Add GitHub Actions, fix #11

.Rbuildignore

@@ -6,4 +6,8 @@ unpub
 ^Meta$
 ^cran-comments\.md$
 ^CRAN-RELEASE$
+<<<<<<< HEAD
+^\.github$
+=======
 ^CRAN-SUBMISSION$
+>>>>>>> 9bd8e8b6b425851ab94e90ad9e345eaa2d6e7c25

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

@@ -0,0 +1,35 @@
+on:
+  push:
+  pull_request:
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Install libcurl4-openssl-dev
+        run: sudo apt install -qq libcurl4-openssl-dev
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_bioc("snpStats")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
+        shell: Rscript {0}
+

.github/workflows/run_issue_6.yaml

@@ -0,0 +1,31 @@
+on:
+  push:
+  pull_request:
+
+name: run_issue_6
+
+jobs:
+  run_issue_6:
+
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - name: Install libcurl4-openssl-dev
+        run: sudo apt install -qq libcurl4-openssl-dev
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck", "rappdirs"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_github("OchoaLab/genio")
+        shell: Rscript {0}
+
+      - name: Run the code from https://github.com/OchoaLab/genio/issues/6
+        run: Rscript scripts/issue_6.R
+

scripts/issue_6.R

@@ -0,0 +1,82 @@
+# Code from https://github.com/OchoaLab/genio/issues/6
+
+################################################################################
+#
+# 1. `write_bed` works as expected, from documentation example code
+#
+################################################################################
+file_out <- tempfile('delete-me-example', fileext = '.bed') # will also work without extension
+X <- rbinom(10, 2, 0.5)
+X[sample(10, 3)] <- NA
+X <- matrix(X, nrow = 5, ncol = 2)
+genio::write_bed(file_out, X) # WORKS
+
+################################################################################
+#
+# 2. `write_bed` works as expected, when saving 
+#   * in a normalized path 
+#   * in a sub-folder that exists
+#
+################################################################################
+file_out <- file.path(
+  rappdirs::user_cache_dir(appname = "my_r_package_name"),
+  "sub_folder_2", "my_filename"
+)
+dir.create(dirname(file_out), recursive = TRUE)
+file_out <- normalizePath(file_out, mustWork = FALSE)
+#
+# On my computer: 
+# file_out == "/home/richel/.cache/my_r_package_name/sub_folder/my_filename"
+#
+X <- rbinom(10, 2, 0.5)
+X[sample(10, 3)] <- NA
+X <- matrix(X, nrow = 5, ncol = 2)
+genio::write_bed(file_out, X) # WORKS
+
+################################################################################
+#
+# 3. `write_bed` crashes ruthlessly, when saving 
+#   * in a normalized path 
+#   * in a sub-folder that does not exist
+#
+################################################################################
+file_out <- file.path(
+  rappdirs::user_cache_dir(appname = "my_r_package_name"),
+  "sub_folder_3", "my_filename"
+)
+file_out <- normalizePath(file_out, mustWork = FALSE)
+#
+# On my computer: 
+# file_out == "/home/richel/.cache/my_r_package_name/sub_folder/my_filename"
+#
+X <- rbinom(10, 2, 0.5)
+X[sample(10, 3)] <- NA
+X <- matrix(X, nrow = 5, ncol = 2)
+
+# The original problem:
+#
+# genio::write_bed(file_out, X) # CAUSES ABORT
+#
+# This is fixed now: it is handled with an R error message 
+# (i.e. no system crash)
+testthat::expect_error(
+  genio::write_bed(file_out, X)
+)
+
+################################################################################
+#
+# 4. `write_bed` crashes ruthlessly, when saving 
+#   * in an un-normalized path 
+#   * in a sub-folder that does exist
+#
+################################################################################
+file_out <- file.path(
+  rappdirs::user_cache_dir(appname = "my_r_package_name"),
+  "sub_folder_4", "my_filename"
+)
+dir.create(dirname(file_out), recursive = TRUE)
+testthat::expect_equal(file_out, "~/.cache/my_r_package_name/sub_folder_4/my_filename")
+X <- rbinom(10, 2, 0.5)
+X[sample(10, 3)] <- NA
+X <- matrix(X, nrow = 5, ncol = 2)
+genio::write_bed(file_out, X) # CAUSES ABORT