[Phylobase-commits] r835 - pkg/src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Nov 19 15:46:09 CET 2012
Author: bbolker
Date: 2012-11-19 15:46:09 +0100 (Mon, 19 Nov 2012)
New Revision: 835
Modified:
pkg/src/Makevars
pkg/src/Makevars.win
pkg/src/nxsblock.cpp
pkg/src/nxscxxdiscretematrix.cpp
pkg/src/nxspublicblocks.cpp
pkg/src/nxsreader.cpp
pkg/src/nxstreesblock.cpp
Log:
replace cout/cerr with Rcpp::Rcout/Rcerr
Modified: pkg/src/Makevars
===================================================================
--- pkg/src/Makevars 2012-11-12 14:27:16 UTC (rev 834)
+++ pkg/src/Makevars 2012-11-19 14:46:09 UTC (rev 835)
@@ -1,2 +1,2 @@
-PKG_CPPFLAGS=-I. -DHAVE_INTTYPES_H
+PKG_CPPFLAGS=-I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS
PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`
Modified: pkg/src/Makevars.win
===================================================================
--- pkg/src/Makevars.win 2012-11-12 14:27:16 UTC (rev 834)
+++ pkg/src/Makevars.win 2012-11-19 14:46:09 UTC (rev 835)
@@ -1,5 +1,5 @@
## PKG_LIBS = -s $(shell Rscript -e 'Rcpp:::LdFlags()') -L"$(RHOME)/bin" -lR --no-export-all-symbols --add-stdcall-alias
-PKG_CXXFLAGS = -I. -DHAVE_INTTYPES_H
+PKG_CXXFLAGS = -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS
PKG_LIBS = $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()")
Modified: pkg/src/nxsblock.cpp
===================================================================
--- pkg/src/nxsblock.cpp 2012-11-12 14:27:16 UTC (rev 834)
+++ pkg/src/nxsblock.cpp 2012-11-19 14:46:09 UTC (rev 835)
@@ -20,6 +20,9 @@
#include "ncl/nxsdefs.h"
#include "ncl/nxsblock.h"
#include "ncl/nxsreader.h"
+
+#include <Rcpp.h>
+
#include <cstdlib>
using namespace std;
@@ -31,7 +34,7 @@
# if defined (ASSERTS_TO_EXCEPTIONS)
NxsString err;
# else
- std::ostream & err(cerr);
+ std::ostream & err(Rcerr);
# endif
err << "\nNCL assertion failed:";
err << "\n expr: " << expr;
@@ -41,7 +44,7 @@
# if defined (ASSERTS_TO_EXCEPTIONS)
throw NxsNCLAPIException(err);
# else
- std::cerr << std::endl;
+ Rcpp::Rcerr << std::endl;
std::exit(1);
# endif
}
Modified: pkg/src/nxscxxdiscretematrix.cpp
===================================================================
--- pkg/src/nxscxxdiscretematrix.cpp 2012-11-12 14:27:16 UTC (rev 834)
+++ pkg/src/nxscxxdiscretematrix.cpp 2012-11-19 14:46:09 UTC (rev 835)
@@ -22,7 +22,7 @@
#include <cassert>
using std::string;
using std::vector;
-using std::cout;
+//using std::cout;
using std::endl;
/**===========================================================================
Modified: pkg/src/nxspublicblocks.cpp
===================================================================
--- pkg/src/nxspublicblocks.cpp 2012-11-12 14:27:16 UTC (rev 834)
+++ pkg/src/nxspublicblocks.cpp 2012-11-19 14:46:09 UTC (rev 835)
@@ -23,6 +23,9 @@
#include <fstream>
#include "ncl/nxspublicblocks.h"
#include "ncl/nxsreader.h"
+
+#include <Rcpp.h>
+
using namespace std;
@@ -680,7 +683,7 @@
throw NxsException(msg);
}
if (verbose)
- std::cerr << "Writing \"" << fn << "\" to store the translation of names\n";
+ Rcpp::Rcerr << "Writing \"" << fn << "\" to store the translation of names\n";
writeTaxonNameTranslationStream(tnf, nameTrans, tb);
tnf.close();
}
Modified: pkg/src/nxsreader.cpp
===================================================================
--- pkg/src/nxsreader.cpp 2012-11-12 14:27:16 UTC (rev 834)
+++ pkg/src/nxsreader.cpp 2012-11-19 14:46:09 UTC (rev 835)
@@ -23,6 +23,9 @@
#include <climits>
#include <sstream>
#include <iterator>
+
+#include <Rcpp.h>
+
#include "ncl/nxsreader.h"
