Merge branch 'release/2.4.0' into stable

.Rbuildignore

@@ -17,3 +17,4 @@
 ^doc$
 ^Meta$
 ^CRAN-RELEASE$
+^\.lintr$

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

@@ -6,6 +6,7 @@ on:
       - devel
       - stable
       - release/*
+      - feature/*
   pull_request:
     branches:
       - devel
@@ -58,36 +59,47 @@ jobs:
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-
 
-      - name: Install system dependencies
+      - name: Install system dependencies on Linux
         if: runner.os == 'Linux'
         run: |
           while read -r cmd
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
-      - name: Install X11 dependencies on MacOS
+      - name: Install system dependencies on MacOS (X11, gdal)
         if: runner.os == 'macOS'
         run: |
           brew install --cask xquartz
-      
+          brew install pkg-config
+          brew install proj@8
+          brew install gdal
+
       - name: Install dependencies
         run: |
-          remotes::install_cran("Matrix")
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
-          sessionInfo()
-          print(getNamespaceVersion("Matrix"))
-          print(.libPaths())
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Full testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main

.github/workflows/lint.yaml

@@ -0,0 +1,47 @@
+on:
+  push:
+    branches:
+      - devel
+  pull_request:
+    branches:
+      - devel
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_github("jimhester/lintr")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}

.github/workflows/test-coverage.yaml

@@ -10,7 +10,7 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-20.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
@@ -34,6 +34,13 @@ jobs:
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-
 
+      - name: Install system dependencies
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
       - name: Install dependencies
         run: |
           install.packages(c("remotes"))

.lintr

@@ -0,0 +1,164 @@
+linters: with_defaults(
+    line_length_linter = NULL, # 866
+    object_name_linter = NULL, # 618
+    commented_code_linter = NULL, # 121
+    object_usage_linter = NULL, # 54
+    object_length_linter = NULL, # 28
+    cyclocomp_linter = NULL, # 27
+    dummy_linter = NULL
+  )
+exclusions: list(
+    "data/gorillas.rda",
+    "data/mexdolphin.rda",
+    "data/mrsea.rda",
+    "data/Poisson1_1D.rda",
+    "data/Poisson2_1D.rda",
+    "data/Poisson3_1D.rda",
+    "data/seals.rda",
+    "data/shrimp.rda",
+    "data/toygroups.rda",
+    "inst/examples/bru.R",
+    "inst/examples/data.toygroups.R",
+    "inst/examples/devel.cvmeasure.R",
+    "inst/examples/generate.bru.R",
+    "inst/examples/gg.inla.mesh.R",
+    "inst/examples/gg.prediction.R",
+    "inst/examples/gg.spatial.R",
+    "inst/examples/like.R",
+    "inst/examples/predict.bru.R",
+    "inst/examples/prediction.bru.R",
+    "inst/examples/rgl.R",
+    "inst/examples/spde.posterior.R",
+    "man/add_mappers.Rd",
+    "man/amatrix_eval.Rd",
+    "man/bincount.Rd",
+    "man/bru_call_options.Rd",
+    "man/bru_compute_linearisation.Rd",
+    "man/bru_env_get.Rd",
+    "man/bru_fill_missing.Rd",
+    "man/bru_info.Rd",
+    "man/bru_int_polygon.Rd",
+    "man/bru_log.Rd",
+    "man/bru_make_stack.Rd",
+    "man/bru_mapper_methods.Rd",
+    "man/bru_mapper.Rd",
+    "man/bru_model.Rd",
+    "man/bru_options.Rd",
+    "man/bru_safe_inla.Rd",
+    "man/bru_standardise_names.Rd",
+    "man/bru.Rd",
+    "man/code.components.Rd",
+    "man/component_list.Rd",
+    "man/component.Rd",
+    "man/cprod.Rd",
+    "man/deltaIC.Rd",
+    "man/devel.cvmeasure.Rd",
+    "man/evaluate_A.Rd",
+    "man/evaluate_effect.Rd",
+    "man/evaluate_index.Rd",
+    "man/evaluate_model.Rd",
+    "man/evaluate_predictor.Rd",
+    "man/expand_labels.Rd",
+    "man/extract_property.Rd",
+    "man/figures/README-example-1.png",
+    "man/fm_crs_wkt.Rd",
+    "man/fm_CRS.Rd",
+    "man/fm_CRSargs.Rd",
+    "man/fm_has_PROJ6.Rd",
+    "man/fm_identical_CRS.Rd",
+    "man/fm_sp_get_crs.Rd",
+    "man/fm_spTransform.Rd",
+    "man/generate.Rd",
+    "man/gg.data.frame.Rd",
+    "man/gg.inla.mesh.1d.Rd",
+    "man/gg.inla.mesh.Rd",
+    "man/gg.matrix.Rd",
+    "man/gg.prediction.Rd",
+    "man/gg.RasterLayer.Rd",
+    "man/gg.Rd",
+    "man/gg.SpatialGridDataFrame.Rd",
+    "man/gg.SpatialLines.Rd",
+    "man/gg.SpatialPixels.Rd",
+    "man/gg.SpatialPixelsDataFrame.Rd",
+    "man/gg.SpatialPoints.Rd",
+    "man/gg.SpatialPolygons.Rd",
+    "man/globe.Rd",
+    "man/glplot.inla.mesh.Rd",
+    "man/glplot.Rd",
+    "man/glplot.SpatialLines.Rd",
+    "man/glplot.SpatialPoints.Rd",
+    "man/gm.Rd",
+    "man/gmap.Rd",
+    "man/gorillas.Rd",
+    "man/iinla.Rd",
+    "man/import.gorillas.Rd",
+    "man/import.mexdolphin.Rd",
+    "man/import.mrsea.Rd",
+    "man/import.seals.Rd",
+    "man/import.shrimp.Rd",
+    "man/index_eval.Rd",
+    "man/inla.stack.mjoin.Rd",
+    "man/inlabru-deprecated.Rd",
+    "man/inlabru.Rd",
+    "man/input_eval.Rd",
+    "man/int.polygon.Rd",
+    "man/int.Rd",
+    "man/integration_weight_aggregation.Rd",
+    "man/intersection_mesh.Rd",
+    "man/ipoints.Rd",
+    "man/is.inside.Rd",
+    "man/lgcp.Rd",
+    "man/like.Rd",
+    "man/local_testthat.Rd",
+    "man/make_stable_integration_points.Rd",
+    "man/materncov.bands.Rd",
+    "man/mexdolphin.Rd",
+    "man/mrsea.Rd",
+    "man/multiplot.Rd",
+    "man/parse_inclusion.Rd",
+    "man/pixels.Rd",
+    "man/plot.bru.Rd",
+    "man/plot.prediction.Rd",
+    "man/plotsample.Rd",
+    "man/point2count.Rd",
+    "man/Poisson1_1D.Rd",
+    "man/Poisson2_1D.Rd",
+    "man/Poisson3_1D.Rd",
+    "man/predict.bru.Rd",
+    "man/predict.inla.Rd",
+    "man/refine.inla.mesh.Rd",
+    "man/row_kron.Rd",
+    "man/sample.lgcp.Rd",
+    "man/seals.Rd",
+    "man/shrimp.Rd",
+    "man/sline.Rd",
+    "man/spatial.to.ppp.Rd",
+    "man/spde.posterior.Rd",
+    "man/split_lines.Rd",
+    "man/spoly.Rd",
+    "man/stransform.Rd",
+    "man/summary.bru_options.Rd",
+    "man/summary.bru.Rd",
+    "man/summary.component.Rd",
+    "man/toygroups.Rd",
+    "man/tsplit.inla.mesh.Rd",
+    "man/vertices.inla.mesh.Rd",
+    "man/vertices.Rd",
+    "man/wkt_tree.Rd",
+    "vignettes/linearapprox.Rmd",
+    "vignettes/method.Rmd",
+    "vignettes/web/1d_lgcp.Rmd",
+    "vignettes/web/2d_lgcp_covars.Rmd",
+    "vignettes/web/2d_lgcp_distancesampling.Rmd",
+    "vignettes/web/2d_lgcp_multilikelihood.Rmd",
+    "vignettes/web/2d_lgcp_plotsampling.Rmd",
+    "vignettes/web/2d_lgcp_spatiotemporal.Rmd",
+    "vignettes/web/2d_lgcp.Rmd",
+    "vignettes/web/cache/2d_lgcp_covars/efit.rds",
+    "vignettes/web/cache/2d_lgcp_covars/fit1.rds",
+    "vignettes/web/cache/2d_lgcp_covars/fit2.rds",
+    "vignettes/web/cache/2d_lgcp_covars/fit3.rds",
+    "vignettes/web/publications.Rmd",
+    "vignettes/web/random_fields_2d.Rmd",
+    "vignettes/web/random_fields.Rmd"
+  )

