Fix gcc6 C++11 warnings. Issue marbl#270.

src/AS_RUN/fragmentDepth.C

@@ -99,7 +99,7 @@ computeStuff(uint32 *V, uint32 N,
   }
 
   if (histogramBig) {
-    fprintf(stderr, "histogramBig: "F_U32"\n", histogramBig);
+    fprintf(stderr, "histogramBig: " F_U32 "\n", histogramBig);
     exit(1);
   }
 
@@ -197,7 +197,7 @@ void outputResult(AS_IID lastiid,
               if (E > N) { E = N; }
 
               computeStuff(V, N, i, E, &mode, &mean, &median);
-              fprintf(stdout, "%s\t"F_U32"\t"F_U32"\t"F_U32"\t%f\t"F_U32"\n", lastiid, i, E, mode, mean, median);
+              fprintf(stdout, "%s\t" F_U32 "\t" F_U32 "\t" F_U32 "\t%f\t" F_U32 "\n", lastiid, i, E, mode, mean, median);
             }
             safe_free(V);
           }

src/AS_UTL/AS_UTL_fileIO.C

@@ -76,7 +76,7 @@ AS_UTL_safeWrite(FILE *file, const void *buffer, const char *desc, size_t size,
 
     if (errno) {
       fprintf(stderr, "safeWrite()-- Write failure on %s: %s\n", desc, strerror(errno));
-      fprintf(stderr, "safeWrite()-- Wanted to write "F_SIZE_T" objects (size="F_SIZE_T"), wrote "F_SIZE_T".\n",
+      fprintf(stderr, "safeWrite()-- Wanted to write " F_SIZE_T " objects (size=" F_SIZE_T "), wrote " F_SIZE_T ".\n",
               towrite, size, written);
       assert(errno == 0);
     }
@@ -92,7 +92,7 @@ AS_UTL_safeWrite(FILE *file, const void *buffer, const char *desc, size_t size,
 #ifdef VERIFY_WRITE_POSITIONS
   if ((expectedposition > 0) &&
       (AS_UTL_ftell(file) != expectedposition)) {
-    fprintf(stderr, "safeWrite()-- EXPECTED "F_OFF_T", ended up at "F_OFF_T"\n",
+    fprintf(stderr, "safeWrite()-- EXPECTED " F_OFF_T ", ended up at " F_OFF_T "\n",
             expectedposition, AS_UTL_ftell(file));
     assert(AS_UTL_ftell(file) == expectedposition);
   }
@@ -121,7 +121,7 @@ AS_UTL_safeRead(FILE *file, void *buffer, const char *desc, size_t size, size_t
 
     if ((errno) && (errno != EINTR)) {
       fprintf(stderr, "safeRead()-- Read failure on %s: %s.\n", desc, strerror(errno));
-      fprintf(stderr, "safeRead()-- Wanted to read "F_SIZE_T" objects (size="F_SIZE_T"), read "F_SIZE_T".\n",
+      fprintf(stderr, "safeRead()-- Wanted to read " F_SIZE_T " objects (size=" F_SIZE_T "), read " F_SIZE_T ".\n",
               toread, size, written);
       assert(errno == 0);
     }
@@ -130,7 +130,7 @@ AS_UTL_safeRead(FILE *file, void *buffer, const char *desc, size_t size, size_t
  finish:
   //  Just annoys developers.  Stop it.
   //if (position != nobj)
-  //  fprintf(stderr, "AS_UTL_safeRead()--  Short read; wanted "F_SIZE_T" objects, read "F_SIZE_T" instead.\n",
+  //  fprintf(stderr, "AS_UTL_safeRead()--  Short read; wanted " F_SIZE_T " objects, read " F_SIZE_T " instead.\n",
   //          nobj, position);
   return(position);
 }
@@ -291,7 +291,7 @@ AS_UTL_sizeOfFile(const char *path) {
     sprintf(cmd, "gzip -l %s", path);
     F = popen(cmd, "r");
     fscanf(F, " %*s %*s %*s %*s ");
-    fscanf(F, " %*d "F_OFF_T" %*s %*s ", &size);
+    fscanf(F, " %*d " F_OFF_T " %*s %*s ", &size);
     pclose(F);
   } else if (strcasecmp(path+strlen(path)-4, ".bz2") == 0) {
     size = s.st_size * 14 / 10;
@@ -345,7 +345,7 @@ AS_UTL_fseek(FILE *stream, off_t offset, int whence) {
   if ((whence == SEEK_SET) && (beginpos == offset)) {
 #ifdef DEBUG_SEEK
     //  This isn't terribly informative, and adds a lot of clutter.
-    //fprintf(stderr, "AS_UTL_fseek()--  seek to "F_OFF_T" (whence=%d); already there\n", offset, whence);
+    //fprintf(stderr, "AS_UTL_fseek()--  seek to " F_OFF_T " (whence=%d); already there\n", offset, whence);
 #endif
     return;
   }
@@ -357,7 +357,7 @@ AS_UTL_fseek(FILE *stream, off_t offset, int whence) {
   }
 
