### Build and Install R

Source: https://github.com/igraph/rigraph/wiki/Testing-with-sanitizers

Build R using the 'make' command, optionally setting parallel job flags for faster builds. Install R to the configured prefix using 'make install'.

```bash
export MAKEFLAGS=-j8
make
make install
```

--------------------------------

### Install Library Targets

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/src/CMakeLists.txt

Installs the main library targets, including executables and libraries, to their designated installation directories.

```cmake
install(
  TARGETS igraph bliss cliquer cxsparse_vendored pcg prpack
  EXPORT igraph_targets
  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
  INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
)
```

--------------------------------

### Run R Script Example

Source: https://github.com/igraph/rigraph/blob/main/revdep/examples/README.md

Demonstrates how to run a reverse dependency example script using Rscript.

```bash
Rscript revdep/examples/tidygraph-bfs-father-issue.R
```

--------------------------------

### Install Header Files from Source Directory

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/src/CMakeLists.txt

Installs header files from the project's source directory to the installation's include directory.

```cmake
install(
  DIRECTORY ${PROJECT_SOURCE_DIR}/include/
  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/igraph
  FILES_MATCHING PATTERN "*.h"
)
```

--------------------------------

### Run R Script with source() Example

Source: https://github.com/igraph/rigraph/blob/main/revdep/examples/README.md

Demonstrates how to run a reverse dependency example script using the source() function in R.

```r
source("revdep/examples/tidygraph-bfs-father-issue.R")
```

--------------------------------

### Installation Failure Summary

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

This snippet shows a general installation failure message for the spopt package. It indicates that the installation process failed and directs the user to a log file for more details.

```text
* checking whether package ‘spopt’ can be installed ... ERROR
     Installation failed.
     See ‘/tmp/workdir/spopt/new/spopt.Rcheck/00install.out’ for details.
```

--------------------------------

### Install Recommended R Packages

Source: https://github.com/igraph/rigraph/wiki/Testing-with-sanitizers

Installs the recommended packages for R. This is a necessary step before building R, ensuring all dependencies are met.

```bash
tools/rsync-recommended
```

--------------------------------

### Install Documentation Tools

Source: https://github.com/igraph/rigraph/blob/main/CONTRIBUTING.md

Installs the necessary R packages for documentation, including roxygen2 and igraph.r2cdocs.

```r
install.packages("roxygen2")
pak::pak("igraph/igraph.r2cdocs")
```

--------------------------------

### Install Library Targets

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/simpleraytracer/CMakeLists.txt

Defines installation rules for the simpleraytracer library, specifying where to place the library, archive, and runtime files on the system.

```cmake
install(
  TARGETS simpleraytracer
  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
)
```

--------------------------------

### Install Pkg-config File

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/src/CMakeLists.txt

Installs the pkg-config file for the igraph library.

```cmake
install(
  FILES ${PROJECT_BINARY_DIR}/igraph.pc
  DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig
)
```

--------------------------------

### Install CMake Configuration Files

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/src/CMakeLists.txt

Installs the main CMake configuration files for the igraph package.

```cmake
install(
  FILES ${PROJECT_BINARY_DIR}/igraph-config.cmake
        ${PROJECT_BINARY_DIR}/igraph-config-version.cmake
  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/igraph
)
```

--------------------------------

### Install Header Files from Build Directory

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/src/CMakeLists.txt

Installs header files generated during the build process from the project's binary directory.

```cmake
install(
  DIRECTORY ${PROJECT_BINARY_DIR}/include/
  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/igraph
  FILES_MATCHING PATTERN "*.h"
)
```

--------------------------------

### Install R/igraph Dependencies on Windows (R >= 4.0)

Source: https://github.com/igraph/rigraph/blob/main/README.md

Install required glpk and libxml2 development libraries for R/igraph compilation on Windows using pacman, assuming RTools is installed.

```bash
pacman -Sy mingw-w64-{i686,x86_64}-glpk mingw-w64-{i686,x86_64}-libxml2
```

--------------------------------

### Community Leading Eigenvector Callback with Start

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the usage of `community_leading_eigenvector_callback_closure_impl` with a starting membership vector. Shows the resulting membership and modularity.

```R
cat("Result with start membership:\n")
cat("Membership length:\n")
print(length(result$membership))
cat("\nModularity:\n")
print(result$modularity)
```

--------------------------------

### Configure R Build with Custom Prefix

Source: https://github.com/igraph/rigraph/wiki/Testing-with-sanitizers

Run the configure script to set up the R build, specifying a custom installation prefix. Ensure required libraries are installed and flags are correctly set if errors occur.

```bash
./configure --prefix=$HOME/rsan
```

