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// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; indent-tabs-mode: nil; -*-
//
// attributes.cpp: Rcpp R/C++ interface class library -- Rcpp attributes
//
// Copyright (C) 2012 - 2013 JJ Allaire, Dirk Eddelbuettel and Romain Francois
//
// This file is part of Rcpp.
//
// Rcpp is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 2 of the License, or
// (at your option) any later version.
//
// Rcpp is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Rcpp. If not, see <http://www.gnu.org/licenses/>.
#define COMPILING_RCPP
#include <sys/types.h>
#include <sys/stat.h>
#include <errno.h>
#include <cstring>
#include <string>
#include <vector>
#include <map>
#include <set>
#include <algorithm>
#include <fstream>
#include <sstream>
#define RCPP_NO_SUGAR
#include <Rcpp.h>
/*******************************************************************
* AttributesUtil.h
*******************************************************************/
namespace Rcpp {
namespace attributes {
// Utility class for getting file existence and last modified time
class FileInfo {
public:
explicit FileInfo(const std::string& path);
std::string path() const { return path_; }
bool exists() const { return exists_; }
time_t lastModified() const { return lastModified_; }
private:
std::string path_;
bool exists_;
time_t lastModified_;
};
// Remove a file
bool removeFile(const std::string& path);
// Recursively create a directory
void createDirectory(const std::string& path);
// Known whitespace chars
extern const char * const kWhitespaceChars;
// Query whether a character is whitespace
bool isWhitespace(char ch);
// Trim a string
void trimWhitespace(std::string* pStr);
// Strip trailing line comments
void stripTrailingLineComments(std::string* pStr);
// Strip balanced quotes from around a string (assumes already trimmed)
void stripQuotes(std::string* pStr);
// is the passed string quoted?
bool isQuoted(const std::string& str);
// show a warning message
void showWarning(const std::string& msg);
// is the line a C++ roxygen comment? (started with //')
bool isRoxygenCpp(const std::string& str);
} // namespace attributes
} // namespace Rcpp
/*******************************************************************
* AttributesTypes.h
*******************************************************************/
namespace Rcpp {
namespace attributes {
// Known attribute names & parameters
const char * const kExportAttribute = "export";
const char * const kDependsAttribute = "depends";
const char * const kPluginsAttribute = "plugins";
const char * const kInterfacesAttribute = "interfaces";
const char * const kInterfaceR = "r";
const char * const kInterfaceCpp = "cpp";
// Type info
class Type {
public:
Type() {}
Type(const std::string& name, bool isConst, bool isReference)
: name_(name), isConst_(isConst), isReference_(isReference)
{
}
bool empty() const { return name().empty(); }
const std::string& name() const { return name_; }
std::string full_name() const {
std::string res ;
if( isConst() ) res += "const " ;
res += name() ;
if( isReference() ) res += "&" ;
return res ;
}
bool isVoid() const { return name() == "void"; }
bool isConst() const { return isConst_; }
bool isReference() const { return isReference_; }
private:
std::string name_;
bool isConst_;
bool isReference_;
};
// Argument info
class Argument {
public:
Argument() {}
Argument(const std::string& name,
const Type& type,
const std::string& defaultValue)
: name_(name), type_(type), defaultValue_(defaultValue)
{
}
bool empty() const { return type().empty(); }
const std::string& name() const { return name_; }
const Type& type() const { return type_; }
const std::string& defaultValue() const { return defaultValue_; }
private:
std::string name_;
Type type_;
std::string defaultValue_;
};
// Function info
class Function {
public:
Function() {}
Function(const Type& type,
const std::string& name,
const std::vector<Argument>& arguments,
const std::string& source)
: type_(type), name_(name), arguments_(arguments), source_(source)
{
}
Function renamedTo(const std::string& name) const {
return Function(type(), name, arguments(), source());
}
std::string signature() const { return signature(name()); }
std::string signature(const std::string& name) const;
bool isHidden() const {
return name().find_first_of('.') == 0;
}
bool empty() const { return name().empty(); }