 #ifdef DEBUG_SEEK
-  fprintf(stderr, "AS_UTL_fseek()--  seek to "F_OFF_T" (requested "F_OFF_T", whence=%d) from "F_OFF_T"\n",
+  fprintf(stderr, "AS_UTL_fseek()--  seek to " F_OFF_T " (requested " F_OFF_T ", whence=%d) from " F_OFF_T "\n",
           AS_UTL_ftell(stream), offset, whence, beginpos);
 #endif
 

src/AS_UTL/AS_UTL_stackTrace.C

@@ -82,7 +82,7 @@ AS_UTL_envokeGDB(void) {
 
   //  Child
 
-  sprintf(cmd, "gdb -quiet -silent -p "F_U64" -batch -x commands", pid);
+  sprintf(cmd, "gdb -quiet -silent -p " F_U64 " -batch -x commands", pid);
   system(cmd);
   exit(0);
 #endif

src/AS_UTL/bitPackedArray.C

@@ -66,7 +66,7 @@ bitPackedArray::get(uint64 idx) {
   uint64 p = _valueWidth * (idx % _valuesPerSegment);
 
   if (idx >= _nextElement) {
-    fprintf(stderr, "bitPackedArray::get()-- element index "F_U64" is out of range, only "F_U64" elements.\n",
+    fprintf(stderr, "bitPackedArray::get()-- element index " F_U64 " is out of range, only " F_U64 " elements.\n",
             idx, _nextElement-1);
     return(0xdeadbeefdeadbeefULL);
   }
@@ -80,7 +80,7 @@ bitPackedArray::set(uint64 idx, uint64 val) {
   uint64 s = idx / _valuesPerSegment;
   uint64 p = _valueWidth * (idx % _valuesPerSegment);
 
-  //fprintf(stderr, "s="F_U64" p="F_U64" segments="F_U64"/"F_U64"\n", s, p, _numSegments, _maxSegments);
+  //fprintf(stderr, "s=" F_U64 " p=" F_U64 " segments=" F_U64 "/" F_U64 "\n", s, p, _numSegments, _maxSegments);
 
   if (idx >= _nextElement)
     _nextElement = idx+1;

src/AS_UTL/bitPackedArray.H

@@ -164,20 +164,20 @@ public:
       }
 
 #ifdef DEBUG_BPH_GET
-      fprintf(stderr, "test c="F_U64" and p="F_U64" lastVal="F_U64"\n",
+      fprintf(stderr, "test c=" F_U64 " and p=" F_U64 " lastVal=" F_U64 "\n",
               cidx, pidx, _lastVal);
-      fprintf(stderr, "test c="F_U64"="F_U64"\n",
+      fprintf(stderr, "test c=" F_U64 "=" F_U64 "\n",
               cidx, cval);
-      fprintf(stderr, "test p="F_U64"="F_U64"\n",
+      fprintf(stderr, "test p=" F_U64 "=" F_U64 "\n",
               pidx, pval);
-      fprintf(stderr, "test c="F_U64"="F_U64" and p="F_U64"="F_U64"\n",
+      fprintf(stderr, "test c=" F_U64 "=" F_U64 " and p=" F_U64 "=" F_U64 "\n",
               cidx, cval, pidx, pval);
 #endif
 
       if (cval < pval) {
 
 #ifdef DEBUG_BPH_GET
-        fprintf(stderr, "swap c="F_U64"="F_U64" and p="F_U64"="F_U64"\n",
+        fprintf(stderr, "swap c=" F_U64 "=" F_U64 " and p=" F_U64 "=" F_U64 "\n",
                 cidx, cval, pidx, pval);
 #endif
 