--------------------------------

### spopt Package Installation (CRAN)

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

This log shows the source installation attempt for the spopt package in a CRAN context. Similar to the devel installation, it fails due to a Rust compiler version incompatibility, this time with the 'rayon-core' crate requiring Rustc 1.80+ while 1.75.0 is active.

```text
* installing *source* package ‘spopt’ ...
** this is package ‘spopt’ version ‘0.1.2’
** package ‘spopt’ successfully unpacked and MD5 sums checked
** using staged installation
Using cargo 1.75.0
Using rustc 1.75.0 (82e1608df 2023-12-21) (built from a source tarball)
Building for CRAN.
Writing `src/Makevars`.
`tools/config.R` has finished.
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/opt/R/4.5.1/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c entrypoint.c -o entrypoint.o
if [ -d ./vendor ]; then \
	echo "=== Using offline vendor directory ==="; \
	mkdir -p /tmp/workdir/spopt/old/spopt.Rcheck/00_pkg_src/spopt/src/.cargo && \
	cp rust/vendor-config.toml /tmp/workdir/spopt/old/spopt.Rcheck/00_pkg_src/spopt/src/.cargo/config.toml; \
elif [ -f ./rust/vendor.tar.xz ]; then \
	echo "=== Using offline vendor tarball ==="; \
	tar xf rust/vendor.tar.xz && \
	mkdir -p /tmp/workdir/spopt/old/spopt.Rcheck/00_pkg_src/spopt/src/.cargo && \
	cp rust/vendor-config.toml /tmp/workdir/spopt/old/spopt.Rcheck/00_pkg_src/spopt/src/.cargo/config.toml; \
fi
=== Using offline vendor tarball ===
export CARGO_HOME=/tmp/workdir/spopt/old/spopt.Rcheck/00_pkg_src/spopt/src/.cargo && \
export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/.cargo/bin" && \
RUSTFLAGS=" --print=native-static-libs" cargo build -j 2 --offline --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target 
error: package `rayon-core v1.13.0` cannot be built because it requires rustc 1.80 or newer, while the currently active rustc version is 1.75.0
Either upgrade to rustc 1.80 or newer, or use
cargo update rayon-core@1.13.0 --precise ver
where `ver` is the latest version of `rayon-core` supporting rustc 1.75.0
make: *** [Makevars:27: rust/target/release/libspopt.a] Error 101
ERROR: compilation failed for package ‘spopt’
* removing ‘/tmp/workdir/spopt/old/spopt.Rcheck/spopt’
```

--------------------------------

### get_all_shortest_paths_impl basic usage

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Provides a basic example of `get_all_shortest_paths_impl` with a valid graph.

```R
get_all_shortest_paths_impl(graph = g, from = 1, to = 3)
```

--------------------------------

### Install UUID Library

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/uuid/CMakeLists.txt

Installs the UUID library targets (library, archive, runtime) to their respective destinations.

```cmake
install(
  TARGETS uuid
  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
)
```

--------------------------------

### Install igraph Development Version

Source: https://github.com/igraph/rigraph/blob/main/CONTRIBUTING.md

Install the development version of igraph from GitHub using remotes or pak. Optionally, specify a separate library location to avoid conflicts with a stable installation.

```R
remotes::install_github("igraph/rigraph")
```

```R
pak::pak("igraph/rigraph")
```

```R
remotes::install_github("igraph/rigraph", lib = "~/testing/")
```

--------------------------------

### Basic Usage of get_all_simple_paths_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Provides a basic example of finding all simple paths between two vertices using `get_all_simple_paths_impl`.

```R
get_all_simple_paths_impl(graph = g, from = 1, to = 3)
```

--------------------------------

### Install GitHub CLI on macOS

Source: https://github.com/igraph/rigraph/blob/main/revdep/NOTIFY-README.md

Installs the GitHub CLI using Homebrew on macOS. This is a prerequisite for creating GitHub issues.

```bash
# Install GitHub CLI
# On macOS:
brew install gh
```

--------------------------------

### Installation Failure Message

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

Indicates that the installation of the 'scAnnotate' package failed. Details can be found in the specified log file.

```text
Installation failed.
See ‘/tmp/workdir/scAnnotate/new/scAnnotate.Rcheck/00install.out’ for details.
```

--------------------------------

### Install git-subrepo on macOS

Source: https://github.com/igraph/rigraph/blob/main/tools/README.md

Install the git-subrepo tool on macOS using Homebrew. Alternatively, you can install from source and source the rc file.

```sh
# On macOS with Homebrew
brew install git-subrepo

# Or install from source
git clone https://github.com/ingydotnet/git-subrepo /path/to/git-subrepo
echo 'source /path/to/git-subrepo/.rc' >> ~/.zshrc
```

--------------------------------

### Install Windows Dependencies

Source: https://github.com/igraph/rigraph/blob/main/CONTRIBUTING.md

Install required system dependencies (glpk and libxml2) for building the igraph package from source on Windows using RTools.

```sh
pacman -Sy mingw-w64-{i86,x86_64}-glpk mingw-w64-{i86,x86_64}-libxml2
```

--------------------------------

### Install All Dependencies with pak

Source: https://github.com/igraph/rigraph/blob/main/AGENTS.md

Installs all necessary package dependencies for the igraph project using the pak package manager.

```r
pak::pak()
```

