Fix buglets spotted by new compiler on Fedora 17

13 files changed, 16 insertions, 57 deletions

diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index b6ea010b..84361414 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -895,7 +895,7 @@ UnitCell *match_cell_ab(UnitCell *cell, UnitCell *template)
 	int used[3];
 	struct rvec real_a, real_b, real_c;
 	struct rvec params[3];
-	double alen, blen, clen;
+	double alen, blen;
 	float ltl = 5.0;     /* percent */
 	int have_real_a;
 	int have_real_b;
@@ -911,7 +911,6 @@ UnitCell *match_cell_ab(UnitCell *cell, UnitCell *template)
 	}
 	alen = modulus(ax, ay, az);
 	blen = modulus(bx, by, bz);
-	clen = modulus(cx, cy, cz);
 
 	/* Get the lengths from the cell and turn them into anonymous vectors */
 	if ( cell_get_cartesian(cell, &ax, &ay, &az,
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index f212821d..5f138eac 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -750,7 +750,6 @@ struct detector *get_detector_geometry(const char *filename)
 		char line[1024];
 		struct badregion *badregion = NULL;
 		struct panel *panel = NULL;
-		char *key;
 		char wholeval[1024];
 
 		rval = fgets(line, 1023, fh);
@@ -802,8 +801,6 @@ struct detector *get_detector_geometry(const char *filename)
 			}
 		}
 
-		key = path[1];
-
 		if ( panel != NULL ) {
 			if ( parse_field_for_panel(panel, path[1],
 			                           wholeval, det) )
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index 259ec199..5cfa908a 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -467,7 +467,6 @@ static void find_candidates(struct reax_private *p,
                             const char *rg, struct detector *det)
 {
 	int i;
-	double th, ph;
 
 	for ( i=0; i<s->n_search; i++ ) {
 		s->search[i].cand = calloc(MAX_CANDIDATES,
@@ -475,7 +474,6 @@ static void find_candidates(struct reax_private *p,
 		s->search[i].n_cand = 0;
 	}
 
-	th = 0.0;  ph = 0.0;
 	for ( i=0; i<p->n_dir; i++ ) {
 		check_dir(&p->directions[i], flist,
 		                    p->nel, pmax, fft_in, fft_out, p->plan,
@@ -492,7 +490,10 @@ static void find_candidates(struct reax_private *p,
 		int j;
 
 		sv = &s->search[i];
-		refine_vector(flist, &sv->cand[j].v);
+
+		for ( j=0; j<sv->n_cand; j++ ) {
+			refine_vector(flist, &sv->cand[j].v);
+		}
 
 	}
 
@@ -593,7 +594,6 @@ static void refine_rigid_group(struct image *image, UnitCell *cell,
 	double bx, by, bz, mb;
 	double cx, cy, cz, mc;
 	double pha, phb, phc;
-	struct panel *p;
 	int i, j;
 	fftw_complex *r_fft_in;
 	fftw_complex *r_fft_out;
@@ -618,13 +618,6 @@ static void refine_rigid_group(struct image *image, UnitCell *cell,
 	                      pr->nel, pmax, fft_in, fft_out, plan,
 	                      smin, smax, rg, det);
 
-	for ( i=0; i<det->n_panels; i++ ) {
-		if ( det->panels[i].rigid_group == rg ) {
-			p = &det->panels[i];
-			break;
-		}
-	}
-
 	r_fft_in = fftw_malloc(pr->cw*pr->ch*sizeof(fftw_complex));
 	r_fft_out = fftw_malloc(pr->cw*pr->ch*sizeof(fftw_complex));
 	for ( i=0; i<pr->cw; i++ ) {
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index ce0ee33e..6627e7ea 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -335,7 +335,6 @@ int read_chunk(FILE *fh, struct image *image)
 	int have_bs = 0;
 	int have_cs = 0;
 	int have_filename = 0;
-	int have_cell = 0;
 	int have_ev = 0;
 
 	if ( find_start_of_chunk(fh) ) return 1;
@@ -410,7 +409,6 @@ int read_chunk(FILE *fh, struct image *image)
 			image->indexed_cell = cell_new_from_reciprocal_axes(as,
 			                                                    bs,
 			                                                    cs);
-			have_cell = 1;
 			have_as = 0;  have_bs = 0;  have_cs = 0;
 		}
 
diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c
index ab837ec0..0352e441 100644
--- a/libcrystfel/src/symmetry.c
+++ b/libcrystfel/src/symmetry.c
@@ -1275,8 +1275,7 @@ SymOpList *get_ambiguities(const SymOpList *source, const SymOpList *target)
 	SymOpList *src_reordered;
 	SymOpMask *used;
 	char *name;
-	int index;
-
+	
 	n_src = num_ops(source);
 	n_tgt = num_ops(target);
 
