public static void SetEnvironmentVariables()
{
var rhome = Environment.GetEnvironmentVariable("R_HOME");
var currentPath = Environment.GetEnvironmentVariable("PATH");
switch (NativeUtility.GetPlatform())
{
case PlatformID.Win32NT:
Environment.SetEnvironmentVariable("PATH", FindRPathFromRegistry() + Path.PathSeparator + currentPath);
break;
case PlatformID.MacOSX:
if (string.IsNullOrEmpty(rhome))
{
Environment.SetEnvironmentVariable("R_HOME", "/Library/Frameworks/R.framework/Resources");
}
Environment.SetEnvironmentVariable("PATH", "/Library/Frameworks/R.framework/Libraries" + Path.PathSeparator + currentPath);
break;
case PlatformID.Unix:
if (string.IsNullOrEmpty(rhome))
{
Environment.SetEnvironmentVariable("R_HOME", "/usr/lib/R");
}
// TODO: cater for cases where user has build R from source and installed to e.g. /usr/local/lib
Environment.SetEnvironmentVariable("PATH", "/usr/lib" + Path.PathSeparator + currentPath);
break;
}
}
public void TestUsingDefaultRPackages()
{
// This test was designed to look at a symptom observed alongside the issue https://github.com/rdotnet/rdotnet/issues/127
SetUpTest();
var engine = this.Engine;
var se = engine.Evaluate("set.seed");
if (NativeUtility.GetPlatform() == PlatformID.Win32NT)
{
Assert.True(engine.Evaluate("Sys.which('R.dll')").AsCharacter()[0].Length > 0);
Assert.True(engine.Evaluate("Sys.which('RBLAS.dll')").AsCharacter()[0].Length > 0);
}
string[] expected = { "base", "methods", "utils", "grDevices", "graphics", "stats" };
var loadedDlls = engine.Evaluate("getLoadedDLLs()").AsList();
string[] dllnames = loadedDlls.Select(x => x.AsCharacter().ToArray()[0]).ToArray();
IEnumerable <string> query = from x in expected.Intersect(dllnames)
select x;
Assert.Equal(expected, query.ToArray());
se = engine.Evaluate("set.seed(0)");
se = engine.Evaluate("blah <- rnorm(4)");
}
/// <summary>
/// Initializes a new instance of the <see cref="MultiCatchmentCompositeObjectiveEvaluator" /> class.
/// </summary>
/// <param name="objDefn"> The objective definition. </param>
private RCompositeObjectiveEvaluator(RexpObjectiveDefinition objDefn)
{
objectiveDefinition = objDefn;
string pathToRDynLib = objDefn.DirectoryForRLibrary;
string rhome = Environment.GetEnvironmentVariable("R_HOME");
if (!Directory.Exists(pathToRDynLib))
{
REngine.SetEnvironmentVariables();
}
else
{
if (string.IsNullOrEmpty(rhome))
{
var plat = NativeUtility.GetPlatform();
switch (plat)
{
case PlatformID.Win32NT:
if (string.IsNullOrEmpty(rhome))
{
rhome = Path.Combine(pathToRDynLib, @"..\.."); // Assume R more recent than 2.12 : binaries under bin\x64 for instance; folder containing 'bin' is R_HOME
Log.WarnFormat("R_HOME environment variable not set. Setting R_HOME = {0}", rhome);
}
break;
case PlatformID.Unix:
Log.Debug("R init: detected Unix platform");
if (String.IsNullOrEmpty(rhome))
{
throw new Exception("R_HOME environment variable is not set");
}
break;
default:
throw new NotSupportedException(string.Format("Platform not supported: {0}", plat));
}
}
Log.Debug("R init: R_HOME = " + rhome);
REngine.SetEnvironmentVariables(pathToRDynLib, rhome);
}
Log.Debug("R init: creating R engine");
rEngine = REngine.GetInstance(dll: null, initialize: false, parameter: null, device: null);
Log.Debug("R init: initialising R engine");
StartupParameter rStartParams = new StartupParameter
{
Quiet = true,
SaveAction = StartupSaveAction.NoSave,
Slave = false,
Interactive = true,
Verbose = false,
LoadInitFile = true,
LoadSiteFile = true,
RestoreAction = StartupRestoreAction.NoRestore,
NoRenviron = false
};
rEngine.Initialize(rStartParams);
Log.Debug("Created rEngine: " + rEngine.ToString());
}
private void SetCstackChecking()
{
// Don't do any stack checking, see R Exts, '8.1.5 Threading issues',
// https://rdotnet.codeplex.com/discussions/462947
// https://rdotnet.codeplex.com/workitem/115
WriteInt32("R_CStackLimit", -1);
switch (NativeUtility.GetPlatform())
{
case PlatformID.MacOSX:
case PlatformID.Unix:
WriteInt32("R_SignalHandlers", 0);
// RInside does this for non-WIN32.