const Type& type() const { return type_; }
const std::string& name() const { return name_; }
const std::vector<Argument>& arguments() const { return arguments_; }
const std::string& source() const { return source_; }
private:
Type type_;
std::string name_;
std::vector<Argument> arguments_;
std::string source_;
};
// Attribute parameter (with optional value)
class Param {
public:
Param() {}
explicit Param(const std::string& paramText);
bool empty() const { return name().empty(); }
const std::string& name() const { return name_; }
const std::string& value() const { return value_; }
private:
std::string name_;
std::string value_;
};
// Attribute (w/ optional params and signature of function it qualifies)
class Attribute {
public:
Attribute() {}
Attribute(const std::string& name,
const std::vector<Param>& params,
const Function& function,
const std::vector<std::string>& roxygen)
: name_(name), params_(params), function_(function), roxygen_(roxygen)
{
}
bool empty() const { return name().empty(); }
const std::string& name() const { return name_; }
const std::vector<Param>& params() const { return params_; }
Param paramNamed(const std::string& name) const;
bool hasParameter(const std::string& name) const {
return !paramNamed(name).empty();
}
const Function& function() const { return function_; }
bool isExportedFunction() const {
return (name() == kExportAttribute) && !function().empty();
}
std::string exportedName() const {
if (!params().empty())
return params()[0].name();
else
return function().name();
}
const std::vector<std::string>& roxygen() const { return roxygen_; }
private:
std::string name_;
std::vector<Param> params_;
Function function_;
std::vector<std::string> roxygen_;
};
class FunctionMap {
std::map< std::string, std::vector<Function> > map_ ;
public:
FunctionMap(){};
~FunctionMap(){} ;
void insert( const Function& fun ){
map_[ fun.name() ].push_back( fun ) ;
}
} ;
// Operator << for parsed types
std::ostream& operator<<(std::ostream& os, const Type& type);
std::ostream& operator<<(std::ostream& os, const Argument& argument);
std::ostream& operator<<(std::ostream& os, const Function& function);
std::ostream& operator<<(std::ostream& os, const Param& param);
std::ostream& operator<<(std::ostream& os, const Attribute& attribute);
// interface to source file attributes
class SourceFileAttributes
{
public:
virtual ~SourceFileAttributes() {};
virtual const std::string& sourceFile() const = 0;
virtual bool hasInterface(const std::string& name) const = 0;
typedef std::vector<Attribute>::const_iterator const_iterator;
virtual const_iterator begin() const = 0;
virtual const_iterator end() const = 0;
virtual const std::vector<std::string>& modules() const = 0;
virtual const std::vector<std::vector<std::string> >& roxygenChunks() const = 0;
virtual bool hasGeneratorOutput() const = 0;
};
} // namespace attributes
} // namespace Rcpp
/*******************************************************************
* AttributesParser.h
*******************************************************************/
namespace Rcpp {
namespace attributes {
// Helper class for determining whether we are in a comment
class CommentState {
public:
CommentState() : inComment_(false) {}
private:
// prohibit copying
CommentState(const CommentState&);
CommentState& operator=(const CommentState&);
public:
bool inComment() const { return inComment_; }
void submitLine(const std::string& line);
void reset() { inComment_ = false; }
private:
bool inComment_;
};
// Class used to parse and return attribute information from a source file
class SourceFileAttributesParser : public SourceFileAttributes {
public:
explicit SourceFileAttributesParser(const std::string& sourceFile);
private:
// prohibit copying
SourceFileAttributesParser(const SourceFileAttributesParser&);
SourceFileAttributesParser& operator=(const SourceFileAttributesParser&);
public:
// implemetnation of SourceFileAttributes interface
virtual const std::string& sourceFile() const {
return sourceFile_;
}
virtual const_iterator begin() const { return attributes_.begin(); }
virtual const_iterator end() const { return attributes_.end(); }
virtual const std::vector<std::string>& modules() const
{
return modules_;
}
virtual const std::vector<std::vector<std::string> >& roxygenChunks() const {
return roxygenChunks_;
}
virtual bool hasGeneratorOutput() const
{
return !attributes_.empty() ||
!modules_.empty() ||
