Understanding the Issue with External C Libraries in R

When working with external C libraries in R, it’s not uncommon to encounter issues related to dynamic linking and library loading. One common error message is “cannot open shared object file” while LD_LIBRARY_PATH is set.

In this article, we’ll delve into the details of this issue and explore the reasons behind it, as well as potential solutions.

The Problem: Unable to Load Shared Object File

The problem arises when trying to load a dynamic library using dyn.load() or load.dynamic.libraries(). When the library is loaded, R attempts to resolve symbols in the shared object file. However, if the shared object file cannot be found, or if its contents are not compatible with the system’s ELF (Executable and Linkable Format) format, the loading process fails.

In this case, we’re using a C extension built with the gcc compiler, which generates a shared object file (libmy.so). The issue arises when trying to load this library from the directory /path/to/my/src, even though LD_LIBRARY_PATH is set.

Setting up LD_LIBRARY_PATH

LD_LIBRARY_PATH is an environment variable that specifies the directories where R should look for shared libraries. When LD_LIBRARY_PATH is set, R will attempt to find and load shared object files in those directories before searching elsewhere. In this case, we’ve set LD_LIBRARY_PATH to include /path/to/hdf5/lib:/path/to/my/lib, which suggests that the library should be found.

The Solution: Understanding dyn.load() and dlopen()

However, as noted by John McKown in his response on the R-Help mailing list, the dyn.load() function does not use the dlopen() routine to load shared object files. Instead, it uses an open() function that requires a specific file name, including path information.

This is where the issue arises: even though we’ve set LD_LIBRARY_PATH, dyn.load() is not aware of this environment variable and will not look for shared object files in those directories.

Creating a Custom Load Dynamic Libraries Function

To address this issue, we can create a custom function called load.dynamic.libraries() that uses the open() function to load shared object files. This function takes a list of library names as input and attempts to find and load each one using the specified method.

Here is an example implementation:

## R Code

load.dynamic.libraries <- function(libnames) {
  # Iterate over each library name
  for (libname in libnames) {
    # Find a matching file, including path information
    found_file = libname
    
    # Check if the environment variable LD_LIBRARY_PATH is set
    if (Sys.getenv("LD_LIBRARY_PATH")) {
      # Split the LD_LIBRARY_PATH value into individual directories
      paths <- unlist(strsplit(Sys.getenv("LD_LIBRARY_PATH"), ":", fixed = TRUE))
      
      # Iterate over each directory in the path
      for (path in paths) {
        try_file <- paste0(path, "/", libname)
        
        # Check if a matching file exists
        if (file.exists(try_file)) {
          found_file = try_file
          break
        }
      }
    }
    
    # Print a message indicating the library being loaded
    write(paste("Loading:", try_file), stderr())
    
    # Attempt to load the shared object file using dyn.load()
    dyn.load(found_file)
  }
}

Using the Custom Load Dynamic Libraries Function

To use this custom function, simply call it with a list of library names as arguments:

# R Code

# Create a list of library names
libnames <- c("libmy.so")

# Call the load.dynamic.libraries function
load.dynamic.libraries(libnames)

By using this custom function, we can ensure that dyn.load() loads shared object files in the correct order and location, even when LD_LIBRARY_PATH is set.

Conclusion

In conclusion, understanding how dyn.load() works and creating a custom load dynamic libraries function can help resolve issues related to loading external C libraries in R. By following these steps and using this custom function, you should be able to successfully load shared object files and resolve any errors that may occur due to incompatible library formats or incorrect directory paths.

References

• John McKown’s response on the R-Help mailing list
• The dlopen() routine
• ELF (Executable and Linkable Format)
• Dynamic linking in C

Last modified on 2025-01-30