Final checks / modifications before submitting to CRAN (#74)

* Removing configure from the package and addressing compiler warnings in comparing int with uword

* Fixing missing image

Author: gvegayon

.Rbuildignore

@@ -32,7 +32,6 @@ README[.](R|q)md
 ^next_release\.md$
 ^src/rgraph_scale_free.+$
 makefile
-^src/Makevars$
 ^docs$
 ^LICENSE\.md$
 ^_pkgdown\.yml$

.devcontainer/Containerfile

@@ -1,16 +1,20 @@
-FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.5
+FROM ghcr.io/rocker-org/devcontainer/r-ver:4.5
 
-# RUN \
-#   echo 'options(repos=c(CRAN="https://packagemanager.posit.co/cran/__linux__/bookworm/latest"))' >> ~/.Rprofile && \
-#   Rscript --vanilla -e 'getOption("repos")'
+# Architecture-specific variable (built in Docker BuildKit)
+ARG TARGETARCH
 
-RUN install2.r --error languageserver && installGithub.r nx10/httpgd
+# Install quarto-cli and the orange-book extension
+RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.9.35/quarto-1.9.35-linux-${TARGETARCH}.deb && \
+    dpkg -i quarto-1.9.35-linux-${TARGETARCH}.deb && \
+    rm quarto-1.9.35-linux-${TARGETARCH}.deb
 
 RUN apt-get update && apt-get install --no-install-recommends -y valgrind gdb \
   libglpk-dev
 
 # Adding R packages
-RUN install2.r --error Rcpp sna network networkDynamic Matrix MASS MatchIt SparseM igraph \
-  viridisLite covr testthat knitr rmarkdown ape RSiena survival RcppArmadillo
+RUN install2.r --error -n4 Rcpp sna network networkDynamic Matrix MASS \
+  MatchIt SparseM igraph \
+  viridisLite covr testthat knitr rmarkdown ape RSiena survival \
+  RcppArmadillo
 
 CMD ["bash"]

.devcontainer/devcontainer.json

@@ -12,7 +12,8 @@
 				"rdebugger.r-debugger",
 				"quarto.quarto",
 				"tianyishi.rmarkdown",
-				"github.vscode-github-actions"
+				"github.vscode-github-actions",
+				"openai.chatgpt"
 			]
 		}
 	},

.github/workflows/pkgdown.yml

@@ -24,7 +24,7 @@ jobs:
         id-token: write
         pages: write
       steps:
-        - uses: actions/checkout@v5
+        - uses: actions/checkout@v6
 
         - uses: r-lib/actions/setup-pandoc@v2
           with:
@@ -65,4 +65,4 @@ jobs:
 
       steps:
         - name: Deploy to GitHub pages
-          uses: actions/deploy-pages@v4
+          uses: actions/deploy-pages@v5

.github/workflows/r.yml

@@ -39,7 +39,7 @@ jobs:
       - name: Configure git
         run: git config --global core.autocrlf false
 
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -78,7 +78,7 @@ jobs:
   build-pkg:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -93,7 +93,7 @@ jobs:
         run: R CMD build .
 
       - name: Upload package artifact
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v7
         with:
           name: R-package
           path: '*.tar.gz'

Makefile

@@ -9,7 +9,7 @@ help:
 	@echo "  make docs        - Generate documentation"
 
 install: 
-	Rscript --vanilla -e 'devtools::install()'
+	Rscript -e 'devtools::install()'
 
 build:
 	R CMD build . 
@@ -18,7 +18,7 @@ README.md: README.qmd
 	quarto render README.qmd
 
 check:
-	Rscript --vanilla -e 'devtools::check()'
+	Rscript -e 'devtools::check()'
 
 checkv: netdiffuseR_$(VERSION).tar.gz
 	R CMD check --as-cran --use-valgrind netdiffuseR_$(VERSION).tar.gz
@@ -27,6 +27,6 @@ clean:
 	rm -rf netdiffuseR.Rcheck src/*.so src/*.o
 
 docs:
-	Rscript --vanilla -e 'devtools::document()'
+	Rscript -e 'devtools::document()'
 
 .PHONY: check checkv clean install docs

NEWS.md

@@ -1,4 +1,6 @@
-# Changes in netdiffuseR version 1.25.0 (2026-03-14)
+# Changes in netdiffuseR version 1.25.0 (2026-03-27)
+
+## User-visible changes
 
 * New function `collapse_timeframes()`: aggregates high-resolution or
   continuous-time longitudinal edgelists into discrete time windows, ready
@@ -9,10 +11,15 @@
 * New dataset `epigames` and `epigamesDiffNet`: a simulated epidemic game
   network with 594 nodes and 15 time periods from the WKU Epi Games study.
 
