GitHub - LTLA/rds2cpp: Read and write RDS files in C++

Overview

This repository contains a header-only C++ library for reading and writing RDS files (created with saveRDS()) without the need to link to R's libraries. In this manner, we can use RDS as a flexible data exchange format across different frameworks that have C++ bindings, e.g., Python, Javascript (via Wasm). We currently support most user-visible data structures such as atomic vectors, lists, environments and S4 classes.

Quick start

Given a path to an RDS file, the parse_rds() function will return a pointer to an RObject interface:

#include "rds2cpp/rds2cpp.hpp"

// Returns an object containing the file information,
// e.g., R version used to read/write the file.
auto file_info = rds2cpp::parse_rds(fpath, {});

// Get the pointer to the actual R object.
const auto& ptr = file_info->object;

The type of the underlying object can then be queried for further examination. For example, if we wanted to process integer vectors:

if (ptr->type() == rds2cpp::SEXPType::INT) {
    auto iptr = static_cast<const rds2cpp::IntegerVector*>(ptr.get());
    const auto& values = iptr->data; // vector of int32_t's.
    const auto& attr_names = iptr->attributes.names; // vector of attribute names.
}

See the reference documentation for a list of known representations.

More reading examples

rds2cpp can extract ordinary lists from an RDS file. Users can inspect the attributes to determine if the list is named.

if (ptr->type() == rds2cpp::SEXPType::VEC) {
    auto lptr = static_cast<const rds2cpp::GenericVector*>(ptr.get());
    const auto& elements = lptr->data; // vector of pointers to list elements.

    const auto& attr = lptr->attributes; 
    const auto& attr_names = sptr->attributes.names;
    const auto& attr_values = sptr->attributes.values;

    // Scanning for the list names.
    auto nIt = std::find(attr_names.begin(), attr_names.end(), std::string("names"));
    if (nIt != attr_names.end()) {
        size_t nindex = nIt - attr_names.begin();
        if (attr_values[nindex]->type() == rds2cpp::SEXPType::STR) {
            auto nptr = static_cast<const rds2cpp::StringVector*>(attr_values[nindex].get());
        }
    }
}

Slots of S4 instances are similarly encoded in the attributes - except for the class name, which is extracted into its own member.

if (ptr->type() == rds2cpp::SEXPType::S4) {
    auto sptr = static_cast<const rds2cpp::S4Object*>(ptr.get());
    sptr->class_name;
    sptr->package_name;
    const auto& slot_names = sptr->attributes.names;
    const auto& slot_values = sptr->attributes.values;
}

Advanced users can also pull out serialized environments. These should be treated as file-specific globals that may be referenced one or more times inside the R object.

if (ptr->type() == rds2cpp::SEXPType::ENV) {
    const auto& env = file_info->environments[eptr->index];
    const auto& vnames = env.variable_names;
    const auto& vvalues = env.variable_values;
}

NULLs are supported but not particularly interesting:

if (ptr->type() == rds2cpp::SEXPType::NIL) {
   // Do something.
}

Writing RDS files

The write_rds() function will write RDS files from an rds2cpp::RObject representation:

rds2cpp::RdsFile file_info;

// Setting up an integer vector.
auto vec = new rds2cpp::IntegerVector;
file_info.object.reset(vec);

// Storing data in the integer vector.
vec->data = std::vector<int32_t>{ 0, 1, 2, 3, 4, 5 };

rds2cpp::write_rds(file_info, "some_file_path.rds");

Here's a more complicated example that saves a sparse matrix (as a dgCMatrix from the Matrix package) to file.

rds2cpp::RdsFile file_info;
auto ptr = new rds2cpp::S4Object;
file_info.object.reset(ptr);
auto& obj = *ptr;

obj.class_name = "dgCMatrix";
obj.package_name = "Matrix";

auto ivec = new rds2cpp::IntegerVector;
obj.attributes.add("i", ivec);
ivec->data = std::vector<int32_t>{ 6, 8, 0, 3, 5, 6, 0, 1, 3, 7 };

auto pvec = new rds2cpp::IntegerVector;
obj.attributes.add("p", pvec);
pvec->data = std::vector<int32_t>{ 0, 0, 2, 3, 4, 5, 6, 8, 8, 8, 10 };

auto xvec = new rds2cpp::DoubleVector;
obj.attributes.add("x", xvec);
xvec->data = std::vector<double>{ 0.96, -0.34, 0.82, -2, -0.72, 0.39, 0.16, 0.36, -1.5, -0.47 };

auto dims = new rds2cpp::IntegerVector;
obj.attributes.add("Dim", dims);
dims->data = std::vector<int32_t>{ 10, 10 };

auto dimnames = new rds2cpp::GenericVector;
obj.attributes.add("Dimnames", dimnames);
dimnames->data.emplace_back(new rds2cpp::Null);
dimnames->data.emplace_back(new rds2cpp::Null);

auto factors = new rds2cpp::GenericVector;
obj.attributes.add("factors", factors);

rds2cpp::write_rds(file_info, "my_matrix.rds");

We can also create environments by registering the environment before creating indices to it.

rds2cpp::RdsFile file_info;

// Creating an environment with a 'foo' variable containing c('bar', NA, 'whee')
file_info.environments.resize(1);
auto& current_env = file_info.environments[0];

auto sptr = new rds2cpp::StringVector;
current_env.add("foo", sptr);
sptr->add("bar");
sptr->add(); // NA string
sptr->add("whee");

// Referencing the environment: 
auto eptr = new rds2cpp::EnvironmentIndex(0);
file_info.object.reset(eptr);

rds2cpp::write_rds(file_info, "my_env.rds");

Building projects

CMake with `FetchContent`

If you're using CMake, you just need to add something like this to your CMakeLists.txt:

include(FetchContent)

FetchContent_Declare(
  rds2cpp
  GIT_REPOSITORY https://github.com/LTLA/rds2cpp
  GIT_TAG master # or any version of interest
)

FetchContent_MakeAvailable(rds2cpp)

Then you can link to rds2cpp to make the headers available during compilation:

# For executables:
target_link_libraries(myexe rds2cpp)

# For libaries
target_link_libraries(mylib INTERFACE rds2cpp)

CMake using `find_package()`

You can install the library by cloning a suitable version of this repository and running the following commands:

mkdir build && cd build
cmake .. 
cmake --build . --target install

Then you can use find_package() as usual:

find_package(ltla_rds2cpp CONFIG REQUIRED)
target_link_libraries(mylib INTERFACE ltla::rds2cpp)

Manual

If you're not using CMake, the simple approach is to just copy the files in the include/ subdirectory - either directly or with Git submodules - and include their path during compilation with, e.g., GCC's -I.

You'll also need to add the byteme header-only library to the compiler's search path. Normally, when using CMake, this is automatically linked to Zlib; this will now need to be done manually.

Known limitations

This library may not support RDS files created using saveRDS() with non-default parameters.

Environments are written without a hash table, so as to avoid the need to replicate R's string hashing logic. This may result in slower retrieval of variables when those environments are loaded into an R session.

Currently, no support is provided for unserializing built-in functions or user-defined closures.