--------------------------------

### Basic layout_sphere_impl (example 1)

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the basic usage of the layout_sphere_impl function to generate a spherical layout for a graph.

```R
layout_sphere_impl(graph = g)
```

--------------------------------

### R6causal Install Warnings

Source: https://github.com/igraph/rigraph/blob/main/revdep/examples/r6causal-attribute-deprecations-issue.md

Shows the deprecation warnings generated during the R6causal package installation check.

```text
checking whether package ‘R6causal’ can be installed ... WARNING
Found the following significant warnings:
  Warning: `set.edge.attribute()` was deprecated in igraph 2.0.0.
  Warning: `induced.subgraph()` was deprecated in igraph 2.0.0.
  Warning: `get.vertex.attribute()` was deprecated in igraph 2.0.0.
```

--------------------------------

### migraph: Tutorial Code Example

Source: https://github.com/igraph/rigraph/blob/main/revdep/problems-analysis.md

Illustrates a specific line of code from a migraph tutorial that triggered a deprecation warning on an older igraph version.

```R
rg <- create_ring(32, width = 2)
```

--------------------------------

### random_walk_impl Basic Usage

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Provides an example of random_walk_impl with default settings.

```R
random_walk_impl(graph = g, start = 1, steps = 2)
```

--------------------------------

### min_st_separators Example Output

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/flow.md

Shows the successful output for the `min_st_separators` function in a note case.

```r
min_st_separators(g_note)
```

--------------------------------

### Basic Vertex Connectivity

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates a basic example of calculating vertex connectivity for a graph using `vertex_connectivity_impl`.

```R
vertex_connectivity_impl(graph = g)
```

--------------------------------

### Install R/igraph Dependencies on Fedora

Source: https://github.com/igraph/rigraph/blob/main/README.md

Install the necessary development packages for glpk and libxml2 on Fedora systems to compile R/igraph from source.

```bash
yum install glpk-devel libxml2-devel
```

--------------------------------

### Reproducible Example of defunct method in sample_degseq

Source: https://github.com/igraph/rigraph/blob/main/revdep/examples/qgraph-sample-degseq-method-issue.md

Demonstrates the error when using the defunct 'simple.no.multiple' method and shows the correct replacement using 'fast.heur.simple'.

```r
library(igraph)

deg <- rep(2, 10)

sample_degseq(deg, method = "simple.no.multiple")
#> Error:
#> ! The `method` argument of `sample_degseq()` must be fast.heur.simple
#>   instead of simple.no.multiple as of igraph 2.1.0.

# Working replacement
sample_degseq(deg, method = "fast.heur.simple")
```

--------------------------------

### Basic Usage of get_widest_path_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Shows a basic example of finding the widest path between two vertices using get_widest_path_impl with specified weights.

```R
get_widest_path_impl(graph = g, from = 1, to = 3, weights = c(1, 2))
```

--------------------------------

### Install CMake Export File

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/src/CMakeLists.txt

Installs the CMake export file that defines targets for imported igraph components.

```cmake
install(
  EXPORT igraph_targets
  FILE igraph-targets.cmake
  NAMESPACE igraph::
  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/igraph
)
```

--------------------------------

### igraph subgraph output example

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/trees.md

Example output from an igraph operation, showing graph attributes and edge list.

```text
IGRAPH U--- 13 11 -- 
+ attr: name_1 (g/c), name_2 (g/c), loops_1 (g/l), loops_2 (g/l)
+ edges: 
 [1]  1-- 2  1-- 8  3-- 6  3-- 8  4-- 5  5-- 7  6-- 7  9--11  9--13 10--13
[11] 12--13
```