!roxygenChunks_.empty();
}
virtual bool hasInterface(const std::string& name) const {
for (const_iterator it=begin(); it != end(); ++it) {
if (it->name() == kInterfacesAttribute) {
return it->hasParameter(name);
}
}
// if there's no interfaces attrbute we default to R
if (name == kInterfaceR)
return true;
else
return false;
}
// Get lines of embedded R code
const std::vector<std::string>& embeddedR() const {
return embeddedR_;
}
private:
// Parsing helpers
Attribute parseAttribute(const std::vector<std::string>& match,
int lineNumber);
std::vector<Param> parseParameters(const std::string& input);
Function parseFunction(size_t lineNumber);
std::string parseSignature(size_t lineNumber);
std::vector<std::string> parseArguments(const std::string& argText);
Type parseType(const std::string& text);
// Validation helpers
bool isKnownAttribute(const std::string& name) const;
void attributeWarning(const std::string& message,
const std::string& attribute,
size_t lineNumber);
void attributeWarning(const std::string& message, size_t lineNumber);
void rcppExportWarning(const std::string& message, size_t lineNumber);
void rcppExportNoFunctionFoundWarning(size_t lineNumber);
void rcppExportInvalidParameterWarning(const std::string& param,
size_t lineNumber);
void rcppInterfacesWarning(const std::string& message,
size_t lineNumber);
private:
std::string sourceFile_;
CharacterVector lines_;
std::vector<Attribute> attributes_;
FunctionMap functionMap_ ;
std::vector<std::string> modules_;
std::vector<std::string> embeddedR_;
std::vector<std::vector<std::string> > roxygenChunks_;
std::vector<std::string> roxygenBuffer_;
};
} // namespace attributes
} // namespace Rcpp
/*******************************************************************
* AttributesGen.h
*******************************************************************/
namespace Rcpp {
namespace attributes {
// Abstract class which manages writing of code for compileAttributes
class ExportsGenerator {
protected:
ExportsGenerator(const std::string& targetFile,
const std::string& package,
const std::string& commentPrefix);
private:
// prohibit copying
ExportsGenerator(const ExportsGenerator&);
ExportsGenerator& operator=(const ExportsGenerator&);
public:
virtual ~ExportsGenerator() {}
// Name of target file and package
const std::string& targetFile() const { return targetFile_; }
const std::string& package() const { return package_; }
// Abstract interface for code generation
virtual void writeBegin() = 0;
void writeFunctions(const SourceFileAttributes& attributes,
bool verbose); // see doWriteFunctions below
virtual void writeEnd() = 0;
virtual bool commit(const std::vector<std::string>& includes) = 0;
// Remove the generated file entirely
bool remove();
// Allow generator to appear as a std::ostream&
operator std::ostream&() {
return codeStream_;
}
protected:
// Allow access to the output stream
std::ostream& ostr() {
return codeStream_;
}
bool hasCppInterface() const {
return hasCppInterface_;
}
// Shared knowledge about function namees
std::string exportValidationFunction() {
return "RcppExport_validate";
}
std::string exportValidationFunctionRegisteredName() {
return package() + "_" + exportValidationFunction();
}
std::string registerCCallableExportedName() {
return package() + "_RcppExport_registerCCallable";
}
// Commit the stream -- is a no-op if the existing code is identical
// to the generated code. Returns true if data was written and false
// if it wasn't (throws exception on io error)
bool commit(const std::string& preamble = std::string());
private:
// Private virtual for doWriteFunctions so the base class
// can always intercept writeFunctions
virtual void doWriteFunctions(const SourceFileAttributes& attributes,
bool verbose) = 0;
// Check whether it's safe to overwrite this file (i.e. whether we
// generated the file in the first place)
bool isSafeToOverwrite() const {
return existingCode_.empty() ||
(existingCode_.find(generatorToken()) != std::string::npos);
}
// UUID that we write into a comment within the file (so that we can
// strongly identify that a file was generated by us before overwriting it)
std::string generatorToken() const {
return "10BE3573-1514-4C36-9D1C-5A225CD40393";
}
private:
std::string targetFile_;
std::string package_;
std::string commentPrefix_;
std::string existingCode_;
std::ostringstream codeStream_;
bool hasCppInterface_;
};
