"Cereal Headers for R and C++ Serialization".

Rcereal: cereal headers for R and C++ serialization

This package provides R with access to cereal header files. cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON.

For more information, please visit the official website of the cereal project: https://uscilab.github.io/cereal/.

The headers in this package can be used via:

• the LinkingTo: field in the DESCRIPTION of an R package;
• the [[cpp11::linking_to("Rcereal")]] attribute and cpp11::source from the cpp11 package, or;
• the [[Rcpp::depends(Rcereal)]]Rcpp attribute.

Installation

Latest release

The latest release can be installed from CRAN via:

install.packages('Rcereal')

Development version

Use remotes::install_github to install the latest version of Rcereal. Optionally: use Rcereal::update_version to over-write the header files in the R library with a version from https://github.com/USCiLab/cereal.

remotes::install_github("wush978/Rcereal")
Rcereal::update_version() # optional

Usage

See the official cerealQuick Start guide for further details about using cereal in C++11.

Using cpp11

The following example shows how to use Rcereal alongside cpp11 to serialize and deserialize a user-defined struct using raw vectors:

// path/to/example.cpp
#include <sstream>

#include <cpp11/raws.hpp>

#include <cereal/archives/binary.hpp>

struct MyClass
{
    int x, y, z;
  // This method lets cereal know which data members to serialize
    template<class Archive>
    void serialize(Archive & archive)
    {
        archive( x, y, z ); // serialize things by passing them to the archive
    }
};

[[cpp11::linking_to("Rcereal")]]
[[cpp11::register]]
cpp11::raws serialize_myclass(int x = 1, int y = 2, int z = 3) {
    MyClass my_instance { x, y, z };
    std::stringstream ss;
    {
        cereal::BinaryOutputArchive oarchive(ss); // Create an output archive
        oarchive(my_instance);
    }
    ss.seekg(0, ss.end);
    cpp11::writable::raws result(ss.tellg());
    ss.seekg(0, ss.beg);
    std::copy(std::istreambuf_iterator<char>{ss},
              std::istreambuf_iterator<char>(),
              result.begin());
    return result;
}

[[cpp11::register]]
void deserialize_myclass(cpp11::raws src) {
    std::stringstream ss;
    std::copy(src.cbegin(), src.cend(), std::ostream_iterator<char>(ss));
    MyClass my_instance;
    {
        cereal::BinaryInputArchive iarchive(ss); // Read from input archive
        iarchive(my_instance);
    }
    Rprintf("%i,%i,%i\n", my_instance.x, my_instance.y, my_instance.z);
}

Then, provided C++11 is enabled by default (see this tidyverse post 03/2023), in R:

cpp11::cpp_source(file='path/to/example.cpp')
raw_vector <- serialize_myclass(1, 2, 4)
deserialize_myclass(raw_vector)

Using Rcpp

The following example shows how to use Rcereal alongside Rcpp to serialize and deserialize a user-defined struct using raw vectors:

// path/to/example.cpp

//[[Rcpp::depends(Rcereal)]]
#include <sstream>

#include <cereal/archives/binary.hpp>

#include <Rcpp.h>
using namespace Rcpp;

struct MyClass
{
    /* same as cpp11 example above */
};

//[[Rcpp::export]]
Rcpp::RawVector serialize_myclass(int x = 1, int y = 2, int z = 3) {
    MyClass my_instance { x, y, z };
    std::stringstream ss;
    {
        cereal::BinaryOutputArchive oarchive(ss); // Create an output archive
        oarchive(my_instance);
    }
    ss.seekg(0, ss.end);
    Rcpp::RawVector result(ss.tellg());
    ss.seekg(0, ss.beg);
    ss.read(reinterpret_cast<char*>(&result[0]), result.size());
    return result;
}

//[[Rcpp::export]]
void deserialize_myclass(Rcpp::RawVector src) {
    std::stringstream ss;
    ss.write(reinterpret_cast<char*>(&src[0]), src.size());
    ss.seekg(0, ss.beg);
    MyClass my_instance;
    {
        cereal::BinaryInputArchive iarchive(ss);
        iarchive(my_instance);
    }
    Rcpp::Rcout << my_instance.x << "," << my_instance.y << "," <<
        my_instance.z << std::endl;
}

Then in R, provided C++ is enabled by default:

Rcpp::sourceCpp("path/to/example.cpp")
raw_vector <- serialize_myclass(1, 2, 4)
deserialize_myclass(raw_vector)

Troubleshooting

C++11 may not be enabled by default for some compilers, if not; ensure that PKG_CXXFLAGS contains -std=c++11, e.g. if you use pkgbuild::compile_dll() to build a package (similarly for devtools::build):

withr::with_makevars(c("PKG_CXXFLAGS"="std=c++11"),
                     pkgbuild::compile_dll(),
                     assignment="+=")

If the compiler reports missing header files, try Rcereal::update_version() to update the content of cereal from GitHub. Check that a directory named cereal is in the folder system.file("include", package = "Rcereal").