--------------------------------

### spopt Package Installation (Devel)

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

This log details the source installation process for the spopt package in a development environment. It highlights a critical error where a Rust dependency ('indexmap') requires a newer Rust compiler version (1.82+) than the one detected (1.75.0), leading to compilation failure.

```text
* installing *source* package ‘spopt’ ...
** this is package ‘spopt’ version ‘0.1.2’
** package ‘spopt’ successfully unpacked and MD5 sums checked
** using staged installation
Using cargo 1.75.0
Using rustc 1.75.0 (82e1608df 2023-12-21) (built from a source tarball)
Building for CRAN.
Writing `src/Makevars`.
`tools/config.R` has finished.
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/opt/R/4.5.1/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c entrypoint.c -o entrypoint.o
if [ -d ./vendor ]; then \
	echo "=== Using offline vendor directory ==="; \
	mkdir -p /tmp/workdir/spopt/new/spopt.Rcheck/00_pkg_src/spopt/src/.cargo && \
	cp rust/vendor-config.toml /tmp/workdir/spopt/new/spopt.Rcheck/00_pkg_src/spopt/src/.cargo/config.toml; \
elif [ -f ./rust/vendor.tar.xz ]; then \
	echo "=== Using offline vendor tarball ==="; \
	tar xf rust/vendor.tar.xz && \
	mkdir -p /tmp/workdir/spopt/new/spopt.Rcheck/00_pkg_src/spopt/src/.cargo && \
	cp rust/vendor-config.toml /tmp/workdir/spopt/new/spopt.Rcheck/00_pkg_src/spopt/src/.cargo/config.toml; \
fi
=== Using offline vendor tarball ===
export CARGO_HOME=/tmp/workdir/spopt/new/spopt.Rcheck/00_pkg_src/spopt/src/.cargo && \
export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/.cargo/bin" && \
RUSTFLAGS=" --print=native-static-libs" cargo build -j 2 --offline --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target 
error: package `indexmap v2.12.1` cannot be built because it requires rustc 1.82 or newer, while the currently active rustc version is 1.75.0
Either upgrade to rustc 1.82 or newer, or use
cargo update indexmap@2.12.1 --precise ver
where `ver` is the latest version of `indexmap` supporting rustc 1.75.0
make: *** [Makevars:27: rust/target/release/libspopt.a] Error 101
ERROR: compilation failed for package ‘spopt’
* removing ‘/tmp/workdir/spopt/new/spopt.Rcheck/spopt’
```

--------------------------------

### Check if a Graph is Chordal (Example 2)

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

This example uses `is_chordal_impl` on a different graph (`g2`) to demonstrate a non-chordal graph and its fill-in edges.

```R
is_chordal_impl(graph = g2, alpha = alpha_vec2, alpham1 = alpham1_vec2)
```

--------------------------------

### Install R/igraph Development Version from GitHub using pak

Source: https://github.com/igraph/rigraph/blob/main/README.md

Install the development version of R/igraph directly from its GitHub repository using the 'pak' package manager. This is useful for testing the latest features.

```r
pak::pak("igraph/rigraph")
```

--------------------------------

### Get girth of a graph using girth_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Basic usage example for `girth_impl` to retrieve the girth of a graph. The result is accessed via the '$girth' attribute.

```R
result$girth
```

--------------------------------

### Configure R-universe Repository for R/igraph

Source: https://github.com/igraph/rigraph/blob/main/README.md

Set up your R session to use the igraph R-universe repository for installing the development version. This ensures you get the latest updates.

```r
options(
  repos = c(
    igraph = 'https://igraph.r-universe.dev',
    CRAN = 'https://cloud.r-project.org'
  )
)
install.packages('igraph')
```

--------------------------------

### Caugi Package Installation Failure (Devel)

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

Illustrates an installation failure for the 'caugi' package in development mode, specifically due to an unsupported Rust version.

```R
* installing *source* package ‘caugi’ ...
** this is package ‘caugi’ version ‘1.2.0’
** package ‘caugi’ successfully unpacked and MD5 sums checked
** using staged installation
Error in eval(ei, envir) :
------------------ [UNSUPPORTED RUST VERSION]------------------
- Minimum supported Rust version is 1.80.0.
- Installed Rust version is 1.75.0.
---------------------------------------------------------------
Calls: source -> withVisible -> eval -> eval
Execution halted
ERROR: configuration failed for package ‘caugi’
* removing ‘/tmp/workdir/caugi/new/caugi.Rcheck/caugi’
```

--------------------------------

### ggpicrust2 Package Installation Check Log

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

This log details the checks performed by revdepcheck for the ggpicrust2 package. It covers environment setup, package integrity, dependency checks, code and documentation validation, and test execution. The output indicates that the package can be installed and loaded without critical errors.

```log
* using log directory ‘/tmp/workdir/ggpicrust2/new/ggpicrust2.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘ggpicrust2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggpicrust2’ version ‘2.5.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘lefser’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ggpicrust2’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   1.0Mb
    help      1.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

```

--------------------------------

### Usage of maximal_cliques_hist_impl with size constraints

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates using `maximal_cliques_hist_impl` with `min_size` and `max_size` to get a histogram of maximal cliques within a specific size range. This example focuses on cliques of size 2.

```R
maximal_cliques_hist_impl(graph = g, min_size = 2, max_size = 2)
```

--------------------------------

### Basic Moran process implementation

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the basic usage of `moran_process_impl` with a graph, weights, quantities, strategies, and 'in' mode.

```R
moran_process_impl(graph = g, weights = c(1, 1), quantities = c(1, 2, 3),
      strategies = c(1, 2, 3), mode = "in")
```

--------------------------------

### Basic rooted_product_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the basic usage of the rooted_product_impl function with two graphs and a specified root.

```R
rooted_product_impl(g1 = g1, g2 = g2, root = 1)
```

--------------------------------

### Basic usage of random_spanning_tree_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates how to generate a random spanning tree from a graph `g` starting from vertex 1 using `random_spanning_tree_impl`.

```R
random_spanning_tree_impl(graph = g, vid = 1)
```

