Fix build errors (#1)

* First sweep of docs etc.

* More cleanup

* Fix remaining check errors

* Add github actions

* Update RoxygenNote

* Add basic pkgdown site

.Rbuildignore

@@ -1,2 +1,11 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^LICENSE\.md$
+^exec$
+^test-dataset\.RDS$
+^sandbox$
+^example\.R$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - 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")'

.gitignore

@@ -3,3 +3,4 @@
 .RData
 *.DS_Store*
 *.Rproj
+docs

DESCRIPTION

@@ -1,31 +1,36 @@
 Package: CVN
 Title: Covariate-varying Networks
 Version: 1.1
-Date: 2022-09-05
 Author: Louis Dijkstra [aut, cre]
 Maintainer: Louis Dijkstra <[email protected]>
-Description: A package for inferring high-dimensional 
-  Gaussian graphical networks that change with 
-  multiple discrete covariates
+Description: A package for inferring high-dimensional Gaussian graphical
+    networks that change with multiple discrete covariates
+License: GPL (>= 3)
+URL: https://github.com/bips-hb/CVN
+BugReports: https://github.com/bips-hb/CVN/issues
+Depends:
+    R (>= 4.0.2),
 Imports: 
-Depends: 
-	R (>= 4.0.2), 
-	Rcpp,
-	doSNOW, 
-	visNetwork,
-	parallel,
-	progress,
-	Matrix,
-	huge, 
-	glasso,
-	crayon, 
-	ggplot2, 
-	reshape2,
-	dplyr
-LinkingTo: Rcpp
-License: GPL-3
+    crayon,
+    doSNOW,
+    dplyr,
+    foreach,
+    ggplot2,
+    glasso,
+    magrittr,
+    Matrix,
+    parallel,
+    progress,
+    Rcpp,
+    reshape2,
+    snow,
+    stats,
+    utils,
+    visNetwork
+LinkingTo: 
+    Rcpp
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
-URL: https://github.com/bips-hb/CVN
-BugReports: https://github.com/bips-hb/CVN/issues
+RoxygenNote: 7.3.2
+Suggests: 
+    igraph