Merge pull request #86 from albersonmiranda/dev

chore: Update R package build configuration and install necessary packages

.devcontainer/Dockerfile

@@ -7,6 +7,8 @@ RUN install2.r --error --skipinstalled -n -1 \
         # pacotes R
         leontief \
         microbenchmark \
+        Rdpack \
+        emoji \
     && rm -rf /tmp/downloaded_packages
 
 # Pacotes Python (digitar nomes em requirements.txt)

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main]
   pull_request:
-    branches: [main, master]
+    branches: [main]
     types:
       - opened
       - reopened
@@ -26,11 +26,30 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: macos-14,      r: 'release'}
+          - {os: macos-14,      r: 'devel'}
+          - {os: macos-14,      r: 'oldrel-1'}
+          - {os: macos-13,      r: 'release'}
+          - {os: macos-13,      r: 'devel'}
+          - {os: macos-13,      r: 'oldrel-1'}
+          - {os: macos-12,      r: 'release'}
+          - {os: macos-12,      r: 'devel'}
+          - {os: macos-12,      r: 'oldrel-1'}
+          - {os: windows-2022,  r: 'release'}
+          - {os: windows-2022,  r: 'devel'}
+          - {os: windows-2022,  r: 'oldrel-1'}
+          - {os: windows-2019,  r: 'release'}
+          - {os: windows-2019,  r: 'devel'}
+          - {os: windows-2019,  r: 'oldrel-1'}
+          - {os: ubuntu-24.04,  r: 'devel'}
+          - {os: ubuntu-24.04,  r: 'release'}
+          - {os: ubuntu-24.04,  r: 'oldrel-1'}
+          - {os: ubuntu-22.04,  r: 'devel'}
+          - {os: ubuntu-22.04,  r: 'release'}
+          - {os: ubuntu-22.04,  r: 'oldrel-1'}
+          - {os: ubuntu-20.04,  r: 'devel'}
+          - {os: ubuntu-20.04,  r: 'release'}
+          - {os: ubuntu-20.04,  r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -56,3 +75,134 @@ jobs:
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+
+  Fedora-36:
+    runs-on: ubuntu-latest
+    container:
+      image: fedora:36
+
+    steps:
+      - name: Install Fedora dependencies
+        run: |
+          sudo dnf install -y --allowerasing pip rust gcc llvm libxml2-devel libcurl-devel harfbuzz-devel \
+          fribidi-devel openssl-devel freetype-devel libpng-devel libtiff-devel libjpeg-devel qpdf xz \
+          glibc-langpack-en devscripts-checkbashisms gcc-c++ gcc-gfortran readline-devel xz-devel bzip2-devel \
+          zlib-devel pcre2-devel cairo-devel libgit2-devel libX11-devel libXt-devel which
+
+      - name: Compile R from source
+        run: |
+          # download R 4.2.0
+          curl https://cran.r-project.org/src/base/R-4/R-4.2.0.tar.gz -O
+          # extract R 4.2.0
+          tar -xvf R-4.2.0.tar.gz
+          # build R 4.2.0
+          cd R-4.2.0 && ./configure --prefix=/usr/local && make && make install
+          # back to the root directory
+          cd ~
+
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+
+  Fedora-37:
+    runs-on: ubuntu-latest
+    container:
+      image: fedora:37
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Fedora dependencies
+        run: |
+          sudo dnf install -y rust libxml2-devel libcurl-devel harfbuzz-devel fribidi-devel openssl-devel freetype-devel libpng-devel libtiff-devel libjpeg-devel qpdf xz devscripts glibc-langpack-en
+
+      - name: Setup R
+        run: |
+          sudo dnf install -y R
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+
+  Fedora-38:
+    runs-on: ubuntu-latest
+    container:
+      image: fedora:38
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Fedora dependencies
+        run: |
+          sudo dnf install -y rust cargo libxml2-devel libcurl-devel harfbuzz-devel fribidi-devel openssl-devel freetype-devel libpng-devel libtiff-devel libjpeg-devel qpdf xz devscripts glibc-langpack-en pandoc
+
+      - name: Setup R
+        run: |
+          sudo dnf install -y R
+          # install R packages
+          R -e 'install.packages(c("remotes", "rcmdcheck", "emoji", "Rdpack", "readxl", "clipr", "fs", "miniUI", "shiny", "knitr", "rmarkdown", "spelling", "microbenchmark", "leontief", "ggplot2", "writexl", "testthat"), repos = "http://cloud.r-project.org")'
+      
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+
+  Fedora-39:
+    runs-on: ubuntu-latest
+    container:
+      image: fedora:39
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Fedora dependencies
+        run: |
+          sudo dnf install -y rust cargo libxml2-devel libcurl-devel harfbuzz-devel fribidi-devel openssl-devel freetype-devel libpng-devel libtiff-devel libjpeg-devel qpdf xz devscripts glibc-langpack-en pandoc
+
+      - name: Setup R
+        run: |
+          sudo dnf install -y R
+          # install R packages
+          R -e 'install.packages(c("remotes", "rcmdcheck", "emoji", "Rdpack", "readxl", "clipr", "fs", "miniUI", "shiny", "knitr", "rmarkdown", "spelling", "microbenchmark", "leontief", "ggplot2", "writexl", "testthat"), repos = "http://cloud.r-project.org")'
+      
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+
+  Fedora-40:
+    runs-on: ubuntu-latest
+    container:
+      image: fedora:40
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Fedora dependencies
+        run: |
+          sudo dnf install -y rust cargo libxml2-devel libcurl-devel harfbuzz-devel fribidi-devel openssl-devel freetype-devel libpng-devel libtiff-devel libjpeg-devel qpdf xz devscripts glibc-langpack-en pandoc
+
+      - name: Setup R
+        run: |
+          sudo dnf install -y R
+          # install R packages
+          R -e 'install.packages(c("remotes", "rcmdcheck", "emoji", "Rdpack", "readxl", "clipr", "fs", "miniUI", "shiny", "knitr", "rmarkdown", "spelling", "microbenchmark", "leontief", "ggplot2", "writexl", "testthat"), repos = "http://cloud.r-project.org")'
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -2,5 +2,5 @@
 inst/doc
 docs
 revdep/
+src/vendor
 src/rust/vendor
-.vscode/