break;
}
}
internal void Install(REngine engine, StartupParameter parameter)
{
this.engine = engine;
switch (NativeUtility.GetPlatform())
{
case PlatformID.Win32NT:
SetupWindowsDevice(parameter);
break;
case PlatformID.MacOSX:
case PlatformID.Unix:
SetupUnixDevice();
break;
}
}
/// <summary>
/// Creates the command line arguments corresponding to the specified startup parameters
/// </summary>
/// <param name="parameter"></param>
/// <returns></returns>
/// <remarks>While not obvious from the R documentation, it seems that command line arguments need to be passed
/// to get the startup parameters taken into account. Passing the StartupParameter to the API seems not to work as expected.
/// While this function may appear like an oddity to a reader, it proved necessary to the initialisation of the R engine
/// after much trial and error.</remarks>
public static string[] BuildRArgv(StartupParameter parameter)
{
var platform = NativeUtility.GetPlatform();
var argv = new List <string>();
argv.Add("rdotnet_app");
// Not sure whether I should add no-readline
//[MarshalAs(UnmanagedType.Bool)]
//public bool R_Quiet;
if (parameter.Quiet && !parameter.Interactive)
{
argv.Add("--quiet"); // --quite --interactive to R embedded crashed...
}
//[MarshalAs(UnmanagedType.Bool)]
//public bool R_Slave;
if (parameter.Slave)
{
argv.Add("--slave");
}
//[MarshalAs(UnmanagedType.Bool)]
//public bool R_Interactive;
if (platform != PlatformID.Win32NT) // RTerm.exe --help shows no such option; Unix only.
{
if (parameter.Interactive)
{
argv.Add("--interactive");
}
}
//[MarshalAs(UnmanagedType.Bool)]
//public bool R_Verbose;
if (parameter.Verbose)
{
argv.Add("--verbose");
}
//[MarshalAs(UnmanagedType.Bool)]
//public bool LoadSiteFile;
if (!parameter.LoadSiteFile)
{
argv.Add("--no-site-file");
}
//[MarshalAs(UnmanagedType.Bool)]
//public bool LoadInitFile;
if (!parameter.LoadInitFile)
{
argv.Add("--no-init-file");
}
//[MarshalAs(UnmanagedType.Bool)]
//public bool DebugInitFile;
//if (parameter.Quiet) argv.Add("--quiet");
//public StartupRestoreAction RestoreAction;
//public StartupSaveAction SaveAction;
//internal UIntPtr vsize;
//internal UIntPtr nsize;
//internal UIntPtr max_vsize;
//internal UIntPtr max_nsize;
//internal UIntPtr ppsize;
//[MarshalAs(UnmanagedType.Bool)]
//public bool NoRenviron;
if (parameter.NoRenviron)
{
argv.Add("--no-environ");
}
switch (parameter.SaveAction)
{
case StartupSaveAction.NoSave:
argv.Add("--no-save");
break;
case StartupSaveAction.Save:
argv.Add("--save");
break;
}
switch (parameter.RestoreAction)
{
case StartupRestoreAction.NoRestore:
argv.Add("--no-restore-data");
break;
case StartupRestoreAction.Restore:
argv.Add("--restore");
break;
}
if (parameter.MaxMemorySize == (Environment.Is64BitProcess ? ulong.MaxValue : uint.MaxValue))
{
// This creates a nasty crash if using the default MaxMemorySize. found out in Rdotnet workitem 72
// do nothing
}
else
{
if (platform == PlatformID.Win32NT) // On unix, otherwise led to https://rdotnet.codeplex.com/workitem/137
{
argv.Add("--max-mem-size=" + parameter.MaxMemorySize);
}
}
argv.Add("--max-ppsize=" + parameter.StackSize);
return(argv.ToArray());
}
/// <summary>
/// Initialize this REngine object. Only the first call has an effect. Subsequent calls to this function are ignored.
