Silenced various compiler warnings (some are real bugs!)

src/gui_jobwindow.cpp

@@ -18,7 +18,7 @@
  * author citations must be preserved.
  ***************************************************************************/
 #include "src/gui_jobwindow.h"
-JobWindow::JobWindow(int _x, int _y, int _w, int _h, const char* title ) : Fl_Box(x,y,w,h,title)
+JobWindow::JobWindow(int _x, int _y, int _w, int _h, const char* title ) : Fl_Box(_x,_y,_w,_h,title)
 {
 	clear();
 	x = _x; y = _y; w = _w; h = _h;

src/jaz/gravis/StringFormat.h

@@ -24,10 +24,12 @@ namespace gravis
         s << start.string();
       };
 
-      const char*   c_str()  const
+// Takanori removed this because this is broken and not used.
+/*    const char*   c_str()  const
       {
         return s.str().c_str();
       }
+*/
       std::string   string() const
       {
         return s.str();

src/jaz/image_log.h

@@ -67,6 +67,9 @@ void ImageLog::write(
 
     switch (center)
     {
+        case NoCenter:
+	    break;
+
         case CenterXY:
         {
             Image<T> img2(w,h,d);

src/jaz/micrograph_handler.cpp

@@ -50,8 +50,6 @@ void MicrographHandler::init(
 		std::string& metaFn)
 {
 	this->nr_omp_threads = nr_omp_threads;
-	this->firstFrame = firstFrame;
-	this->lastFrame = lastFrame;
 
 	if (corrMicFn != "")
 	{

src/jaz/obs_model.cpp

@@ -760,7 +760,7 @@ int ObservationModel::getOpticsGroup(const MetaDataTable &particlesMdt, long int
 {
 	int opticsGroup = -1;
 	if (!particlesMdt.getValue(EMDL_IMAGE_OPTICS_GROUP, opticsGroup, particle))
-		REPORT_ERROR("ObservationModel::getOpticsGroup: Failed to get optics group for particle #" + particle);
+		REPORT_ERROR("ObservationModel::getOpticsGroup: Failed to get optics group for particle #" + std::to_string(particle));
 	opticsGroup--;
 
 	return opticsGroup;

src/pipeline_jobs.cpp

@@ -218,13 +218,6 @@ float JobOption::getNumber(std::string &errmsg)
 	}
 	else
 	{
-
-		if (&value == NULL)
-		{
-			errmsg = "Error in textToFloat of " + value;
-			return 0.;
-		}
-
 		float retval;
 		int ok = sscanf(value.c_str(), "%f", &retval);
 

src/pipeliner.cpp

@@ -1904,7 +1904,7 @@ void PipeLine::read(bool do_lock, std::string lock_message)
 #ifdef DEBUG_LOCK
 		std::cerr <<  " A status= " << status << std::endl;
 #endif
-		while (!status == 0)
+		while (status != 0)
 		{
 			if (errno == EACCES) // interestingly, not EACCESS!
 				REPORT_ERROR("ERROR: PipeLine::read cannot create a lock directory " + dir_lock + ". You don't have write permission to this project. If you want to look at other's project directory (but run nothing there), please start RELION with --readonly.");

src/scheduler.cpp

@@ -620,7 +620,7 @@ void Schedule::read(bool do_lock, FileName fn)
 #ifdef DEBUG_LOCK
 		std::cerr <<  " A status= " << status << std::endl;
 #endif
-		while (!status == 0)
+		while (status != 0)
 		{
 			if (errno == EACCES) // interestingly, not EACCESS!
 				REPORT_ERROR("ERROR: Schedule::read cannot create a lock directory " + dir_lock + ". You don't have write permission to this project. If you want to look at other's project directory (but run nothing there), please start RELION with --readonly.");

src/tiff_converter.cpp

@@ -138,7 +138,7 @@ void TIFFConverter::estimate(FileName fn_movie)
 				stable++;
 		}
 
-		printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n",
+		printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10ld / %10ld\n",
 		       fn_movie.c_str(), iframe + 1, changed, error, negative, YXSIZE(defects()) - stable, YXSIZE(defects()));
 	}
 }