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Merged
gvegayon merged 2 commits into from
Apr 7, 2026
Merged

Final checks / modifications before submitting to CRAN #74

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6c14668
Removing configure from the package and addressing compiler warnings …
gvegayon Mar 27, 2026
1b5325d
Fixing missing image
gvegayon Apr 7, 2026
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1 change: 0 additions & 1 deletion .Rbuildignore
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Expand Up @@ -32,7 +32,6 @@ README[.](R|q)md
^next_release\.md$
^src/rgraph_scale_free.+$
makefile
^src/Makevars$
^docs$
^LICENSE\.md$
^_pkgdown\.yml$
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18 changes: 11 additions & 7 deletions .devcontainer/Containerfile
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@@ -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
Comment on lines +6 to +9
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Copilot AI Apr 7, 2026

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The devcontainer downloads and installs the Quarto .deb directly via wget without any integrity verification (checksum/signature). Even though this is “dev-only”, it’s still a supply-chain risk; consider verifying a published SHA256 (or using a package manager / pinned digest) before installing.

Copilot uses AI. Check for mistakes.

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"]
3 changes: 2 additions & 1 deletion .devcontainer/devcontainer.json
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Expand Up @@ -12,7 +12,8 @@
"rdebugger.r-debugger",
"quarto.quarto",
"tianyishi.rmarkdown",
"github.vscode-github-actions"
"github.vscode-github-actions",
"openai.chatgpt"
]
}
},
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4 changes: 2 additions & 2 deletions .github/workflows/pkgdown.yml
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Expand Up @@ -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:
Expand Down Expand Up @@ -65,4 +65,4 @@ jobs:

steps:
- name: Deploy to GitHub pages
uses: actions/deploy-pages@v4
uses: actions/deploy-pages@v5
6 changes: 3 additions & 3 deletions .github/workflows/r.yml
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Expand Up @@ -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:
Expand Down Expand Up @@ -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:
Expand All @@ -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'
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6 changes: 3 additions & 3 deletions Makefile
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Expand Up @@ -9,7 +9,7 @@ help:
@echo " make docs - Generate documentation"

install:
Rscript --vanilla -e 'devtools::install()'
Rscript -e 'devtools::install()'

build:
R CMD build .
Expand All @@ -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
Expand All @@ -27,6 +27,6 @@ clean:
rm -rf netdiffuseR.Rcheck src/*.so src/*.o

docs:
Rscript --vanilla -e 'devtools::document()'
Rscript -e 'devtools::document()'
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Removing --vanilla from these Rscript invocations means user/site profiles and environment variables can influence devtools::install(), check(), and document(), which reduces reproducibility across machines. If the intent is reliable, “clean” local/CI builds, consider keeping --vanilla at least for check/docs targets.

Suggested change
Rscript -e 'devtools::document()'
Rscript --vanilla -e 'devtools::document()'

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.PHONY: check checkv clean install docs
9 changes: 8 additions & 1 deletion NEWS.md
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@@ -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
Expand All @@ -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
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40 changes: 20 additions & 20 deletions README.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
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3 changes: 0 additions & 3 deletions cleanup
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