--------------------------------

### sbm_game_impl with Directed and Loops

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Shows how to use `sbm_game_impl` to generate a directed graph with self-loops. This example highlights the parameters for controlling graph directionality and the inclusion of loops.

```R
sbm_game_impl(n = 5, pref_matrix = matrix(0.5, 2, 2), block_sizes = c(2, 3),
      directed = TRUE, loops = TRUE)
```

--------------------------------

### Basic Usage of get_k_shortest_paths_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Illustrates how to find the k-shortest paths between two vertices using `get_k_shortest_paths_impl`.

```R
get_k_shortest_paths_impl(graph = g, from = 1, to = 3, k = 2)
```

--------------------------------

### blavaan Package Installation Error

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

This snippet shows the general error message when the blavaan package fails to install. It indicates that the installation failed and directs the user to a log file for details.

```text
* checking whether package ‘blavaan’ can be installed ... ERROR
     Installation failed.
     See ‘/tmp/workdir/blavaan/new/blavaan.Rcheck/00install.out’ for details.
```

--------------------------------

### scAnnotate Package Installation Error (Devel)

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

Shows the build process for the 'scAnnotate' package (devel version) failing during byte-compilation due to an unexported object from the 'harmony' namespace.

```r
* installing *source* package ‘scAnnotate’ ...
** this is package ‘scAnnotate’ version ‘0.3’
** package ‘scAnnotate’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘HarmonyMatrix’ is not exported by 'namespace:harmony'
Execution halted
ERROR: lazy loading failed for package ‘scAnnotate’
* removing ‘/tmp/workdir/scAnnotate/new/scAnnotate.Rcheck/scAnnotate’


```

--------------------------------

### asymmetric_preference_game_impl basic usage

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Provides a basic example of generating a directed graph with asymmetric preferences using asymmetric_preference_game_impl.

```R
asymmetric_preference_game_impl(nodes = 5, out_types = 2, in_types = 2,
 type_dist_matrix = matrix(c(0.5, 0.5, 0.5, 0.5), 2, 2), pref_matrix = matrix(
 c(0.5, 0.5, 0.5, 0.5), 2, 2))
```

--------------------------------

### preference_game_impl basic usage

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Shows a basic example of creating a graph using preference_game_impl with specified node types and preferences.

```R
preference_game_impl(nodes = 5, types = 2, type_dist = c(0.5, 0.5),
 fixed_sizes = FALSE, pref_matrix = matrix(c(0.5, 0.5, 0.5, 0.5), 2, 2))
```

--------------------------------

### Basic cycle finding with callback

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Illustrates the basic usage of `simple_cycles_callback_closure_impl` for finding simple cycles and processing them with a callback. Shows how to print the result and the details of the first cycle found.

```R
cat("Result:\n")
print(result)
cat("\nNumber of cycles found:", length(cycle_data), "\n")
cat("First cycle:\n")
print(cycle_data[[1]])
```

--------------------------------

### Perform Simple Breadth-First Search (BFS)

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Performs a simple BFS starting from a specified root vertex, returning traversal order, layers, and parents.

```R
bfs_simple_impl(graph = g, root = 1)
```

--------------------------------

### laplacian_spectral_embedding_impl Basic Usage

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Shows a basic usage example of laplacian_spectral_embedding_impl with a valid graph object and outputs the resulting embedding matrices and options.

```R
laplacian_spectral_embedding_impl(graph = g, no = 2)
```

--------------------------------

### Basic Edge Connectivity

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Shows a basic example of calculating edge connectivity for a graph using `edge_connectivity_impl`.

```R
edge_connectivity_impl(graph = g)
```

--------------------------------

### Site Percolation Error Handling

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Shows an example of an error condition when site_percolation_impl is called with a NULL graph object.

```R
site_percolation_impl(graph = NULL)
```

--------------------------------

### k_regular_game_impl Error Example

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates an error case for `k_regular_game_impl` when a negative number of nodes is provided. The function requires a non-negative node count.

```R
k_regular_game_impl(no_of_nodes = -1, k = 2)
```

--------------------------------

### Vertex Dependency Example

Source: https://github.com/igraph/rigraph/blob/main/tools/py-stimulus/docs/index.mdx

Shows a specific dependency for vertex specification, where 'vids' depends on 'graph'. 'R' ensures vertex sequences are correct, translating names to indices.

```text
DEPS: vids ON graph
```

--------------------------------

### Generate Pkgconfig File

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/src/CMakeLists.txt

Includes helper functions for generating pkgconfig files. This is essential for making the installed library discoverable by other projects using pkg-config.

```cmake
# Generate pkgconfig file
include(pkgconfig_helpers)
```

--------------------------------

### solve_lsap_impl Basic Usage

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the basic usage of solve_lsap_impl with a cost matrix and number of agents.

```R
solve_lsap_impl(c = matrix(1:4, ncol = 2), n = 2)
```