#include "ncl/nxsdefs.h"
@@ -1305,19 +1308,19 @@
return;
if (warnMode == NxsReader::WARNINGS_TO_STDERR)
{
- std::cerr << "\nWarning: ";
- std::cerr << "\n " << msg << std::endl;
+ Rcpp::Rcerr << "\nWarning: ";
+ Rcpp::Rcerr << "\n " << msg << std::endl;
if (line > 0 || pos > 0)
- std::cerr << "at line " << line << ", column (approximately) " << col << " (file position " << pos << ")\n";
+ Rcpp::Rcerr << "at line " << line << ", column (approximately) " << col << " (file position " << pos << ")\n";
}
else if (warnMode != NxsReader::WARNINGS_TO_STDOUT)
{
- std::cout << "\nWarning: ";
+ Rcpp::Rcout << "\nWarning: ";
if (line > 0 || pos > 0)
- std::cout << "at line " << line << ", column " << col << " (file position " << pos << "):\n";
- std::cout << "\n " << msg << '\n';
+ Rcpp::Rcout << "at line " << line << ", column " << col << " (file position " << pos << "):\n";
+ Rcpp::Rcout << "\n " << msg << '\n';
if (line > 0 || pos > 0)
- std::cout << "at line " << line << ", column (approximately) " << col << " (file position " << pos << ')' << std::endl;
+ Rcpp::Rcout << "at line " << line << ", column (approximately) " << col << " (file position " << pos << ')' << std::endl;
}
else
{
@@ -1332,9 +1335,9 @@
if (warnMode == NxsReader::IGNORE_WARNINGS)
return;
if (warnMode == NxsReader::WARNINGS_TO_STDERR)
- std::cerr << "[!Skipping unknown block (" << blockName << ")...]" << std::endl;
+ Rcpp::Rcerr << "[!Skipping unknown block (" << blockName << ")...]" << std::endl;
else if (warnMode != NxsReader::WARNINGS_TO_STDOUT)
- std::cout << "[!Skipping unknown block (" << blockName << ")...]" << std::endl;
+ Rcpp::Rcout << "[!Skipping unknown block (" << blockName << ")...]" << std::endl;
}
void ExceptionRaisingNxsReader::SkippingDisabledBlock(NxsString blockName)
@@ -1342,15 +1345,15 @@
if (warnMode == NxsReader::IGNORE_WARNINGS)
return;
if (warnMode == NxsReader::WARNINGS_TO_STDERR)
- std::cerr << "[!Skipping disabled block (" << blockName << ")...]" << std::endl;
+ Rcpp::Rcerr << "[!Skipping disabled block (" << blockName << ")...]" << std::endl;
else if (warnMode != NxsReader::WARNINGS_TO_STDOUT)
- std::cout << "[!Skipping disabled block (" << blockName << ")...]" << std::endl;
+ Rcpp::Rcout << "[!Skipping disabled block (" << blockName << ")...]" << std::endl;
}
void NxsReader::statusMessage(const std::string & m) const
{
if (alwaysReportStatusMessages || currentWarningLevel == UNCOMMON_SYNTAX_WARNING) {
- std::cerr << m << std::endl;
+ Rcpp::Rcerr << m << std::endl;
}
}
Modified: pkg/src/nxstreesblock.cpp
===================================================================
--- pkg/src/nxstreesblock.cpp 2012-11-12 14:27:16 UTC (rev 834)
+++ pkg/src/nxstreesblock.cpp 2012-11-19 14:46:09 UTC (rev 835)
@@ -19,6 +19,8 @@
#include <climits>
#include "ncl/nxstreesblock.h"
+#include <Rcpp.h>
+
#include <sstream>
#include <stack>
@@ -1003,13 +1005,13 @@
if (nd->IsTip())
{
nodeIndex = nd->GetTaxonIndex();
- std::cout << " leaf node # = " << nodeIndex << '\n';
+ Rcpp::Rcout << " leaf node # = " << nodeIndex << '\n';
}
else
{
nodeIndex = internalNdIndex++;
nd->SetTaxonIndex(nodeIndex);
- std::cout << " internal node # = " << nd->GetTaxonIndex() << '\n';
+ Rcpp::Rcout << " internal node # = " << nd->GetTaxonIndex() << '\n';
}
if (parentVector.size() < nodeIndex + 1)
{
@@ -1034,17 +1036,17 @@
branchLengthVector[nodeIndex] = -1.0;
}
}
- std::cout << "Parents = [";
+ Rcpp::Rcout << "Parents = [";
for (std::vector<unsigned>::const_iterator nIt = parentVector.begin(); nIt != parentVector.end(); ++nIt)
- {
- std::cout << *nIt << ", ";