@@ -1290,8 +1289,7 @@ SymOpList *get_ambiguities(const SymOpList *source, const SymOpList *target)
 		ERROR("Subgroup index would be fractional.\n");
 		return NULL;
 	}
-	index = n_src / n_tgt;
-
+	
 	src_reordered = new_symoplist();
 	used = new_symopmask(source);
 
diff --git a/src/check_hkl.c b/src/check_hkl.c
index fbc29f00..a1688ad2 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -68,8 +68,6 @@ static void show_help(const char *s)
 static void plot_shells(RefList *list, UnitCell *cell, const SymOpList *sym,
                         double rmin_fix, double rmax_fix)
 {
-	double num[NBINS];
-	int cts[NBINS];
 	int possible[NBINS];
 	unsigned int measurements[NBINS];
 	unsigned int measured[NBINS];
@@ -104,8 +102,6 @@ static void plot_shells(RefList *list, UnitCell *cell, const SymOpList *sym,
 	}
 
 	for ( i=0; i<NBINS; i++ ) {
-		num[i] = 0.0;
-		cts[i] = 0;
 		possible[i] = 0;
 		measured[i] = 0;
 		snr_measured[i] = 0;
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 2f846087..fb1ac117 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -96,12 +96,9 @@ static void plot_shells(RefList *list1, RefList *list2, double scale,
 {
 	double num[NBINS];
 	int cts[NBINS];
-	unsigned int measurements[NBINS];
-	unsigned int measured[NBINS];
 	double total_vol, vol_per_shell;
 	double rmins[NBINS];
 	double rmaxs[NBINS];
-	double snr[NBINS];
 	double rmin, rmax;
 	int i;
 	Reflection *refl1;
@@ -119,9 +116,6 @@ static void plot_shells(RefList *list1, RefList *list2, double scale,
 		num[i] = 0.0;
 		den[i] = 0.0;
 		cts[i] = 0;
-		measured[i] = 0;
-		measurements[i] = 0;
-		snr[i] = 0;
 	}
 
 	/* Find resolution limits */
diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index de03c62b..54d0bdea 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -77,13 +77,13 @@ static gint displaywindow_closed(GtkWidget *window, DisplayWindow *dw)
 	if ( dw->pixbufs != NULL ) {
 		int i;
 		for ( i=0; i<dw->n_pixbufs; i++ ) {
-			gdk_pixbuf_unref(dw->pixbufs[i]);
+			g_object_unref(dw->pixbufs[i]);
 		}
 		free(dw->pixbufs);
 	}
 
 	if ( dw->col_scale != NULL ) {
-		gdk_pixbuf_unref(dw->col_scale);
+		g_object_unref(dw->col_scale);
 	}
 
 	if ( dw->image != NULL ) {
@@ -189,12 +189,8 @@ static void show_ring(cairo_t *cr, DisplayWindow *dw,
 static void show_simple_ring(cairo_t *cr, DisplayWindow *dw,
                              double d, cairo_matrix_t *basic_m)
 {
-	struct detector *det;
-
 	if ( !dw->use_geom ) return;
 
-	det = dw->image->det;
-
 	cairo_identity_matrix(cr);
 	cairo_translate(cr, -dw->min_x/dw->binning,
 	                     dw->max_y/dw->binning);
@@ -431,7 +427,7 @@ static void set_window_size(DisplayWindow *dw)
 static void update_colscale(DisplayWindow *dw)
 {
 	if ( dw->col_scale != NULL ) {
-		gdk_pixbuf_unref(dw->col_scale);
+		g_object_unref(dw->col_scale);
 	}
 	dw->col_scale = render_get_colour_scale(20, dw->height, dw->scale);
 }
@@ -446,7 +442,7 @@ static void displaywindow_update(DisplayWindow *dw)
 	if ( dw->pixbufs != NULL ) {
 		int i;
 		for ( i=0; i<dw->n_pixbufs; i++ ) {
-			gdk_pixbuf_unref(dw->pixbufs[i]);
+			g_object_unref(dw->pixbufs[i]);
 		}
 		free(dw->pixbufs);
 	}
diff --git a/src/get_hkl.c b/src/get_hkl.c
index e298680d..00de38a5 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -270,10 +270,8 @@ static RefList *expand_reflections(RefList *in, const SymOpList *target,
 