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+  "rust-analyzer.linkedProjects": [
+    "${workspaceFolder}/src/rust/Cargo.toml"
+  ],
+}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fio
 Title: Friendly Input-Output Analysis
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: c(
   person(
     given = "Alberson",
@@ -29,7 +29,7 @@ Roxygen: list(markdown = TRUE, r6 = TRUE)
 RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.0)
-SystemRequirements: Cargo (Rust's package manager), rustc >= 1.67
+SystemRequirements: Cargo (Rust's package manager), rustc >= 1.67.1
 LazyData: true
 Imports: 
     cli,
@@ -42,7 +42,7 @@ Imports:
     shiny,
     Rdpack
 License: MIT + file LICENSE
-Config/rextendr/version: 0.3.1
+Config/rextendr/version: 0.3.1.9000
 Suggests: 
     knitr,
     rmarkdown,

NEWS.md

@@ -1,3 +1,11 @@
+# fio 0.1.1
+
+## 🛠️ Other improvements
+
+* Update `extraction.rs`and `multipliers.rs` in order to lower minimum supported Rust version from 1.71 to 1.67.
+* Set minimum version of rustc >= 1.67.1 in `SystemRequirements`.
+* Add system checks to rustc and prompt users either install, if missing, or update when version is lower than specified in `DESCRIPTION`.
+
 # fio 0.1.0
 
 ## ✨ Enhancements

README.Rmd

@@ -36,13 +36,13 @@ You can install the released version of `{fio}` from CRAN with:
 ```r
 install.packages("fio")
 ```
-For the latest development version, you'll find precompiled binaries at [R-universe](https://albersonmiranda.r-universe.dev/fio):
+For the latest tested but unreleased version ([main branch](https://github.com/albersonmiranda/fio/tree/main)), you'll find precompiled binaries at [R-universe](https://albersonmiranda.r-universe.dev/fio):
 
 ```r
 install.packages("fio", repos = c("https://albersonmiranda.r-universe.dev", "https://cloud.r-project.org"))
 ```
 
-If you wish to compile the latest development version from source, you'll need [Rust](https://www.rust-lang.org/) installed on your system. You can install Rust with the following commands:
+For the development version, you can compile the [dev branch](https://github.com/albersonmiranda/fio/tree/dev) from source, you'll need [Rust](https://www.rust-lang.org/) installed on your system. You can install Rust with the following commands:
 
 - Debian/Ubuntu: `apt-get install cargo`
 - Fedora/CentOS: `dnf install cargo`

README.md

@@ -39,14 +39,17 @@ You can install the released version of `{fio}` from CRAN with:
 install.packages("fio")
 ```
 
-For the latest development version, you’ll find precompiled binaries at
+For the latest tested but unreleased version ([main
+branch](https://github.com/albersonmiranda/fio/tree/main)), you’ll find
+precompiled binaries at
 [R-universe](https://albersonmiranda.r-universe.dev/fio):
 