/// </summary>
/// <param name="parameter">The optional startup parameters</param>
/// <param name="device">The optional character device to use for the R engine</param>
/// <param name="setupMainLoop">if true, call the functions to initialise the embedded R</param>
public void Initialize(StartupParameter parameter = null, ICharacterDevice device = null, bool setupMainLoop = true)
{
// Console.WriteLine("REngine.Initialize start");
if (this.isRunning)
{
return;
}
// Console.WriteLine("REngine.Initialize, after isRunning checked as false");
this.parameter = parameter ?? new StartupParameter();
this.adapter = new CharacterDeviceAdapter(device ?? DefaultDevice);
// Disabling the stack checking here, to try to avoid the issue on Linux.
// The disabling used to be here around end Nov 2013. Was moved later in this
// function to cater for disabling on Windows, @ rev 305, however this may have
// re-broken on Linux. so we may need to call it twice.
SetCstackChecking();
// Console.WriteLine("Initialize-SetCstackChecking; R_CStackLimit value is " + GetDangerousInt32("R_CStackLimit"));
if (!setupMainLoop)
{
this.isRunning = true;
return;
}
string[] R_argv = BuildRArgv(this.parameter);
//string[] R_argv = new[]{"rdotnet_app", "--interactive", "--no-save", "--no-restore-data", "--max-ppsize=50000"};
//rdotnet_app --quiet --interactive --no-save --no-restore-data --max-mem-size=18446744073709551615 --max-ppsize=50000
GetFunction <R_setStartTime>()();
int R_argc = R_argv.Length;
// Console.WriteLine("Initialize-R_setStartTime; R_CStackLimit value is " + GetDangerousInt32("R_CStackLimit"));
if (NativeUtility.GetPlatform() == PlatformID.Win32NT)
{
// Attempted Fix for https://rdotnet.codeplex.com/workitem/110; not working
// Tried to make sure that the command line options are taken into account. They are NOT effectively so via Rf_initialize_R only.
// The problem is that cmdlineoptions assumes it is called by RGui.exe or RTerm.exe, and overrides R_HOME
// GetFunction<R_set_command_line_arguments>()(R_argc, R_argv);
// GetFunction<cmdlineoptions>()(R_argc, R_argv);
}
var status = GetFunction <Rf_initialize_R>()(R_argc, R_argv);
if (status != 0)
{
throw new Exception("A call to Rf_initialize_R returned a non-zero; status=" + status);
}
// Console.WriteLine("Initialize-Rf_initialize_R; R_CStackLimit value is " + GetDangerousInt32("R_CStackLimit"));
SetCstackChecking();
// following in RInside: may not be needed.
//GetFunction<R_ReplDLLinit> () ();
//this.parameter.Interactive = true;
this.adapter.Install(this, this.parameter);
//Console.WriteLine("Initialize-adapter installation; R_CStackLimit value is " + GetDangerousInt32("R_CStackLimit"));
switch (NativeUtility.GetPlatform())
{
case PlatformID.Win32NT:
GetFunction <R_SetParams_Windows>("R_SetParams")(ref this.parameter.start);
break;
case PlatformID.MacOSX:
case PlatformID.Unix:
GetFunction <R_SetParams_Unix>("R_SetParams")(ref this.parameter.start.Common);
//Console.WriteLine("Initialize-R_SetParams_Unix; R_CStackLimit value is " + GetDangerousInt32("R_CStackLimit"));
break;
}
GetFunction <setup_Rmainloop>()();
//Console.WriteLine("Initialize-after setup_Rmainloop; R_CStackLimit value is " + GetDangerousInt32("R_CStackLimit"));
// See comments in the first call to SetCstackChecking in this function as to why we (may) need it twice.
SetCstackChecking();
this.isRunning = true;
//Console.WriteLine("Initialize-just before leaving; R_CStackLimit value is " + GetDangerousInt32("R_CStackLimit"));
// Partial Workaround (hopefully temporary) for https://rdotnet.codeplex.com/workitem/110
if (NativeUtility.GetPlatform() == PlatformID.Win32NT)
{
Evaluate(string.Format("invisible(memory.limit({0}))", (this.parameter.MaxMemorySize / 1048576UL)));
}
}
