    expect(await classes.toArray()).toEqual(["abc", "def"]);
+  });
+
+  test('Get S4 R object class vector', async () => {
+    const rClass = await webR.evalR('getClass("MethodDefinition")');
+    const classes = await rClass.class();
+    const attrs = await rClass.attrs();
+    const attrPackage = await attrs.get('package');
+    expect(await classes.toArray()).toEqual(["classRepresentation"]);
+    expect(await attrPackage.toString()).toEqual("methods");
+  });
+});
+
 describe('Working with R lists and vectors', () => {
   test('Get R object attributes', async () => {
     const vector = await webR.evalR('c(a=1, b=2, c=3)');

src/tests/webR/webr-worker.test.ts

@@ -15,8 +15,7 @@ beforeAll(async () => {
 
 describe('Download and install binary webR packages', () => {
   test('Install packages via evalR', async () => {
-    // eslint-disable-next-line @typescript-eslint/no-empty-function
-    const warnSpy = jest.spyOn(console, 'warn').mockImplementation(() => { });
+    const warnSpy = jest.spyOn(console, 'warn').mockImplementation(() => null);
 
     // Downloading and extracting a .tgz package
     await webR.evalR(
@@ -36,8 +35,7 @@ describe('Download and install binary webR packages', () => {
   });
 
   test('Install packages quietly', async () => {
-    // eslint-disable-next-line @typescript-eslint/no-empty-function
-    const warnSpy = jest.spyOn(console, 'warn').mockImplementation(() => { });
+    const warnSpy = jest.spyOn(console, 'warn').mockImplementation(() => null);
     await webR.evalR(
       'webr::install("Matrix", repos="https://repo.r-wasm.org/", mount = FALSE, quiet = TRUE)'
     );
@@ -46,13 +44,22 @@ describe('Download and install binary webR packages', () => {
   });
 
   test('Install packages via API', async () => {
-    // eslint-disable-next-line @typescript-eslint/no-empty-function
-    const warnSpy = jest.spyOn(console, 'warn').mockImplementation(() => { });
+    const warnSpy = jest.spyOn(console, 'warn').mockImplementation(() => null);
     await webR.installPackages(['MASS'], { mount: false });
     const pkg = (await webR.evalR('"MASS" %in% library(MASS)')) as RLogical;
     expect(await pkg.toBoolean()).toEqual(true);
     warnSpy.mockRestore();
   });
+
+  test('Install packages via package shim', async () => {
+    const warnSpy = jest.spyOn(console, 'warn').mockImplementation(() => null);
+    const pkg = (await webR.evalR(`
+      webr::shim_install()
+      "rlang" %in% library("rlang", character.only = TRUE, show_menu = FALSE, quiet = TRUE)
+    `)) as RLogical;
+    expect(await pkg.toBoolean()).toEqual(true);
+    warnSpy.mockRestore();
+  });
 });
 
 describe('Test webR virtual filesystem', () => {

src/webR/robj-worker.ts

@@ -243,6 +243,17 @@ export class RObject extends RObjectBase {
     return RPairlist.wrap(Module._ATTRIB(this.ptr));
   }
 
+  class(): RCharacter {
+    const prot = { n: 0 };
+    const classCall = new RCall([new RSymbol('class'), this]);
+    protectInc(classCall, prot);
+    try {
+      return classCall.eval() as RCharacter;
+    } finally {
+      unprotect(prot.n);
+    }
+  }
+
   setNames(values: (string | null)[] | null): this {
     let namesObj: RObject;