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: inlabru
 Type: Package
 Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
-Version: 2.3.1
+Version: 2.4.0
 Authors@R: c(
   person("Finn", "Lindgren", email = "finn.lindgren@gmail.com",
          role = c("aut", "cre", "cph"),
@@ -20,7 +20,9 @@ Authors@R: c(
          role = c("ctb", "dtc", "cph"),
          comment = "Lindesay Scott-Howard provided MRSea data import code"),
   person("Seaton", "Andy", email = "andy.e.seaton@gmail.com", role = c("ctb"),
-         comment = "Andy Seaton provided testing and bugfixes")
+         comment = "Andy Seaton provided testing and bugfixes"),
+  person("Suen", "Man Ho", email = "M.H.Suen@sms.ed.ac.uk", role = c("ctb", "cph"),
+         comment = "Man Ho Suen contributed features for aggregated responses")
   )
 URL: http://www.inlabru.org, https://inlabru-org.github.io/inlabru/
 BugReports: https://github.com/inlabru-org/inlabru/issues
@@ -38,27 +40,29 @@ Description: Facilitates spatial and general latent Gaussian modeling using
   <doi:10.1111/2041-210X.13168>.
 License: GPL (>= 2)
 Additional_repositories: https://inla.r-inla-download.org/R/testing
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Encoding: UTF-8
 Depends:
-    ggplot2,
     methods,
     R (>= 3.5),
     sp (>= 1.4-5),
     stats
 Imports:
+    plyr,
     Matrix,
     rgdal (>= 1.5.8),
     rgeos,
+    rlang,
     utils,
     withr
 Suggests:
     covr,
     dplyr,
     ggmap,
+    ggplot2,
     ggpolypath,
     graphics,
-    INLA (>= 20.06.18),
+    INLA (>= 21.08.31),
     knitr,
     maptools,
     mgcv,