Merge pull request #7 from andyquinterom/T6

Changes @param name in `as.list` method

.Rbuildignore

@@ -1,6 +1,25 @@
-^src/\.cargo$
+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^README\.Rmd$
+^README\.md$
+^man/figures/.*$
 ^\.github$
+^fonts$
+
+^src/.cargo$
+^src/rust/.cargo$
+^src/rust/.vscode$
+^src/rust/vendor$
+
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-^LICENSE\.md$
+
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^CRAN-RELEASE$
+
+^check$
+
+^update_authors\.R$

.github/workflows/check-full.yaml

@@ -0,0 +1,50 @@
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: "${{ matrix.config.os }} (R: ${{ matrix.config.r }}, Rust: ${{ matrix.config.rust }})"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release',  rust: 'stable-msvc'}
+          - {os: windows-latest, r: 'devel',    rust: 'stable-msvc'}
+          - {os: macOS-latest,   r: 'release',  rust: 'stable'     }
+          - {os: ubuntu-latest,  r: 'release',  rust: 'stable'     }
+          - {os: ubuntu-latest,  r: 'devel',    rust: 'stable'     }
+          - {os: ubuntu-latest,  r: 'release',  rust: 'nightly'    }
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Rust
+        uses: dtolnay/rust-toolchain@master
+        with:
+          toolchain: ${{ matrix.config.rust }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          rtools-version: ${{ matrix.config.rtools-version }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+
+      - name: debug
+        run: cat ./check/*.Rcheck/00install.out

.gitignore

@@ -48,3 +48,10 @@ po/*~
 # RStudio Connect folder
 rsconnect/
 docs
+
+# Rust Cargo files
+src/.cargo
+src/rust/.cargo
+src/rust/vendor/
+
+docs

DESCRIPTION

@@ -2,10 +2,16 @@ Package: orbweaver
 Title: Fast and Efficient Graph Data Structures
 Version: 0.1.0.9000
 Authors@R: 
-    person("Andres", "Quintero", , "andres@ixpantia.com", role = c("aut", "cre"))
+    c(person("Andres", "Quintero", , "andres@ixpantia.com", role = c("aut", "cre")),
+      person(given = "The authors of the dependency Rust crates",
+             role = c("ctb"),
+             comment = "see inst/AUTHORS file for details"))
 Description: Orbweaver is an R packages that optimizes the processing of graph data structures.
+URL: https://github.com/ixpantia/orbweaver
+BugReports: https://github.com/ixpantia/orbweaver/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Config/rextendr/version: 0.3.1
+SystemRequirements: Cargo (Rust's package manager), rustc

LICENSE.note

@@ -0,0 +1,91 @@
+This package contains the Rust source code of the dependencies in src/rust/vendor.tar.xz
+The authorships and the licenses are listed below. In summary, all libraries are
+distributed either under the MIT license or under MIT/Apache-2.0 dual license [1].
+
+Note that, when Cargo (Rust’s build system and package manager) is not installed
+on the machine, the pre-compiled binary will be downloaded on building this
+package. The binary is compiled using the same Rust code, so the authorships and
+the licenses are the same as listed here.
+
+[1]: The unicode-indent library shows 'Unicode-DFS-2016' license because it
+     contains some test data generated by using the Unicode Character Database.
+     So, this license is not applied to the actual sources that get compiled.
+     Please refer to the License section of the library's README
+     (https://crates.io/crates/unicode-ident) for the details.
+
+===============================
+
+Name:    either
+Files:   vendor/either/*
+Authors: bluss
+License: MIT OR Apache-2.0
+
+------------------------------
+
+Name:    extendr-api
+Files:   vendor/extendr-api/*
+Authors: andy-thomason, Thomas Down, Mossa Merhi Reimert, Claus O. Wilke, Hiroaki Yutani, Ilia A. Kosenkov, Michael Milton
+License: MIT
+
+------------------------------
+
+Name:    extendr-macros
+Files:   vendor/extendr-macros/*
+Authors: andy-thomason, Thomas Down, Mossa Merhi Reimert, Claus O. Wilke, Hiroaki Yutani, Ilia A. Kosenkov
+License: MIT
+
+------------------------------
+
+Name:    itertools
+Files:   vendor/itertools/*
+Authors: bluss
+License: MIT OR Apache-2.0
+
+------------------------------
+
+Name:    libR-sys
+Files:   vendor/libR-sys/*
+Authors: andy-thomason, Thomas Down, Mossa Merhi Reimert, Claus O. Wilke, Ilia A. Kosenkov, Hiroaki Yutani
+License: MIT
+
+------------------------------
+
+Name:    once_cell
+Files:   vendor/once_cell/*
+Authors: Aleksey Kladov
+License: MIT OR Apache-2.0
+
+------------------------------
+
+Name:    paste
+Files:   vendor/paste/*
+Authors: David Tolnay
+License: MIT OR Apache-2.0
+
+------------------------------
+
+Name:    proc-macro2
+Files:   vendor/proc-macro2/*
+Authors: David Tolnay, Alex Crichton
+License: MIT OR Apache-2.0
+
+------------------------------
+
+Name:    quote
+Files:   vendor/quote/*
+Authors: David Tolnay
+License: MIT OR Apache-2.0
+
+------------------------------
+
+Name:    syn
+Files:   vendor/syn/*
+Authors: David Tolnay
+License: MIT OR Apache-2.0
+
+------------------------------
+
+Name:    unicode-ident
+Files:   vendor/unicode-ident/*
+Authors: David Tolnay
+License: (MIT OR Apache-2.0) AND Unicode-DFS-2016