// Class which manages generating RcppExports.cpp
class CppExportsGenerator : public ExportsGenerator {
public:
explicit CppExportsGenerator(const std::string& packageDir,
const std::string& package,
const std::string& fileSep);
virtual void writeBegin() {};
virtual void writeEnd();
virtual bool commit(const std::vector<std::string>& includes);
private:
virtual void doWriteFunctions(const SourceFileAttributes& attributes,
bool verbose);
std::string registerCCallable(size_t indent,
const std::string& exportedName,
const std::string& name) const;
private:
std::vector<Attribute> cppExports_;
};
// Class which manages generating PackageName_RcppExports.h header file
class CppExportsIncludeGenerator : public ExportsGenerator {
public:
CppExportsIncludeGenerator(const std::string& packageDir,
const std::string& package,
const std::string& fileSep);
virtual void writeBegin();
virtual void writeEnd();
virtual bool commit(const std::vector<std::string>& includes);
private:
virtual void doWriteFunctions(const SourceFileAttributes& attributes,
bool verbose);
std::string getCCallable(const std::string& function) const;
std::string getHeaderGuard() const;
private:
std::string includeDir_;
};
// Class which manages generating PackageName_RcppExports.h header file
class CppPackageIncludeGenerator : public ExportsGenerator {
public:
CppPackageIncludeGenerator(const std::string& packageDir,
const std::string& package,
const std::string& fileSep);
virtual void writeBegin() {}
virtual void writeEnd();
virtual bool commit(const std::vector<std::string>& includes);
private:
virtual void doWriteFunctions(const SourceFileAttributes& attributes,
bool verbose) {}
std::string getHeaderGuard() const;
private:
std::string includeDir_;
};
// Class which manages generator RcppExports.R
class RExportsGenerator : public ExportsGenerator {
public:
RExportsGenerator(const std::string& packageDir,
const std::string& package,
const std::string& fileSep);
virtual void writeBegin() {}
virtual void writeEnd();
virtual bool commit(const std::vector<std::string>& includes);
private:
virtual void doWriteFunctions(const SourceFileAttributes& attributes,
bool verbose);
};
// Class to manage and dispatch to a list of generators
class ExportsGenerators {
public:
typedef std::vector<ExportsGenerator*>::iterator Itr;
ExportsGenerators() {}
virtual ~ExportsGenerators();
void add(ExportsGenerator* pGenerator);
void writeBegin();
void writeFunctions(const SourceFileAttributes& attributes,
bool verbose);
void writeEnd();
// Commit and return a list of the files that were updated
std::vector<std::string> commit(
const std::vector<std::string>& includes);
// Remove and return a list of files that were removed
std::vector<std::string> remove();
private:
// prohibit copying
ExportsGenerators(const ExportsGenerators&);
ExportsGenerators& operator=(const ExportsGenerators&);
private:
std::vector<ExportsGenerator*> generators_;
};
// Standalone generation helpers (used by sourceCpp)
std::string generateRArgList(const Function& function);
void generateCpp(std::ostream& ostr,
const SourceFileAttributes& attributes,
bool includePrototype,
bool cppInterface,
const std::string& contextId);
} // namespace attributes
} // namespace Rcpp
/*******************************************************************
* AttributesParser.cpp
*******************************************************************/
namespace Rcpp {
namespace attributes {
namespace {
Rcpp::List regexMatches(Rcpp::CharacterVector lines,
const std::string& regex)
{
Rcpp::Environment base("package:base");
Rcpp::Function regexec = base["regexec"];
Rcpp::Function regmatches = base["regmatches"];
Rcpp::RObject result = regexec(regex, lines);
Rcpp::List matches = regmatches(lines, result);
return matches;
}
// Parse embedded R code chunks from a file (receives the lines of the
// file as a CharcterVector for using with regexec and as a standard
// stl vector for traversal/insepection)
std::vector<std::string> parseEmbeddedR(
Rcpp::CharacterVector linesVector,
const std::deque<std::string>& lines) {
Rcpp::List matches = regexMatches(linesVector,
"^\\s*/\\*{3,}\\s+[Rr]\\s*$");
bool withinRBlock = false;
CommentState commentState;
std::vector<std::string> embeddedR;
for (int i = 0; i<matches.size(); i++) {
// track comment state
std::string line = lines[i];
commentState.submitLine(line);
// is this a line that begins an R code block?