- }
- std::cout << "]\nbranch lengths = [";
- for (std::vector<double>::const_iterator nIt = branchLengthVector.begin(); nIt != branchLengthVector.end(); ++nIt)
- {
- std::cout << *nIt << ", ";
- }
- std::cout << "]\n";
+ {
+ Rcpp::Rcout << *nIt << ", ";
+ }
+ Rcpp::Rcout << "]\nbranch lengths = [";
+ for (std::vector<double>::const_iterator nIt = branchLengthVector.begin(); nIt != branchLengthVector.end(); ++nIt)
+ {
+ Rcpp::Rcout << *nIt << ", ";
+ }
+ Rcpp::Rcout << "]\n";
#endif
}
}
@@ -1328,9 +1330,9 @@
else if (prevToken == NXS_TREE_COLON_TOKEN)
throw NxsException("Expecting a branch length after a : but found (", token);
nchildren.top() += 1;
- //std::cerr << "Open Parens nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ Rcpp::Rcerr << "Open Parens nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
nchildren.push(0);
- //std::cerr << "Open Parens after push nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ Rcpp::Rcerr << "Open Parens after push nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
newickStream << '(';
prevToken = NXS_TREE_OPEN_PARENS_TOKEN;
handled = true;
@@ -1354,10 +1356,10 @@
else if (nchildren.top() > 3 || nchildren.size() > 1) /* three children are allowed not considered a polytomy */
hasPolytomies = true;
}
- //std::cerr << "close parens nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ Rcpp::Rcerr << "close parens nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
nchildren.pop();
- //if (!nchildren.empty())
- //std::cerr << "close parens post-pop nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ if (!nchildren.empty())
+ Rcpp::Rcerr << "close parens post-pop nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
newickStream << ')';
prevToken = NXS_TREE_CLOSE_PARENS_TOKEN;
handled = true;
@@ -1431,7 +1433,7 @@
NxsString toAppend;
if (prevToken == NXS_TREE_CLOSE_PARENS_TOKEN)
{
- //std::cerr << "validateInternalNodeLabels = " << validateInternalNodeLabels << '\n';
+ Rcpp::Rcerr << "validateInternalNodeLabels = " << validateInternalNodeLabels << '\n';
if (validateInternalNodeLabels)
{
std::map<std::string, unsigned>::const_iterator tt = capNameToInd.find(ucl);
@@ -1515,7 +1517,7 @@
}
taxaEncountered.insert(indWithAdditions);
nchildren.top() += 1;
- //std::cerr << "treating as number " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ Rcpp::Rcerr << "treating as number " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
toAppend += (1 + indWithAdditions);
}
@@ -1541,7 +1543,7 @@
capNameToInd[tasstring] = valueInd;
taxaEncountered.insert(valueInd);
nchildren.top() += 1;
- //std::cerr << "nonnumeric newtaxon " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ Rcpp::Rcerr << "nonnumeric newtaxon " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
toAppend += (1 + valueInd);
}
}
@@ -1557,7 +1559,7 @@
}
taxaEncountered.insert(*cit);
nchildren.top() += 1;
- //std::cerr << "taxon set " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ Rcpp::Rcerr << "taxon set " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
if (!firstTaxonAdded)
toAppend.append(1, ',');
toAppend += (1 + *cit);
@@ -1574,7 +1576,7 @@
{
taxaEncountered.insert(ind);
nchildren.top() += 1;
- //std::cerr << "taxon label " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
+ Rcpp::Rcerr << "taxon label " << ucl << " nchildren.top = " << nchildren.top() << " nchildren.size() = " << nchildren.size() << " rooted = " << rooted << " hasPolytomies = " << hasPolytomies << std::endl;
toAppend += (1 + ind);
}
}
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