--------------------------------

### Basic Usage of get_isomorphisms_vf2_callback_closure_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Illustrates the basic output and results when using `get_isomorphisms_vf2_callback_closure_impl` to find isomorphisms. It shows how to print the results and count the number of isomorphisms found.

```R
cat("Result:\n")
print(result)
cat("\nNumber of isomorphisms found:", length(iso_data), "\n")
cat("First isomorphism:\n")
print(iso_data[[1]])
```

--------------------------------

### Install Build Dependencies with pak

Source: https://github.com/igraph/rigraph/blob/main/AGENTS.md

Installs only the build-specific dependencies for the igraph project using the pak package manager.

```r
pak::pak(dependencies = "Config/Needs/build")
```

--------------------------------

### Basic Usage of get_subisomorphisms_vf2_callback_closure_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the basic output and results when using `get_subisomorphisms_vf2_callback_closure_impl` to find subisomorphisms. It includes printing the results and counting the number of subisomorphisms found.

```R
cat("Result:\n")
print(result)
cat("\nNumber of subisomorphisms found:", length(subiso_data), "\n")
cat("First subisomorphism:\n")
print(subiso_data[[1]])
```

--------------------------------

### Check if a Graph is Chordal (Example 1)

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

The `is_chordal_impl` function checks if a graph is chordal. This example demonstrates a chordal graph.

```R
is_chordal_impl(graph = g, alpha = alpha_vec, alpham1 = alpham1_vec)
```

--------------------------------

### get_all_shortest_paths_dijkstra_impl basic usage

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the basic functionality of `get_all_shortest_paths_dijkstra_impl`.

```R
get_all_shortest_paths_dijkstra_impl(graph = g, from = 1, to = 3)
```

--------------------------------

### Reproducible Example of Defunct layout.spring()

Source: https://github.com/igraph/rigraph/blob/main/revdep/examples/comato-layout-spring-issue.md

Demonstrates the error when calling the defunct igraph::layout.spring() function and shows the working replacement using layout_with_fr().

```r
library(igraph)

g <- make_ring(10)

# Old call -- now defunct
layout.spring(g)
#> Error:
#> ! `layout.spring()` was deprecated in igraph 2.1.0 and is now defunct.
#> i Please use `layout_with_fr()` instead.

# Working replacement
coords <- layout_with_fr(g)
```

--------------------------------

### Correct usage of bfs()

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/structural-properties.md

Shows a working example of the `bfs()` function with various arguments to explore graph structure. This demonstrates how to correctly use arguments like `mode`, `order`, `rank`, `parent`, `pred`, `succ`, and `dist`.

```R
g <- graph_from_literal(a - +b - +c, z - +a, d)
bfs(g, root = 2, mode = "out", unreachable = FALSE, order = TRUE, rank = TRUE,
  parent = TRUE, pred = TRUE, succ = TRUE, dist = TRUE)
```

--------------------------------

### Review Source and Configure Changes

Source: https://github.com/igraph/rigraph/blob/main/src/README.md

Compares the current state of src/ and configure files against the last commit. Use this to review changes after updating sources.

```sh
git diff src/ configure
```

--------------------------------

### Basic usage of sample_sphere_volume_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Illustrates the basic functionality of `sample_sphere_volume_impl` for sampling points within a sphere's volume.

```R
sample_sphere_volume_impl(dim = 3, n = 5)
```

--------------------------------

### stochastic_imitation_impl basic usage (algo 1)

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Basic usage of stochastic_imitation_impl with algorithm 1.

```R
stochastic_imitation_impl(graph = g, vid = 1, algo = 1, quantities = c(1, 2, 3),
  strategies = c(1, 2, 3))

```

--------------------------------

### Caugi Package Installation Failure (CRAN)

Source: https://github.com/igraph/rigraph/blob/main/revdep/failures.md

Details an installation failure for the 'caugi' package from CRAN, also caused by an unsupported Rust version.

```R
* installing *source* package ‘caugi’ ...
** this is package ‘caugi’ version ‘1.2.0’
** package ‘caugi’ successfully unpacked and MD5 sums checked
** using staged installation
Error in eval(ei, envir) :
------------------ [UNSUPPORTED RUST VERSION]------------------
- Minimum supported Rust version is 1.80.0.
- Installed Rust version is 1.75.0.
---------------------------------------------------------------
Calls: source -> withVisible -> eval -> eval
Execution halted
ERROR: configuration failed for package ‘caugi’
* removing ‘/tmp/workdir/caugi/old/caugi.Rcheck/caugi’
```

--------------------------------

### Install R/igraph Dependencies on Debian/Ubuntu

Source: https://github.com/igraph/rigraph/blob/main/README.md

Install the necessary development packages for glpk and libxml2 on Debian or Ubuntu systems to compile R/igraph from source.

```bash
apt install libglpk-dev libxml2-dev
```

--------------------------------

### Basic Site Percolation

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the basic usage of the site_percolation_impl function to calculate giant component size and edge count.

```R
site_percolation_impl(graph = g)
```

