Merge branch 'develop' into develop-64

# Conflicts:
#	libhdt/src/libdcs/CSD_PFC.cpp
#	libhdt/src/triples/TripleIterators.cpp

Author: wouterbeek

.travis.yml

@@ -2,8 +2,6 @@ language: cpp
 env:
   global:
     - LOCAL=$HOME/local
-    - TESTS_HDT="bit375 bitutiltest listener logarr serd streamtest testmax"
-    - TESTS_CDS="testArray testBitSequence testHuffman testLCP testNPR testSequence testSuffixTree testTextIndex timeSequence toArray2 toArray"
 matrix:
   include:
     - os: osx
@@ -50,8 +48,8 @@ script:
   - ./configure --prefix=$LOCAL CXX=$HDT_CPP
   - make -j2
   # Make and run selected tests. Most tests in HDT are failing
-  - TESTS=$TESTS_CDS make -e check -j2 -C libcds || ( cat libcds/tests/test-suite.log && exit -1)
-  - TESTS=$TESTS_HDT make -e check -j2 -C libhdt || ( cat libhdt/tests/test-suite.log && exit -1)
+  - make check -j2 -C libcds || ( cat libcds/tests/test-suite.log && exit -1)
+  - make check -j2 -C libhdt || ( cat libhdt/tests/test-suite.log && exit -1)
   # Install
   - make install
   - hdtSearch -q 0 libhdt/data/literals.hdt

libcds/src/static/coders/huff.cpp

@@ -235,7 +235,7 @@ namespace cds_static
 		if (!enc) {
 			H.fst = new uint[H.depth+1];
 			H.fst[H.depth] = 0; dold = 0;
-			for (d=H.depth-1;d>=0;d--) {
+			for (d=H.depth-1;d!=(uint)-1;d--) {
 				dact = H.num[d+1];
 				H.fst[d] = (H.fst[d+1]+dact) >> 1;
 				H.num[d+1] = dold;

libcds/tests/Makefile.am

@@ -4,13 +4,13 @@ testBitSequence \
 testHuffman \
 testLCP \
 testNPR \
-testQuantile \
 testSequence \
 testSuffixTree \
 testTextIndex \
 timeSequence \
 toArray2 \
 toArray
+#testQuantile
 
 AM_DEFAULT_SOURCE_EXT = .cpp
 AM_CPPFLAGS = -I@top_srcdir@/libcds/include $(WARN_CFLAGS)

libhdt/src/bitsequence/BitSequence375.cpp

@@ -288,7 +288,8 @@ BitSequence375 * BitSequence375::load(istream & in)
 	// Read array from file, byte-aligned.
 	size_t bytes = ret->numBytes(ret->numbits);
 	in.read((char*)&ret->data[0], bytes);
-	if(in.gcount()!=bytes) {
+	streamsize gc = in.gcount();
+	if(gc < 0 || static_cast<size_t>(gc)!=bytes) {
 		throw std::runtime_error("BitSequence375 error reading array of bits.");
 	}
 

libhdt/src/dictionary/FourSectionDictionary.cpp

@@ -582,7 +582,7 @@ void FourSectionDictionary::getSuggestions(const char *base, hdt::TripleComponen
 	merge(v1.begin(),v1.end(), v2.begin(), v2.end(), std::back_inserter(out));
 
 	// Remove possible extra items
-	if(out.size()>maxResults) {
+	if((maxResults>=0) && (out.size()>static_cast<size_t>(maxResults))) {
 		out.resize(maxResults);
 	}
 }

libhdt/src/dictionary/LiteralDictionary.cpp

@@ -430,7 +430,7 @@ size_t LiteralDictionary::substringToId(unsigned char *s, size_t len, size_t off
 
 	if(fmIndex!=NULL) {
 		uint32_t ret = fmIndex->locate_substring(s, len, offset, limit, deduplicate, occs, num_occ);
-		for (int i=0;i<*num_occ;i++){
+		for (size_t i=0;i<*num_occ;i++){
 			(*occs)[i] = this->getGlobalId((*occs)[i], NOT_SHARED_OBJECT);
 		}
 		return ret;
@@ -706,7 +706,7 @@ void LiteralDictionary::getSuggestions(const char *base, hdt::TripleComponentRol
 	merge(v1.begin(), v1.end(), v2.begin(), v2.end(), std::back_inserter(out));
 