R/graph.R

@@ -138,7 +138,7 @@ find_least_common_parents <- function(graph, nodes) {
 #'
 #' @description
 #' Converts the graph to a list.
-#' @param graph The graph to convert to a list.
+#' @param x The graph to convert to a list.
 #' @param ... Ignored.
 #' @return A list representation of the graph.
 #' @export

inst/AUTHORS

@@ -0,0 +1,51 @@
+The authors of the dependency Rust crates:
+
+either (version 1.9.0):
+  bluss
+
+extendr-api (version 0.6.0):
+  andy-thomason
+  Thomas Down
+  Mossa Merhi Reimert
+  Claus O. Wilke
+  Hiroaki Yutani
+  Ilia A. Kosenkov
+  Michael Milton
+
+extendr-macros (version 0.6.0):
+  andy-thomason
+  Thomas Down
+  Mossa Merhi Reimert
+  Claus O. Wilke
+  Hiroaki Yutani
+  Ilia A. Kosenkov
+
+itertools (version 0.11.0):
+  bluss
+
+libR-sys (version 0.6.0):
+  andy-thomason
+  Thomas Down
+  Mossa Merhi Reimert
+  Claus O. Wilke
+  Ilia A. Kosenkov
+  Hiroaki Yutani
+
+once_cell (version 1.18.0):
+  Aleksey Kladov
+
+paste (version 1.0.14):
+  David Tolnay
+
+proc-macro2 (version 1.0.69):
+  David Tolnay
+  Alex Crichton
+
+quote (version 1.0.33):
+  David Tolnay
+
+syn (version 2.0.39):
+  David Tolnay
+
+unicode-ident (version 1.0.12):
+  David Tolnay

src/Makevars

@@ -1,3 +1,7 @@
+# TODO
+VENDORING = yes
+OFFLINE_OPTION = --offline
+
 TARGET_DIR = ./rust/target
 LIBDIR = $(TARGET_DIR)/release
 STATLIB = $(LIBDIR)/liborbweaver.a
@@ -7,24 +11,35 @@ all: C_clean
 
 $(SHLIB): $(STATLIB)
 
-CARGOTMP = $(CURDIR)/.cargo
-
 $(STATLIB):
+	# vendoring (Note: to avoid NOTE of "Found the following hidden files and
+	# directories", .cargo needs to be created here)
+	if [ "$(VENDORING)" = "yes" ]; then \
+	  $(TAR) --extract --xz -f ./rust/vendor.tar.xz -C ./rust && \
+		mkdir -p ./rust/.cargo && \
+		cp ./config/cargo_vendor_config.toml ./rust/.cargo/config.toml; \
+	fi
+
 	# In some environments, ~/.cargo/bin might not be included in PATH, so we need
 	# to set it here to ensure cargo can be invoked. It is appended to PATH and
 	# therefore is only used if cargo is absent from the user's PATH.
 	if [ "$(NOT_CRAN)" != "true" ]; then \
 		export CARGO_HOME=$(CARGOTMP); \
 	fi && \
 		export PATH="$(PATH):$(HOME)/.cargo/bin" && \
-		cargo build --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR)
+		cd ./rust && \
+		cargo build --lib --release \
+			$(OFFLINE_OPTION) \
+			--jobs 1
 	if [ "$(NOT_CRAN)" != "true" ]; then \
 		rm -Rf $(CARGOTMP) && \
 		rm -Rf $(LIBDIR)/build; \
 	fi
 
 C_clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)
+	rm -Rf $(SHLIB) $(OBJECTS) ./rust/.cargo $(STATLIB)
 
 clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) rust/target
+	rm -Rf $(SHLIB) $(OBJECTS) $(STATLIB) ./rust/.cargo ./rust/vendor ./rust/target
+
+.PHONY: all C_clean clean