From f27a2113fa7a471d9e54a2562e02550811e5cfe3 Mon Sep 17 00:00:00 2001
From: randef1ned <46381867+randef1ned@users.noreply.github.com>
Date: Sun, 14 Jan 2024 02:19:10 +0800
Subject: [PATCH] Update docs and bug fixes

---
 .github/workflows/lint.yaml | 32 ++++++++++++++++++++++++++++++++
 .gitignore                  |  1 -
 DESCRIPTION                 |  7 +++----
 R/mat_util.R                |  1 +
 R/mrw.R                     |  2 +-
 man/random.walk.Rd          |  2 +-
 src/Makevars                | 14 ++++++++++++++
 7 files changed, 52 insertions(+), 7 deletions(-)
 create mode 100644 .github/workflows/lint.yaml
 create mode 100644 src/Makevars

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
new file mode 100644
index 0000000..f4c4ef2
--- /dev/null
+++ b/.github/workflows/lint.yaml
@@ -0,0 +1,32 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.gitignore b/.gitignore
index c95bebc..4f392af 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,7 +7,6 @@ src/tests/netreg_benchmarks*
 src/tests/netreg_tests*
 src/test
 src/netReg.dSYM/*
-src/Makevars
 src/stamp-h1
 src/**/*.o
 src/**/*.a
diff --git a/DESCRIPTION b/DESCRIPTION
index e2c167e..8297370 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,10 +3,9 @@ Type: Package
 Title: Network Diffusion Algorithms
 Version: 0.2.1
 Date: 2018-04-20
-Authors@R: c(person("Simon", "Dirmeier",
+Authors@R: person("Simon", "Dirmeier",
                   email = "simon.dirmeier@gmx.de",
-                  role = c("aut")),
-             person("Yinchun", "Su", email = "me@yinchun.su", role = c("ctb", "cre")))
+                  role = c("aut", "cre"))
 Maintainer: Simon Dirmeier <simon.dirmeier@gmx.de>
 Description: Implementation of network diffusion algorithms such as
   heat diffusion or Markov random walks. Network diffusion algorithms generally
@@ -18,7 +17,7 @@ Description: Implementation of network diffusion algorithms such as
 URL: https://github.com/randef1ned/diffusr
 BugReports: https://github.com/randef1ned/diffusr/issues
 License: GPL (>=3)
-Depends: R (>= 3.4)
+Depends: R (>= 4.0)
 LazyData: TRUE
 LinkingTo: Rcpp, RcppEigen
 biocViews: sparseMatrixStats
diff --git a/R/mat_util.R b/R/mat_util.R
index 54aff7f..e45608f 100644
--- a/R/mat_util.R
+++ b/R/mat_util.R
@@ -159,4 +159,5 @@ colSums3 <- function(mat, is.sparse = NULL) {
   } else {
     sums <- colSums2(mat)
   }
+  return(sums)
 }
diff --git a/R/mrw.R b/R/mrw.R
index d539716..06b4197 100644
--- a/R/mrw.R
+++ b/R/mrw.R
@@ -54,7 +54,7 @@
 #'  nodes, such that the random walk gets not biased to nodes with high
 #'  degree. In that case the original input matrix will be normalized as:
 #'  \deqn{ P(j | i) = \dfrac{1}{\text{degree}(i)} \times
-#'    \min \left(1, \dfrac{\text{degree}(j)}{\text{degree}(i)}\right)}
+#'    \min \left(1, \dfrac{\text{degree}(i)}{\text{degree}(j)}\right)}
 #'  \emph{Note that this will not consider edge weights.}
 #'
 #' @param allow.ergodic Allow multiple components in a graph.
diff --git a/man/random.walk.Rd b/man/random.walk.Rd
index 4220e4c..f8689c2 100644
--- a/man/random.walk.Rd
+++ b/man/random.walk.Rd
@@ -45,7 +45,7 @@ computed solving the analytical solution or rather iteratively}
 nodes, such that the random walk gets not biased to nodes with high
 degree. In that case the original input matrix will be normalized as:
 \deqn{ P(j | i) = \dfrac{1}{\text{degree}(i)} \times
-  \min \left(1, \dfrac{\text{degree}(j)}{\text{degree}(i)}\right)}
+  \min \left(1, \dfrac{\text{degree}(i)}{\text{degree}(j)}\right)}
 \emph{Note that this will not consider edge weights.}}
 
 \item{allow.ergodic}{Allow multiple components in a graph.}
diff --git a/src/Makevars b/src/Makevars
new file mode 100644
index 0000000..aecc367
--- /dev/null
+++ b/src/Makevars
@@ -0,0 +1,14 @@
+## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is
+## no user-facing library. The include path to headers is already set by R.
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)
+
+## With R 3.1.0 or later, you can uncomment the following line to tell R to
+## enable compilation with C++11 (or even C++14) where available
+## R 4.0.0 made C++11 the default, R 4.1.0 switched to C++14, R 4.3.0 to C++17
+## _In general_ we should no longer need to set a standard as any recent R
+## installation will do the right thing. Should you need it, uncomment it and
+## set the appropriate value, possibly CXX17.
+CXX_STD = CXX17
+
+PKG_CPPFLAGS = -w -I../inst/include/ -I/opt/intel/oneapi/mkl/latest/include/ -I/usr/include/mkl -Wno-ignored-attributes -DMKL_ILP64 -m64 -DRCPP_USE_UNWIND_PROTECT -fopenmp -O3 -march=native -fno-math-errno -mfma
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl