Merging current development branch into main (#46)

* Starting to work on warnings fixing dependencies and global vars (still some stuff to deal)

* Removal of magrittr #41 and checks for deps. in actions

* Removal of cmdstanr as not on CRAN...

* Update CITATION.cff

* Fix check (#42)

* Install extra-packages in setup-r-deps step

* Fix cmethod consistency

* Linewidth examples (usage still issue but not sure how to break)

* Starting to fix some deps warnings (still some left)

* Forgot cmdstanr not on CRAN

* Fix check (#43)

* Install extra-packages in setup-r-deps step

* Fix cmethod consistency

* Linewidth examples (usage still issue but not sure how to break)

* Starting to fix some deps warnings (still some left)

* Typo in gh-actions

* Trying to fix call to require in write_output. Its not beautiful, but working...I think...

* Remove calls to require()

* Remove not need importFrom and collect them in ibis.iSDM-package.R

* Some smaller cosmetic changes

* No need to specific Namespace for functions from this package

* Remove purrr

* Small fixes to docs, split hyperparameter search and feature selection in `train`. Added Boruta

* Small bug fix introduced with last commit [no-ci]

* Small bug fix introduced with last commit [no-ci]

* Update of citation and prep for release version 0.0.3

* Url fix

* url fix attempt nr 3

* url fix attempt nr 4

---------

Co-authored-by: mhesselbarth <[email protected]>
Co-authored-by: Martin-Jung <[email protected]>

.Rbuildignore

@@ -1,31 +1,32 @@
-^\.travis\.yml$
-^.*\.Rproj$
-^\.Rproj\.user$
-man-roxygen/*
-\.github/*
-vignettes/_output.yaml
-src/stan_files/.*\.o$
-src/stan_files/.*\.cc$
-src/stan_files/.*\.hpp$
-src/stan_files/.*\.exe$
-tests/testthat/stan_files/.*\.o$
-tests/testthat/stan_files/.*\.cc$
-tests/testthat/stan_files/.*\.hpp$
-^\cleanup*
-configure.ac
-^inst/doc/[A-Za-z0-9\-_]+[.]svg$
-^inst/doc/[A-Za-z0-9\-_]+[.]txt$
-^inst/doc/[A-Za-z0-9\-_]+[.]csv
-^inst/doc/\.install_extras$
-^_pkgdown\.yml$
-^docs$
-^\.github$
-^pkgdown$
-LICENSE.md
-README.Rmd
-^CITATION\.cff$
-^vignettes/articles$
-CONTRIBUTING.md
-^cran-comments\.md$
-^revdep$
-^codecov\.yml$
+^\.travis\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
+man-roxygen/*
+\.github/*
+vignettes/_output.yaml
+src/stan_files/.*\.o$
+src/stan_files/.*\.cc$
+src/stan_files/.*\.hpp$
+src/stan_files/.*\.exe$
+tests/testthat/stan_files/.*\.o$
+tests/testthat/stan_files/.*\.cc$
+tests/testthat/stan_files/.*\.hpp$
+^\cleanup*
+configure.ac
+^inst/doc/[A-Za-z0-9\-_]+[.]svg$
+^inst/doc/[A-Za-z0-9\-_]+[.]txt$
+^inst/doc/[A-Za-z0-9\-_]+[.]csv
+^inst/doc/\.install_extras$
+^_pkgdown\.yml$
+^docs$
+^\.github$
+^pkgdown$
+LICENSE.md
+README.Rmd
+^CITATION\.cff$
+^vignettes/articles$
+CONTRIBUTING.md
+^cran-comments\.md$
+^revdep$
+^codecov\.yml$
+.covrignore

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

@@ -40,6 +40,7 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+          extra-repositories: "https://inla.r-inla-download.org/R/testing"
 
       - name: Install gdal and igraph dependencies on Linux (gdal)
         run: |
@@ -60,7 +61,18 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: '"all"'
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck,
+            any::glmnet,
+            any::glmnetUtils,
+            any::pdp,
+            stan-dev/cmdstanr,
+            any::igraph,
+            any::xgboost,
+            any::dbarts,
+            any::mboost,
+            any::inlabru,
+            any::BoomSpikeSlab
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2