--------------------------------

### Stimulus Command Line Usage

Source: https://github.com/igraph/rigraph/blob/main/tools/py-stimulus/docs/index.mdx

This shows the basic command-line arguments for invoking the Stimulus tool. Use definition files for functions and types, specify the target language, input, and output files.

```bash
stimulus -f <function-file>
         -t <type-file>
         -l language
         -i <input-file>
         -o <output-file>
         -h --help -v
```

--------------------------------

### Sample sphere surface with custom radius and sign

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Shows how to use `sample_sphere_surface_impl` with a specified radius and to sample points with both positive and negative coordinates.

```R
sample_sphere_surface_impl(dim = 3, n = 5, radius = 2, positive = FALSE)
```

--------------------------------

### Basic usage of sample_sphere_surface_impl

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Illustrates the basic functionality of `sample_sphere_surface_impl` for sampling points on a sphere's surface.

```R
sample_sphere_surface_impl(dim = 3, n = 5)
```

--------------------------------

### Install Stable R/igraph from CRAN

Source: https://github.com/igraph/rigraph/blob/main/README.md

Use this command to install the latest stable version of the R/igraph package from the Comprehensive R Archive Network (CRAN).

```r
install.packages("igraph")
```

--------------------------------

### Boptbd Example Error: tkplot Deprecation

Source: https://github.com/igraph/rigraph/blob/main/revdep/problems.md

This example from the Boptbd package fails because the `tkplot()` function, used internally by `graphoptBbd`, has been deprecated and is now defunct in igraph version 3.0.0.

```R
##To create the graphical layout of the D-optimal block design
##obtained using the treatment exchange algorithm for 
trt.N <- 10  #Number of treatments
blk.N <- 10  #Number of blocks
alpha <- 0.1 #alpha value 
beta  <- 0.1 #beta value 
OptdesF <- rbind(1:10, c(2:10,1)) #Bayesian A-optimal block design (loop design) 

graphoptBbd(trt.N = 10, blk.N = 10, alpha = 0.1, beta = 0.1, OptdesF, Optcrit = "A")
```

--------------------------------

### Error: Unknown constructor for sample_()

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/make.md

Demonstrates the error message when sample_() is called without arguments or with invalid arguments.

```R
sample_()
```

```R
sample_(1:10)
```

--------------------------------

### ggm package example error with deprecated tkplot

Source: https://github.com/igraph/rigraph/blob/main/revdep/problems.md

This snippet shows an error encountered during the example execution of the 'ggm' package. It highlights the deprecation of 'tkplot' in igraph version 3.0.0.

```R
...
+              0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+              1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,
+              0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0),16,16,byrow=TRUE)
> M <- c(3,5,6,15,16)
> C <- c(4,7)
> AG(ex, M, C, plot = TRUE)
Warning: `graph()` was deprecated in igraph 2.1.0.
ℹ Please use `make_graph()` instead.
ℹ The deprecated feature was likely used in the ggm package.
  Please report the issue to the authors.
Warning: `get.edgelist()` was deprecated in igraph 2.0.0.
ℹ Please use `as_edgelist()` instead.
ℹ The deprecated feature was likely used in the ggm package.
  Please report the issue to the authors.
Error:
! `tkplot()` was deprecated in igraph 3.0.0 and is now defunct.
Backtrace:
    ▆
 1. └─ggm::AG(ex, M, C, plot = TRUE)
 2.   └─ggm (local) plotfun(fr, ...)
 3.     └─igraph::tkplot(...)
 4.       └─lifecycle::deprecate_stop("3.0.0", "tkplot()")
 5.         └─lifecycle:::deprecate_stop0(msg)
 6.           └─rlang::cnd_signal(...)
Execution halted
```

--------------------------------

### Basic deterministic optimal imitation

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Demonstrates the basic usage of `deterministic_optimal_imitation_impl` with specified graph, vertex ID, quantities, and strategies.

```R
deterministic_optimal_imitation_impl(graph = g, vid = 1, quantities = c(1, 2, 3),
      strategies = c(1, 2, 3))
```