 	// Remove possible extra items
-	if (out.size() > maxResults) {
+	if ((maxResults >= 0) && (out.size() > static_cast<size_t>(maxResults))) {
 		out.resize(maxResults);
 	}
 }

libhdt/src/libdcs/CSD_FMIndex.cpp

@@ -445,9 +445,9 @@ void csd::CSD_FMIndex::fillSuggestions(const char *base,
     uint32_t *results = NULL;
     size_t numresults = this->locate_substring(n_s, len + 1, &results);
     int maxIter = maxResults;
-    if (numresults < maxIter)
+    if (maxIter >= 0 && numresults < static_cast<size_t>(maxIter))
         maxIter = numresults;
-    for (int i = 0; i < numresults; i++) {
+    for (size_t i = 0; i < numresults; i++) {
         out.push_back((char*) (this->extract(results[i])));
     }
 }

libhdt/src/sequence/AdjacencyList.cpp

@@ -233,7 +233,7 @@ size_t AdjacencyList::findNextAppearance(size_t oldpos, size_t element) {
 
 size_t AdjacencyList::findPreviousAppearance(size_t oldpos, size_t element) {
 	long long old=oldpos;
-    if(oldpos==-1 || element==0) {
+    if(oldpos==(size_t)-1 || element==0) {
         return -1;
     }
 

libhdt/src/triples/BitmapTriples.cpp

@@ -488,7 +488,7 @@ void BitmapTriples::generateIndexFast(ProgressListener *listener) {
 
 		//cerr << "Item " << i << " in adjlist " << adjZlist << endl;
 		unsigned int pred = arrayY->get(adjZlist);
-		maxpred = pred>maxpred ? pred : maxpred;
+		maxpred = ((maxpred<0) || (pred>static_cast<size_t>(maxpred))) ? pred : maxpred;
 
         index[val-1].push_back(std::make_pair(adjZlist, pred));
 		NOTIFYCOND(&iListener, "Generating Object lists", i, arrayZ->getNumberOfElements());

libhdt/src/triples/BitmapTriplesIterators.cpp

@@ -456,7 +456,7 @@ void MiddleWaveletIterator::skip(size_t pos) {
 
 	int numJumps = 0;
     unsigned int posLeft = pos;
-	while ((numJumps<pos)&&(posZ<maxZ)){
+	while ((numJumps<0 || static_cast<size_t>(numJumps)<pos)&&(posZ<maxZ)){
 		if((posZ+posLeft)>nextZ) {
 			 numJumps += (nextZ-posZ)+1; // count current jump
 			 predicateOcurrence++; // jump to the next occurrence
@@ -611,7 +611,7 @@ void IteratorY::updateOutput() {
 
 bool IteratorY::hasNext()
 {
-    return nextY!=-1 || posZ<=nextZ;
+    return nextY!=(size_t)-1 || posZ<=nextZ;
 }
 
 TripleID *IteratorY::next()
@@ -639,7 +639,7 @@ TripleID *IteratorY::next()
 
 bool IteratorY::hasPrevious()
 {
-	return prevY!=-1 || posZ>=prevZ;
+	return prevY!=(size_t)-1 || posZ>=prevZ;
 }
 
 TripleID *IteratorY::previous()
@@ -785,7 +785,7 @@ void ObjectIndexIterator::updateOutput() {
 
 bool ObjectIndexIterator::hasNext()
 {
-    return posIndex <= maxIndex && maxIndex >= 0;
+    return maxIndex >= 0 && posIndex <= static_cast<size_t>(maxIndex);
 }
 
 TripleID *ObjectIndexIterator::next()
@@ -804,7 +804,7 @@ TripleID *ObjectIndexIterator::next()
 
 bool ObjectIndexIterator::hasPrevious()
 {
-    return posIndex>minIndex;
+    return minIndex<0 || posIndex>static_cast<size_t>(minIndex);
 }
 
 TripleID *ObjectIndexIterator::previous()