 ``` r
 install.packages("fio", repos = c("https://albersonmiranda.r-universe.dev", "https://cloud.r-project.org"))
 ```
 
-If you wish to compile the latest development version from source,
+For the development version, you can compile the [dev
+branch](https://github.com/albersonmiranda/fio/tree/dev) from source,
 you’ll need [Rust](https://www.rust-lang.org/) installed on your system.
 You can install Rust with the following commands:
 

configure

@@ -1,3 +1,3 @@
 #!/usr/bin/env sh
 : "${R_HOME=`R RHOME`}"
-"${R_HOME}/bin/Rscript" tools/msrv.R 
+"${R_HOME}/bin/Rscript" tools/msrv.R 

configure.win

@@ -1,2 +1,2 @@
 #!/usr/bin/env sh
-"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" tools/msrv.R
+"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" tools/msrv.R

cran-comments.md

@@ -1,34 +1,19 @@
-## Third ressubmission
-
-In this version I have:
+## R CMD check results
 
-* Updated `import_iom()` example so it does not require `dontrun` nor `donttest` tag.
-* Added missing `return` tag to `iom` class (previously only on methods).
+0 errors | 0 warnings | 1 notes
 
-## Second Ressubmission
+* NOTE:
+ - installed size is 8.2Mb due to vendored Rust dependencies as per CRAN policy.
 
 In this version I have:
-
-* Rewrite `r6.R` documentation to address Konstanze's instructions.
-* Refactor `$set_max_threads()` method for better parallelism control and error handling.
-* Comply with CRAN's policies by building offline:
-  * Pass "--offline" flag to `cargo build` to avoid online compilation.
-  * Included compressed Rust dependencies in order to compile offline.
-* Added `configure` and `configure.win` files with 'Cargo' installation instructions when needed but not found.
-
-## Ressubmission
-
-This is a resubmission. Previous submission failed due to parallelization by default.
-In this version I have:
-
-* Added "-j 2" flag to `cargo build` to avoid parallelism during building (`makevars` and `makevars.win`).
-* Added `$set_max_threads()` method to provide parallelism control to the user.
-* Added tests.
-
-## R CMD check results
-
-0 errors | 0 warnings | 2 notes
 
-* Check on Ubuntu
-  - Installed size is 9.3Mb: Rust code and dependencies are compiled and statically linked into the shared library `fio.so`.
-  - Build on Ubuntu 24.04 raises non-portable flag due to `-mno-omit-leaf-frame-pointer` which is [set by default in 24.04](https://ubuntu.com/blog/ubuntu-performance-engineering-with-frame-pointers-by-default).
+* Addressed CRAN removal:
+  - Update `extraction.rs`and `multipliers.rs` in order to lower MSRV from 1.71 to 1.67. That fixes previous failure, assuming CRAN lowest 'rustc' version is 1.69.0 (last release in Fedora 36 default repository).
+  - Set minimum version of rustc >= 1.67.1 in `SystemRequirements`. That specific version is due to dependency `faer-entity v0.19.0`.
+  - Update `configure` and `configure.win` to check `SystemRequirements` field in `DESCRIPTION` and performe a system check for both `Rust` and `Cargo` tools. If any of them is not found, build fails with a message to install them. If they are found, it checks for the minimum version of `rustc`. If it is lower than specified in `SystemRequirements`, build fails with a message stating both installed and minimum version required. Finally, if all tests pass, it prints the version of `cargo` and `rustc` found, which will be used to build the package.
+  - CI tests include (all passed R CMD check):
+    - macOS 12, 13 and 14; R release, devel and oldrel-1.
+    - Windows Server 2019, 2022; R release, devel and oldrel-1.
+    - Ubuntu 20.04, 22.04, 24.04; R release, devel and oldrel-1.
+    - Fedora 36; R 4.2 built from source. `cargo` and other dependencies installed from Fedora 36 default repository (`dnf install`).
+    - Fedora 37, 38, 39, 40; R and all dependencies installed from default repository (`dnf install`).

src/Makevars

@@ -26,7 +26,8 @@ $(STATLIB):
 	fi && \
 		export PATH="$(PATH):$(HOME)/.cargo/bin" && \
 			cargo build $(CRAN_FLAGS) --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR) && \
-			echo `cargo --version` && echo `rustc --version`;
+			echo "Rust version:" `rustc --version` && \
+			echo "Cargo version:" `cargo --version`;
 		rm -Rf $(CARGOTMP) $(VENDOR_DIR) $(LIBDIR)/build; \
 
 C_clean:

src/Makevars.win

@@ -13,13 +13,6 @@ CRAN_FLAGS=-j 2 --offline
 CARGOTMP = $(CURDIR)/.cargo
 VENDOR_DIR = $(CURDIR)/vendor
 
-all: C_clean
-
-$(SHLIB): $(STATLIB)
-
-CRAN_FLAGS=-j 2 --offline
-CARGOTMP = $(CURDIR)/.cargo
-
 $(STATLIB):
 	# uncompress vendored deps
 	if [ -f ./rust/vendor.tar.xz ]; then \
@@ -43,7 +36,8 @@ $(STATLIB):
 		export CARGO_TARGET_X86_64_PC_WINDOWS_GNU_LINKER="$(CARGO_LINKER)" && \
 		export LIBRARY_PATH="$${LIBRARY_PATH};$(CURDIR)/$(TARGET_DIR)/libgcc_mock"; \
 		cargo build $(CRAN_FLAGS) --target=$(TARGET) --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR) && \
-		echo `cargo --version` && echo `rustc --version`;
+		echo "Rust version:" `rustc --version` && \
+		echo "Cargo version:" `cargo --version`;
 	if [ "$(NOT_CRAN)" != "true" ]; then \
 		rm -Rf $(CARGOTMP) $(VENDOR_DIR) $(LIBDIR)/build; \
 	fi