From f0fc1421083eb9f461fbc599096ebc7ad0bcf429 Mon Sep 17 00:00:00 2001 From: David Schoch Date: Fri, 24 Jul 2026 09:36:00 +0200 Subject: [PATCH 1/2] Fix R CMD check: rename vendored header to .h, refresh workflows R CMD check (run with error-on = warning) failed on: checking if this is a source package ... WARNING Subdirectory 'src' contains: nanoflann.hpp R does not accept the .hpp extension in src/. Rename the vendored header src/nanoflann.hpp -> src/nanoflann.h and update the include in mingle.cpp. Also: - bump actions/checkout@v3 -> v4 in both workflows (v3 uses deprecated Node 20) - add inst/COPYRIGHTS documenting the bundled nanoflann BSD license - Rbuildignore .claude Local R CMD check --as-cran is now 0 errors / 0 warnings / 0 notes. Co-Authored-By: Claude Opus 4.8 (1M context) --- .Rbuildignore | 1 + .github/workflows/R-CMD-check.yaml | 2 +- .github/workflows/pkgdown.yaml | 2 +- inst/COPYRIGHTS | 12 ++++++++++++ src/mingle.cpp | 2 +- src/{nanoflann.hpp => nanoflann.h} | 0 6 files changed, 16 insertions(+), 3 deletions(-) create mode 100644 inst/COPYRIGHTS rename src/{nanoflann.hpp => nanoflann.h} (100%) diff --git a/.Rbuildignore b/.Rbuildignore index 8fd6c54..bbc651a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -15,3 +15,4 @@ pkgdown/ ^pkgdown$ ^vignettes/articles$ ^_docs$ +^\.claude$ diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac618..74d8c97 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -29,7 +29,7 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index ed7650c..57aba39 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -22,7 +22,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 diff --git a/inst/COPYRIGHTS b/inst/COPYRIGHTS new file mode 100644 index 0000000..f552348 --- /dev/null +++ b/inst/COPYRIGHTS @@ -0,0 +1,12 @@ +The file src/nanoflann.h is a copy of the nanoflann C++ library +(https://github.com/jlblancoc/nanoflann), used for nearest-neighbour search +in edge_bundle_mingle(). + +nanoflann is distributed under the 2-clause BSD license: + + Copyright 2008-2009 Marius Muja (mariusm@cs.ubc.ca). All rights reserved. + Copyright 2008-2009 David G. Lowe (lowe@cs.ubc.ca). All rights reserved. + Copyright 2011-2026 Jose Luis Blanco (joseluisblancoc@gmail.com). + All rights reserved. + +The full license text is retained in the header of src/nanoflann.h. diff --git a/src/mingle.cpp b/src/mingle.cpp index ef97cb6..92f29e6 100644 --- a/src/mingle.cpp +++ b/src/mingle.cpp @@ -10,7 +10,7 @@ // is built once with a kd-tree (vendored nanoflann), giving O(E log E); the // graph is then coarsened combinatorially level by level. #include -#include "nanoflann.hpp" +#include "nanoflann.h" #include #include using namespace Rcpp; diff --git a/src/nanoflann.hpp b/src/nanoflann.h similarity index 100% rename from src/nanoflann.hpp rename to src/nanoflann.h From 377aa1f1702285331129a4e29c03b82f0ed9e502 Mon Sep 17 00:00:00 2001 From: David Schoch Date: Fri, 24 Jul 2026 09:40:32 +0200 Subject: [PATCH 2/2] Bump actions/checkout@v4 -> v5 (Node 24) checkout@v4 still targets the deprecated Node 20 runtime; v5 targets Node 24, silencing the deprecation annotation. Co-Authored-By: Claude Opus 4.8 (1M context) --- .github/workflows/R-CMD-check.yaml | 2 +- .github/workflows/pkgdown.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 74d8c97..21efb73 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -29,7 +29,7 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - uses: r-lib/actions/setup-pandoc@v2 diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 57aba39..4360b25 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -22,7 +22,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - uses: r-lib/actions/setup-pandoc@v2