@@ -204,7 +204,7 @@ public:
     bool    more = false;
 
 #ifdef DEBUG_BPH_ADD
-    fprintf(stderr, "add  c="F_U64"="F_U64" -- lastVal="F_U64"\n",
+    fprintf(stderr, "add  c=" F_U64 "=" F_U64 " -- lastVal=" F_U64 "\n",
             cidx, cval, _lastVal);
 #endif
 
@@ -217,20 +217,20 @@ public:
       pidx = (cidx-1) / 2;
 
 #ifdef DEBUG_BPH_ADD
-      fprintf(stderr, "more c="F_U64" and p="F_U64"\n", cidx, pidx);
+      fprintf(stderr, "more c=" F_U64 " and p=" F_U64 "\n", cidx, pidx);
 #endif
 
       pval = _array->get(pidx);
 
 #ifdef DEBUG_BPH_ADD
-      fprintf(stderr, "test c="F_U64"="F_U64" and p="F_U64"="F_U64"\n",
+      fprintf(stderr, "test c=" F_U64 "=" F_U64 " and p=" F_U64 "=" F_U64 "\n",
               cidx, cval, pidx, pval);
 #endif
 
       if (pval > cval) {
 
 #ifdef DEBUG_BPH_ADD
-        fprintf(stderr, "swap c="F_U64"="F_U64" and p="F_U64"="F_U64"\n",
+        fprintf(stderr, "swap c=" F_U64 "=" F_U64 " and p=" F_U64 "=" F_U64 "\n",
                 cidx, cval, pidx, pval);
 #endif
 
@@ -254,7 +254,7 @@ public:
 
   void      dump(void) {
     for (uint32 i=0; i<_lastVal; i++)
-      fprintf(stderr, "HEAP["F_U32"]="F_U64"\n", i, _array->get(i));
+      fprintf(stderr, "HEAP[" F_U32 "]=" F_U64 "\n", i, _array->get(i));
   }
 
   void      clear(void) {

src/AS_UTL/bitPackedFile.C

@@ -213,7 +213,7 @@ bitPackedFile::bitPackedFile(char const *name, uint64 offset, bool forceTruncate
     fprintf(stderr, "bitPackedFile::bitPackedFile()-- found ");
     for (uint32 i=0; i<16; i++)
       fprintf(stderr, "%c", isascii(c[i]) ? c[i] : '.');
-    fprintf(stderr, " at position "F_X64"\n", file_offset);
+    fprintf(stderr, " at position " F_X64 "\n", file_offset);
     exit(1);
   }
 
@@ -412,7 +412,7 @@ bitPackedFile::seekNormal(uint64 bitpos) {
   errno = 0;
   lseek(_file, _pos * 8 + endianess_offset, SEEK_SET);
   if (errno) {
-    fprintf(stderr, "bitPackedFile::seekNormal() '%s' seek to pos="F_U64" failed: %s\n",
+    fprintf(stderr, "bitPackedFile::seekNormal() '%s' seek to pos=" F_U64 " failed: %s\n",
             _name,
             _pos * 8 + endianess_offset, strerror(errno));
     exit(1);
@@ -421,7 +421,7 @@ bitPackedFile::seekNormal(uint64 bitpos) {
   errno = 0;
   size_t wordsread = read(_file, _bfr, sizeof(uint64) * _bfrmax);
   if (errno) {
-    fprintf(stderr, "bitPackedFile::seekNormal() '%s' read of "F_U64" bytes failed': %s\n",
+    fprintf(stderr, "bitPackedFile::seekNormal() '%s' read of " F_U64 " bytes failed': %s\n",
             _name,
             sizeof(uint64) * _bfrmax,
             strerror(errno));
@@ -459,7 +459,7 @@ bitPackedFile::seek(uint64 bitpos) {
     if ((_pos <= np) && (np <= _pos + _bfrmax - 32)) {
       _bit = bitpos - (_pos << 6);
       stat_seekInside++;
-      //fprintf(stderr, "SEEK INSIDE to _bit="F_U64"\n", _bit);
+      //fprintf(stderr, "SEEK INSIDE to _bit=" F_U64 "\n", _bit);
       return;
     }
   }
@@ -481,7 +481,7 @@ bitPackedFile::seek(uint64 bitpos) {
 