+## Internal changes
+
 * Fixed CRAN example error in `round_to_seq()`: `plot(w, x)` replaced with
   `plot(w)` to avoid `%||%` operator issue in R 4.4.0+'s `formula.default`
   when called via `plot.data.frame()`.
 
+* Removed `configure` framework. R already provides paths and configuration for OpenMP.
+
+
 # Changes in netdiffuseR version 1.24.0 (2025-12-09)
 
 * New function `degree_adoption_diagnostic()` analyzes the correlation between network 

README.md

@@ -52,7 +52,7 @@ And the actual R package:
   Vega Yon G, Olivera Morales A, Valente T (2025). _netdiffuseR:
   Analysis of Diffusion and Contagion Processes on Networks_.
   doi:10.5281/zenodo.1039317 <https://doi.org/10.5281/zenodo.1039317>,
-  R package version 1.24.1, <https://github.com/USCCANA/netdiffuseR>.
+  R package version 1.25.0, <https://github.com/USCCANA/netdiffuseR>.
 
 To see these entries in BibTeX format, use 'print(<citation>,
 bibtex=TRUE)', 'toBibtex(.)', or set
@@ -351,13 +351,13 @@ par(oldpar)
 
 ``` r
 sessionInfo()
-#> R version 4.5.2 (2025-10-31)
-#> Platform: x86_64-pc-linux-gnu
-#> Running under: Ubuntu 24.04.3 LTS
+#> R version 4.5.3 (2026-03-11)
+#> Platform: aarch64-unknown-linux-gnu
+#> Running under: Ubuntu 24.04.4 LTS
 #> 
 #> Matrix products: default
-#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
-#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
+#> BLAS:   /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 
+#> LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
 #> 
 #> locale:
 #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
@@ -374,23 +374,23 @@ sessionInfo()
 #> [1] stats     graphics  grDevices utils     datasets  methods   base     
 #> 
 #> other attached packages:
-#> [1] netdiffuseR_1.24.1
+#> [1] netdiffuseR_1.25.0
 #> 
 #> loaded via a namespace (and not attached):
-#>  [1] Matrix_1.7-4          jsonlite_2.0.0        dplyr_1.1.4          
-#>  [4] compiler_4.5.2        tidyselect_1.2.1      Rcpp_1.1.0           
-#>  [7] networkLite_1.1.0     boot_1.3-32           yaml_2.3.10          
-#> [10] fastmap_1.2.0         lattice_0.22-7        coda_0.19-4.1        
+#>  [1] Matrix_1.7-5          jsonlite_2.0.0        dplyr_1.2.0          
+#>  [4] compiler_4.5.3        tidyselect_1.2.1      Rcpp_1.1.1           
+#>  [7] networkLite_1.1.0     boot_1.3-32           yaml_2.3.12          
+#> [10] fastmap_1.2.0         lattice_0.22-9        coda_0.19-4.1        
 #> [13] R6_2.6.1              generics_0.1.4        MatchIt_4.7.2        
-#> [16] igraph_2.2.1          knitr_1.50            MASS_7.3-65          
-#> [19] backports_1.5.0       tibble_3.3.0          statnet.common_4.12.0
-#> [22] pillar_1.11.1         rlang_1.1.6           xfun_0.53            
-#> [25] viridisLite_0.4.2     cli_3.6.5             magrittr_2.0.4       
-#> [28] network_1.19.0        digest_0.6.37         grid_4.5.2           
-#> [31] lifecycle_1.0.4       vctrs_0.6.5           sna_2.8              
-#> [34] evaluate_1.0.5        SparseM_1.84-2        glue_1.8.0           
-#> [37] rmarkdown_2.30        tools_4.5.2           pkgconfig_2.0.3      
-#> [40] networkDynamic_0.11.5 htmltools_0.5.8.1
+#> [16] igraph_2.2.2          knitr_1.51            MASS_7.3-65          
+#> [19] backports_1.5.0       tibble_3.3.1          statnet.common_4.13.0
+#> [22] pillar_1.11.1         rlang_1.1.7           xfun_0.56            
+#> [25] otel_0.2.0            viridisLite_0.4.3     cli_3.6.5            
+#> [28] magrittr_2.0.4        network_1.20.0        digest_0.6.39        
+#> [31] grid_4.5.3            lifecycle_1.0.5       vctrs_0.7.2          
+#> [34] SparseM_1.84-2        sna_2.8               evaluate_1.0.5       
+#> [37] glue_1.8.0            rmarkdown_2.31        tools_4.5.3          
+#> [40] pkgconfig_2.0.3       networkDynamic_0.11.5 htmltools_0.5.9
 ```
 
 ## To-do list