const Rcpp::CharacterVector match = matches[i];
bool beginRBlock = match.size() > 0;
// check state and do the right thing
if (beginRBlock) {
withinRBlock = true;
}
else if (withinRBlock) {
if (commentState.inComment())
embeddedR.push_back(line);
else
withinRBlock = false;
}
}
return embeddedR;
}
} // anonymous namespace
// Generate a type signature for the function with the provided name
// (type signature == function pointer declaration)
std::string Function::signature(const std::string& name) const {
std::ostringstream ostr;
ostr << type() << "(*" << name << ")(";
const std::vector<Argument>& args = arguments();
for (std::size_t i = 0; i<args.size(); i++) {
ostr << args[i].type();
if (i != (args.size()-1))
ostr << ",";
}
ostr << ")";
return ostr.str();
}
// Parse attribute parameter from parameter text
Param::Param(const std::string& paramText)
{
// parse out name/value pair if there is one
std::string::size_type pos = paramText.find("=") ;
if ( pos != std::string::npos ) {
// name
name_ = paramText.substr(0, pos);
trimWhitespace(&name_);
// value
value_ = paramText.substr(pos + 1) ;
trimWhitespace(&value_);
stripQuotes(&value_);
}
else {
name_ = paramText;
stripQuotes(&name_);
}
}
// Check if the attribute has a parameter of a paricular name
Param Attribute::paramNamed(const std::string& name) const {
for (std::vector<Param>::const_iterator
it = params_.begin(); it != params_.end(); ++it) {
if (it->name() == name)
return *it;
}
return Param();
}
// Type operator <<
std::ostream& operator<<(std::ostream& os, const Type& type) {
if (!type.empty()) {
if (type.isConst())
os << "const ";
os << type.name();
if (type.isReference())
os << "&";
}
return os;
}
// Argument operator <<
std::ostream& operator<<(std::ostream& os, const Argument& argument) {
if (!argument.empty()) {
os << argument.type();
if (!argument.name().empty()) {
os << " ";
os << argument.name();
if (!argument.defaultValue().empty())
os << " = " << argument.defaultValue();
}
}
return os;
}
// Function operator <<
std::ostream& operator<<(std::ostream& os, const Function& function) {
if (!function.empty()) {
if (!function.type().empty()) {
os << function.type();
os << " ";
}
os << function.name();
os << "(";
const std::vector<Argument>& arguments = function.arguments();
for (std::size_t i = 0; i<arguments.size(); i++) {
os << arguments[i];
if (i != (arguments.size()-1))
os << ", ";
}
os << ")";
}
return os;
}
// Param operator <<
std::ostream& operator<<(std::ostream& os, const Param& param) {
if (!param.empty()) {
os << param.name();
if (!param.value().empty())
os << "=" << param.value();
}
return os;
}
// Attribute operator <<
std::ostream& operator<<(std::ostream& os, const Attribute& attribute) {
if (!attribute.empty()) {
os << "[[Rcpp::" << attribute.name();
const std::vector<Param>& params = attribute.params();
if (params.size() > 0) {
os << "(";
for (std::size_t i = 0; i<params.size(); i++) {
os << params[i];
if (i != (params.size()-1))
os << ",";
}
os << ")";
}
os << "]]";
if (!attribute.function().empty())
os << " " << attribute.function();
}
return os;
}
// Parse the attributes from a source file
SourceFileAttributesParser::SourceFileAttributesParser
(const std::string& sourceFile)
: sourceFile_(sourceFile)
{
// First read the entire file into a std::stringstream so we can check
// it for attributes (we don't want to do any of our more expensive
// processing steps if there are no attributes to parse)
std::ifstream ifs(sourceFile_.c_str());
if (ifs.fail())
throw Rcpp::file_io_error(sourceFile_);
std::stringstream buffer;
buffer << ifs.rdbuf();
std::string contents = buffer.str();
// Check for attribute signature
if (contents.find("[[Rcpp::") != std::string::npos ||
contents.find("RCPP_MODULE") != std::string::npos) {
// Now read into a list of strings (which we can pass to regexec)
// First read into a std::deque (which will handle lots of append