   _forceFirstLoad = false;
 
-  //fprintf(stderr, "SEEK OUTSIDE to _pos="F_U64" _bit="F_U64"\n", _pos, _bit);
+  //fprintf(stderr, "SEEK OUTSIDE to _pos=" F_U64 " _bit=" F_U64 "\n", _pos, _bit);
 }
 
 

src/AS_UTL/bitPackedFile.H

@@ -71,7 +71,7 @@ public:
   uint64     loadInCore(void);
 
   void       showStats(FILE *f) {
-    fprintf(f, "inside: "F_U64"  outside: "F_U64"\n", stat_seekInside, stat_seekOutside);
+    fprintf(f, "inside: " F_U64 "  outside: " F_U64 "\n", stat_seekInside, stat_seekOutside);
     fflush(f);
   };
 private:

src/AS_UTL/kMer.C

@@ -300,7 +300,7 @@ kMerBuilder::addBaseCompressed(uint64 cf, uint64 cr) {
     lb = 9;  //  No valid last base (should probably be ~uint64ZERO, but that screws up diagnostic output)
 
 #ifdef DEBUGCOMP
-  fprintf(stderr, "kMerBuilder::addBaseCompressed()--  lb="uint64FMT" cf="uint64FMT" ms="F_U32" ccl="F_U32" lvl="F_U32"\n",
+  fprintf(stderr, "kMerBuilder::addBaseCompressed()--  lb="uint64FMT" cf="uint64FMT" ms=" F_U32 " ccl=" F_U32 " lvl=" F_U32 "\n",
           lb, cf, ms, _compressionCurrentLength, _compression);
 #endif
 
@@ -392,7 +392,7 @@ kMerBuilder::addBaseCompressed(uint64 cf, uint64 cr) {
   ms -= _compressionLength[_compressionIndex];  //  subtract the count for the letter we just shifted out
 
 #ifdef DEBUGCOMP
-  fprintf(stderr, "kMerBuilder::addBaseCompressed()--  ADDNEWBASE shifted out at idx="F_U32" with "F_U32" positions; final span "F_U32"\n",
+  fprintf(stderr, "kMerBuilder::addBaseCompressed()--  ADDNEWBASE shifted out at idx=" F_U32 " with " F_U32 " positions; final span " F_U32 "\n",
           _compressionIndex,
           _compressionLength[_compressionIndex],
           ms + 1);

src/AS_UTL/kMerHuge.H

@@ -260,7 +260,7 @@ public:
     val &= uint64MASK(numbits);
 
     if (wrd >= KMER_WORDS) {
-      fprintf(stderr, "kMer::setBits()-- ERROR: tried to set pos="F_U32" numbits="F_U32" larger than KMER_WORDS=%d\n",
+      fprintf(stderr, "kMer::setBits()-- ERROR: tried to set pos=" F_U32 " numbits=" F_U32 " larger than KMER_WORDS=%d\n",
               pos, numbits, KMER_WORDS), exit(1);
     }
 
@@ -274,7 +274,7 @@ public:
       MERWORD(wrd) |=  val << bit;
     } else {
       if (wrd+1 >= KMER_WORDS) {
-        fprintf(stderr, "kMer::setBits()-- ERROR: tried to set pos="F_U32" numbits="F_U32" larger than KMER_WORDS=%d\n",
+        fprintf(stderr, "kMer::setBits()-- ERROR: tried to set pos=" F_U32 " numbits=" F_U32 " larger than KMER_WORDS=%d\n",
                 pos, numbits, KMER_WORDS), exit(1);
       }
 
@@ -295,15 +295,15 @@ public:
     uint32  bit = pos  & 0x3f;
 
     if (wrd >= KMER_WORDS) {
-      fprintf(stderr, "kMer::getBits()-- ERROR: tried to get pos="F_U32" numbits="F_U32" larger than KMER_WORDS=%d\n",
+      fprintf(stderr, "kMer::getBits()-- ERROR: tried to get pos=" F_U32 " numbits=" F_U32 " larger than KMER_WORDS=%d\n",
               pos, numbits, KMER_WORDS), exit(1);
     }
 
     if (64 - bit >= numbits) {
       val = MERWORD(wrd) >> bit;
     } else {
       if (wrd+1 >= KMER_WORDS) {
-        fprintf(stderr, "kMer::getBits()-- ERROR: tried to get pos="F_U32" numbits="F_U32" larger than KMER_WORDS=%d\n",
+        fprintf(stderr, "kMer::getBits()-- ERROR: tried to get pos=" F_U32 " numbits=" F_U32 " larger than KMER_WORDS=%d\n",
                 pos, numbits, KMER_WORDS), exit(1);
       }
 