 		signed int h, k, l;
 		int n, j;
-		double intensity;
 
 		get_indices(refl, &h, &k, &l);
-		intensity = get_intensity(refl);
 
 		special_position(initial, m, h, k, l);
 		n = num_equivs(initial, m);
@@ -298,7 +296,7 @@ static RefList *expand_reflections(RefList *in, const SymOpList *target,
 
 			/* FIXME: Make phase negative if the reflection is
 			 * separated from the original via an inversion */
-			get_phase(refl, &have_phase);
+			ph = get_phase(refl, &have_phase);
 			if ( have_phase ) set_phase(new, -ph);
 
 		}
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index fdbbf3a3..c9ad5300 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -840,7 +840,6 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
 			char results[1024];
 			char *rval;
 			int fd;
-			int n;
 			char *eptr;
 
 			if ( !sb->running[i] ) {
@@ -863,7 +862,7 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
 
 			chomp(results);
 
-			n = strtol(results, &eptr, 10);
+			strtol(results, &eptr, 10);
 			if ( eptr == results ) {
 				if ( strlen(results) > 0 ) {
 					ERROR("Invalid result '%s'\n", results);
diff --git a/src/powder_plot.c b/src/powder_plot.c
index 049b9c0e..84f292a3 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -725,7 +725,7 @@ int main(int argc, char *argv[])
 	unsigned int n_patterns = 0;
 	unsigned int n_peaks    = 0;
 
-	int c, rval, file_type, data_type;
+	int c, file_type, data_type;
 	int config_satcorr = 1;
 	int need_geometry  = 0;
 	int need_beam      = 0;
@@ -953,7 +953,7 @@ int main(int argc, char *argv[])
 			return 1;
 		}
 		/* Use wavelength from first chunk */
-		rval = read_chunk(fh, &image);
+		read_chunk(fh, &image);
 		rewind(fh);
 	} else if (file_type == FILE_H5) {
 		hdfile = hdfile_open(filename);
diff --git a/src/process_hkl.c b/src/process_hkl.c
index e06270bc..28d54360 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -356,7 +356,6 @@ int main(int argc, char *argv[])
 	unsigned int n_total_patterns;
 	char *sym_str = NULL;
 	SymOpList *sym;
-	char *pdb = NULL;
 	char *histo = NULL;
 	signed int hist_h, hist_k, hist_l;
 	signed int hist_nbins=50;
@@ -387,7 +386,7 @@ int main(int argc, char *argv[])
 	};
 
 	/* Short options */
-	while ((c = getopt_long(argc, argv, "hi:e:o:p:y:g:f:b:z:",
+	while ((c = getopt_long(argc, argv, "hi:e:o:y:g:f:b:z:",
 	                        longopts, NULL)) != -1) {
 
 		switch (c) {
@@ -411,10 +410,6 @@ int main(int argc, char *argv[])
 			config_startafter = atoi(optarg);
 			break;
 
-		case 'p' :
-			pdb = strdup(optarg);
-			break;
-
 		case 'y' :
 			sym_str = strdup(optarg);
 			break;
diff --git a/tests/pr_gradient_check.c b/tests/pr_gradient_check.c
index 8ca8ace5..6972b66a 100644
--- a/tests/pr_gradient_check.c
+++ b/tests/pr_gradient_check.c
@@ -225,10 +225,6 @@ static int test_gradients(struct image *image, double incr_val, int refine,
 
 			double r1, r2, p;
 			int cl, ch;
-			double tt, dstar;
-
-			dstar = 2.0 * resolution(image->indexed_cell, h, k, l),
-			tt = 2.0*asin(image->lambda/(2.0/dstar));
 
 			grad1 = (vals[1][i] - vals[0][i]) / incr_val;
 			grad2 = (vals[2][i] - vals[1][i]) / incr_val;