--------------------------------

### Example Check Error in GoodFitSBM

Source: https://github.com/igraph/rigraph/blob/main/revdep/problems.md

This snippet shows an error encountered during the example checks for the GoodFitSBM package, indicating a problem with deprecated igraph functions and API changes related to edge ID retrieval.

```R
...
ℹ The deprecated feature was likely used in the GoodFitSBM package.
  Please report the issue at <https://github.com/Roy-SR-007/GoodFitSBM/issues>.
Warning: `get.edge.ids()` was deprecated in igraph 2.1.0.
ℹ Please use `get_edge_ids()` instead.
ℹ The deprecated feature was likely used in the GoodFitSBM package.
  Please report the issue at <https://github.com/Roy-SR-007/GoodFitSBM/issues>.
Error:
! The `vp` argument of `get_edge_ids()` supplied as a matrix should be a
  n times 2 matrix, not 2 times n as of igraph 2.1.5.
ℹ either transpose the matrix with t() or convert it to a data.frame with two
  columns.
Backtrace:
     ▆
  1. └─GoodFitSBM::goftest_BetaSBM(adjsymm, C = class, numGraphs = 10)
  2.   └─GoodFitSBM::sample_a_move_BetaSBM(C, G)
  3.     └─GoodFitSBM:::Get.Next.Network(...)
  4.       └─GoodFitSBM:::Get.Move.beta.SBM(b, blocks = SBM.blocks, coin = beta.SBM.coin)
  5.         └─GoodFitSBM:::Get.Induced.Subgraph(g, v.block[[i]])
  6.           └─igraph::get.edge.ids(g, pairs)
  7.             └─igraph::get_edge_ids(...)
  8.               └─igraph:::el_to_vec(vp, call = rlang::caller_env())
  9.                 └─lifecycle::deprecate_stop(...)
  10.                   └─lifecycle:::deprecate_stop0(msg)
  11.                     └─rlang::cnd_signal(...)
Execution halted
```

--------------------------------

### Configure Package Configuration File

Source: https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/src/CMakeLists.txt

Configures the igraph-config.cmake file, which allows users to find the installed igraph library using CMake's FIND_PACKAGE command. It sets the installation destination according to Debian/Ubuntu conventions.

```cmake
# Provide an igraph-config.cmake file in the installation directory so
# users can find the installed igraph library with FIND_PACKAGE(igraph)
# from their CMakeLists.txt files
include(CMakePackageConfigHelpers)
configure_package_config_file(
  ${PROJECT_SOURCE_DIR}/etc/cmake/igraph-config.cmake.in
  ${PROJECT_BINARY_DIR}/igraph-config.cmake
  # Install destination selected according to https://wiki.debian.org/CMake
  # and by looking at how eigen3 does it in Ubuntu
  INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/igraph
)
```

--------------------------------

### simplify_and_colorize_impl Basic Usage

Source: https://github.com/igraph/rigraph/blob/main/tests/testthat/_snaps/aaa-auto.md

Shows the basic output of simplify_and_colorize_impl with a sample graph.

```R
simplify_and_colorize_impl(graph = g)
```

--------------------------------

### Deprecated igraph functions in qgraph examples

Source: https://github.com/igraph/rigraph/blob/main/revdep/problems.md

This snippet shows warnings from qgraph examples using deprecated igraph functions like `watts.strogatz.game()`, `average.path.length()`, and `degree.sequence.game()`. These functions have been replaced by newer alternatives in igraph 2.0.0.

```R
...
     Warning: `watts.strogatz.game()` was deprecated in igraph 2.0.0.
     ℹ Please use `sample_smallworld()` instead.
     > smallworldness(regnet, B=10)
     Warning: `average.path.length()` was deprecated in igraph 2.0.0.
     ℹ Please use `mean_distance()` instead.
     ℹ The deprecated feature was likely used in the qgraph package.
       Please report the issue at <https://github.com/SachaEpskamp/qgraph>.
     Warning: `degree.sequence.game()` was deprecated in igraph 2.0.0.
     ℹ Please use `sample_degseq()` instead.
     ℹ The deprecated feature was likely used in the qgraph package.
       Please report the issue at <https://github.com/SachaEpskamp/qgraph>.
     Error:
     ! The `method` argument of `sample_degseq()` must be fast.heur.simple
       instead of simple.no.multiple as of igraph 2.1.0.
     Backtrace:
         ▆
      1. └─qgraph::smallworldness(regnet, B = 10)
      2.   └─base::lapply(...)
      3.     └─qgraph (local) FUN(X[[i]], ...) 
      4.       └─igraph::degree.sequence.game(deg.dist, method = "simple.no.multiple")
      5.         └─igraph::sample_degseq(out.deg = out.deg, in.deg = in.deg, method = method)
      6.           └─lifecycle::deprecate_stop("2.1.0", "sample_degseq(method = 'must be fast.heur.simple instead of simple.no.multiple')")
      7.             └─lifecycle:::deprecate_stop0(msg)
      8.               └─rlang::cnd_signal(...)
     Execution halted
```

--------------------------------

### c3net Example Warnings and Error: Deprecated igraph Functions

Source: https://github.com/igraph/rigraph/blob/main/revdep/problems.md

This example from the c3net package encounters multiple warnings due to deprecated igraph functions (`graph.adjacency`, `get.edgelist`, `graph.edgelist`) and a fatal error because `tkplot()` is defunct.

```R
net <- c3net(expdata, network=TRUE)
```

--------------------------------

### Dependency Indexing in Templates

Source: https://github.com/igraph/rigraph/blob/main/tools/py-stimulus/docs/index.mdx

Demonstrates how to reference dependencies within type definition templates using the '%I[dependency number]%' format. '%I1%' refers to the first dependency, and '%I2%' to the second.

```text
DEPS: res ON graph vids
%I1% refers to graph, and %I2% refers to vids
```