@@ -395,7 +395,7 @@ kMerHuge::setMerSize(uint32 ms) {
   }
 
   if (_maskWord >= KMER_WORDS) {
-    fprintf(stderr, "kMer::setMerSize()-- ERROR!  Desired merSize of "F_U32" larger than\n", _merSize);
+    fprintf(stderr, "kMer::setMerSize()-- ERROR!  Desired merSize of " F_U32 " larger than\n", _merSize);
     fprintf(stderr, "                     available storage space (KMER_WORDS=%d, max merSize %d).\n", KMER_WORDS, KMER_WORDS*32);
     exit(1);
   }

src/AS_UTL/memoryMappedFile.H

@@ -109,7 +109,7 @@ public:
                                                  : mmap(0L, _length, PROT_READ | PROT_WRITE, MAP_FILE | MAP_SHARED, fd, 0);
 
     if (errno)
-      fprintf(stderr, "memoryMappedFile()-- Couldn't mmap '%s' of length "F_SIZE_T": %s\n", _name, _length, strerror(errno)), exit(1);
+      fprintf(stderr, "memoryMappedFile()-- Couldn't mmap '%s' of length " F_SIZE_T ": %s\n", _name, _length, strerror(errno)), exit(1);
 
     close(fd);
 
@@ -135,7 +135,7 @@ public:
       length = _length - offset;
 
     if (offset + length > _length)
-      fprintf(stderr, "memoryMappedFile()-- Requested "F_SIZE_T" bytes at position "F_SIZE_T" in file '%s', but only "F_SIZE_T" bytes in file.\n",
+      fprintf(stderr, "memoryMappedFile()-- Requested " F_SIZE_T " bytes at position " F_SIZE_T " in file '%s', but only " F_SIZE_T " bytes in file.\n",
               length, offset, _name, _length), exit(1);
 
     _offset = offset + length;

src/AS_UTL/readBuffer.C

@@ -176,7 +176,7 @@ readBuffer::fillBuffer(void) {
   if (errno == EAGAIN)
     goto again;
   if (errno)
-    fprintf(stderr, "readBuffer::fillBuffer()-- only read "F_U64" bytes, couldn't read "F_U64" bytes from '%s': %s\n",
+    fprintf(stderr, "readBuffer::fillBuffer()-- only read " F_U64 " bytes, couldn't read " F_U64 " bytes from '%s': %s\n",
             _bufferLen, _bufferMax, _filename, strerror(errno)), exit(1);
 
   if (_bufferLen == 0)
@@ -209,7 +209,7 @@ readBuffer::seek(uint64 pos) {
     errno = 0;
     lseek(_file, pos, SEEK_SET);
     if (errno)
-      fprintf(stderr, "readBuffer()-- '%s' couldn't seek to position "F_U64": %s\n",
+      fprintf(stderr, "readBuffer()-- '%s' couldn't seek to position " F_U64 ": %s\n",
               _filename, pos, strerror(errno)), exit(1);
 
     _bufferLen = 0;
@@ -272,7 +272,7 @@ readBuffer::read(void *buf, uint64 len) {
     errno = 0;
     bAct = (uint64)::read(_file, bufchar + bCopied + bRead, len - bCopied - bRead);
     if (errno)
-      fprintf(stderr, "readBuffer()-- couldn't read "F_U64" bytes from '%s': n%s\n",
+      fprintf(stderr, "readBuffer()-- couldn't read " F_U64 " bytes from '%s': n%s\n",
               len, _filename, strerror(errno)), exit(1);
 
     //  If we hit EOF, return a short read

src/AS_UTL/stddev.H

@@ -520,7 +520,7 @@ public:
     fprintf(F, "#%s\tquantity\n", label);
 
     for (uint64 ii=0; ii <= _histogramMax; ii++)
-      fprintf(F, F_U64"\t"F_U64"\n", ii, _histogram[ii]);
+      fprintf(F, F_U64"\t" F_U64 "\n", ii, _histogram[ii]);
   };