small updates + add R_CMD_CHECK Action

.Rbuildignore

@@ -5,4 +5,5 @@
 ^pkgdown$
 ^scratch$
 ^codecov\.yml$
-^vignettes/web_only$
+^vignettes/not_on_cran/.*$
+^vignettes/too_slow/.*$

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

@@ -0,0 +1,39 @@
+# 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, dev]
+  pull_request:
+    branches: [main, dev]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies Ubuntu
+        if: runner.os == 'Linux'
+        run: |
+          install.packages('remotes')
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("knitr")
+          remotes::install_cran("rmarkdown")
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

DESCRIPTION

@@ -28,16 +28,6 @@ Imports:
     igraph
 Suggests:
     knitr
-Enhances:
-    spict,
-    JABBA,
-    Rpath,
-    boot
-Remotes:
-    DTUAqua/spict/spict,
-    jabbamodel/JABBA,
-    NOAA-EDAB/Rpath,
-    kaskr/RTMB/RTMBode
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 VignetteBuilder: knitr

vignettes/simulation.Rmd → vignettes/not_on_cran/simulation.Rmd

@@ -7,6 +7,7 @@ vignette: >
   %\VignetteIndexEntry{Demonstrating EcoState via simulation}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
+  %\VignetteDepends{Rpath}
 ---
 
 ```{r, include = FALSE, warning=FALSE, message=FALSE}
@@ -15,6 +16,8 @@ knitr::opts_chunk$set(
   comment = "#>"
 )
 start_time = Sys.time()
+# Dependencies
+#  remotes::install_github( "NOAA-EDAB/Rpath" )
 # Install locally
 #  devtools::install_local( R'(C:\Users\James.Thorson\Desktop\Git\ecostate)', force=TRUE )
 #  devtools::install_github( 'James-Thorson-NOAA/ecostate', force=TRUE )
@@ -25,6 +28,7 @@ start_time = Sys.time()
 
 ```{r setup, echo=TRUE, message=FALSE}
 library(ecostate)
+library(Rpath)
 ```
 
 `ecostate` is an R package for fitting the mass-balance dynamics specified by EcoSim as a state-space model.   We here highlight a few features in particular.
@@ -155,8 +159,6 @@ sim = simulate_data()
 We then load `Rpath` and reformat inputs in the format that it expects to calculate mass-balance:
 
 ```{r, echo=TRUE, message=TRUE, fig.width=7, fig.height=7}
-library(Rpath)
-
 # Rpath needs types in ascending order (EcoState doesn't care)
 types  <- sapply( c(type_i,"fishery"), FUN=switch, 
                   "hetero"==0, "auto"=1, "detritus"=2, "fishery"=3 )

vignettes/surplus_production.Rmd → vignettes/not_on_cran/surplus_production.Rmd

@@ -7,6 +7,7 @@ vignette: >
   %\VignetteIndexEntry{EcoState as surplus production model}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
+  %\VignetteDepends{spict,JABBA}
 ---
 
 ```{r, include = FALSE, warning=FALSE, message=FALSE}
@@ -15,6 +16,9 @@ knitr::opts_chunk$set(
   comment = "#>"
 )
 start_time = Sys.time()
+# Dependencies
+#  remotes::install_github( "jabbamodel/JABBA" )
+#  remotes::install_github( "DTUAqua/spict/spict" )
 # Install locally
 #  devtools::install_local( R'(C:\Users\James.Thorson\Desktop\Git\ecostate)', force=TRUE, dep=FALSE )
 #  devtools::install_github( 'James-Thorson-NOAA/ecostate', force=TRUE )
@@ -25,6 +29,8 @@ start_time = Sys.time()
 
 ```{r setup, echo=TRUE, message=FALSE}
 library(ecostate)
+library(JABBA)
+library(spict)
 set.seed(101)
 ```
 
@@ -513,8 +519,6 @@ The model includes process-errors in the first-stage (eggs to recruits, from age
 We can compare this with a state-space production model in continuous time (SPiCT):
 
 ```{r, echo=TRUE, message=TRUE, fig.width=7, fig.height=7}
-library(spict)
-
 # Format for SPiCT
 datalist = list(
   obsC = C_t[-1],
@@ -531,8 +535,6 @@ plotspict.biomass(res)
 Similarly, we can compare it with Just Another Bayesian Biomass Assessment (JABBA):
 
 ```{r, echo=TRUE, message=TRUE, fig.width=7, fig.height=7}
-library(JABBA)
-
 # Compile JABBA JAGS model and input object
 jbinput = build_jabba( catch = data.frame(Year=years, Total=C_t)[-1,],
                        cpue = data.frame(Year=years, Index=Bobs_t)[-1,],