// operations efficiently) then copy into an R chracter vector
std::string line;
std::deque<std::string> lines;
while(std::getline(buffer, line)) {
// strip \r (for the case of windows line terminators on posix)
if (line.length() > 0 && *line.rbegin() == '\r')
line.erase(line.length()-1, 1);
stripTrailingLineComments(&line);
lines.push_back(line);
}
lines_ = Rcpp::wrap(lines);
// Scan for attributes
CommentState commentState;
Rcpp::List matches = regexMatches(lines_,
"^\\s*//\\s*\\[\\[Rcpp::(\\w+)(\\(.*?\\))?\\]\\]\\s*$");
for (int i = 0; i<matches.size(); i++) {
// track whether we are in a comment and bail if we are in one
std::string line = lines[i];
commentState.submitLine(line);
if (commentState.inComment())
continue;
// attribute line
const Rcpp::CharacterVector match = matches[i];
if (match.size() > 0) {
// if the match size isn't 3 then regmatches has not behaved
// as expected (it should return a vector of either 0 or 3
// elements). we don't ever expect this to occur but if it
// does let's not crash
if (match.size() != 3)
continue;
// add the attribute
Attribute attr = parseAttribute(
Rcpp::as<std::vector<std::string> >(match), i);
attributes_.push_back(attr);
if( attr.isExportedFunction() ){
functionMap_.insert(attr.function());
}
}
// if it's not an attribute line then it could still be a
// line of interest (e.g. roxygen comment)
else {
// save roxygen comments
if (line.find("//'") == 0) {
std::string roxLine = "#" + line.substr(2);
roxygenBuffer_.push_back(roxLine);
}
// a non-roxygen line causes us to clear the roxygen buffer
else if (!roxygenBuffer_.empty()) {
roxygenChunks_.push_back(roxygenBuffer_);
roxygenBuffer_.clear();
}
}
}
// Scan for Rcpp modules
commentState.reset();
Rcpp::List modMatches = regexMatches(lines_,
"^\\s*RCPP_MODULE\\s*\\(\\s*(\\w+)\\s*\\).*$");
for (int i = 0; i<modMatches.size(); i++) {
// track whether we are in a comment and bail if we are in one
std::string line = lines[i];
commentState.submitLine(line);
if (commentState.inComment())
continue;
// get the module declaration
Rcpp::CharacterVector match = modMatches[i];
if (match.size() > 0) {
const char * name = match[1];
modules_.push_back(name);
}
}
// Parse embedded R
embeddedR_ = parseEmbeddedR(lines_, lines);
}
}
// Parse an attribute from the vector returned by regmatches
Attribute SourceFileAttributesParser::parseAttribute(
const std::vector<std::string>& match,
int lineNumber) {
// Attribute name
std::string name = match[1];
// Warn if this is an unknown attribute
if (!isKnownAttribute(name)) {
attributeWarning("Unrecognized attribute Rcpp::" + name,
lineNumber);
}
// Extract params if we've got them
std::vector<Param> params;
std::string paramsText = match[2];
if (!paramsText.empty()) {
// we know from the regex that it's enclosed in parens so remove
// trim before we do this just in case someone updates the regex
// to allow for whitespace around the call
trimWhitespace(¶msText);
paramsText = paramsText.substr(1, paramsText.size()-2);
// parse the parameters
params = parseParameters(paramsText);
}
// Extract function signature if this is a function attribute
// and it doesn't appear at the end of the file
Function function;
// special handling for export
if (name == kExportAttribute) {
// parse the function (unless we are at the end of the file in
// which case we print a warning)
if ((lineNumber + 1) < lines_.size())
function = parseFunction(lineNumber + 1);
else
rcppExportWarning("No function found", lineNumber);
}
// validate interfaces parameter
else if (name == kInterfacesAttribute) {
if (params.empty()) {
rcppInterfacesWarning("No interfaces specified", lineNumber);
}
else {
for (std::size_t i=0; i<params.size(); i++) {
std::string param = params[i].name();
if (param != kInterfaceR && param != kInterfaceCpp) {
rcppInterfacesWarning(
"Unknown interface '" + param + "'", lineNumber);
}