Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv30906
Added Files:
pymol-py-clang.patch
Log Message:
add fixes recommended by clang
--- NEW FILE: pymol-py-clang.patch ---
--- pymol-1.5/layer0/Tetsurf.c.orig 2013-06-07 19:07:33.000000000 -0400
+++ pymol-1.5/layer0/Tetsurf.c 2013-06-07 19:08:35.000000000 -0400
@@ -712,8 +712,7 @@
if(I->Tri) {
VLAFreeP(I->Tri);
}
- if(I->PtLink);
- {
+ if(I->PtLink) {
VLAFreeP(I->PtLink);
}
if(I->VertexCodes) {
--- pymol-1.5/layer1/P.c.orig 2013-06-07 19:19:20.000000000 -0400
+++ pymol-1.5/layer1/P.c 2013-06-07 19:19:39.000000000 -0400
@@ -2618,7 +2618,7 @@
/* don't run if we're currently banned */
char *buffer = 0;
int size, curSize = 0;
- while(size = OrthoCommandOutSize(G)){
+ while((size = OrthoCommandOutSize(G))){
if (!curSize){
buffer = VLACalloc(char, size);
curSize = size;
@@ -2662,7 +2662,7 @@
int did_work = false;
char *buffer = 0;
int size, curSize = 0;
- while(size = OrthoCommandOutSize(G)){
+ while((size = OrthoCommandOutSize(G))){
if (!curSize){
buffer = VLACalloc(char, size);
curSize = size;
--- pymol-1.5/layer1/Ortho.c.orig 2013-06-07 19:10:57.000000000 -0400
+++ pymol-1.5/layer1/Ortho.c 2013-06-07 19:16:16.000000000 -0400
@@ -1088,7 +1088,7 @@
curLine = I->CurLine & OrthoSaveLines;
if(I->PromptChar) {
strcpy(buffer, I->Line[curLine]);
- if(PComplete(G, buffer + I->PromptChar, sizeof(OrthoLineType) -
I->PromptChar)); /* just print, don't complete */
+ PComplete(G, buffer + I->PromptChar, sizeof(OrthoLineType) -
I->PromptChar); /* just print, don't complete */
}
}
break;
--- pymol-1.5/layer1/Control.c.orig 2013-06-07 19:20:31.000000000 -0400
+++ pymol-1.5/layer1/Control.c 2013-06-07 19:20:50.000000000 -0400
@@ -709,7 +709,7 @@
but_bottom = y - (cControlBoxSize - 1);
but_height = cControlBoxSize;
- if((but_num == I->Active)) {
+ if(but_num == I->Active) {
draw_button(but_left, but_bottom,
but_width, but_height, lightEdge, darkEdge, pushed);
} else if(((but_num == 6) && ((int) SettingGet(G, cSetting_seq_view))) ||
--- pymol-1.5/layer1/Scene.c.orig 2013-06-07 19:22:02.000000000 -0400
+++ pymol-1.5/layer1/Scene.c 2013-06-07 19:41:53.000000000 -0400
@@ -7686,7 +7686,7 @@
/* update all gadgets first (single-threaded since they're
thread-unsafe) */
rec = NULL;
while(ListIterate(I->Obj, rec, next)) {
- if((rec->obj->type == cObjectGadget)) {
+ if(rec->obj->type == cObjectGadget) {
if(rec->obj->fUpdate)
rec->obj->fUpdate(rec->obj);
}
--- pymol-1.5/layer2/ObjectMolecule.c.orig 2013-06-07 19:42:56.000000000
-0400
+++ pymol-1.5/layer2/ObjectMolecule.c 2013-06-07 19:46:08.000000000 -0400
@@ -1390,7 +1390,7 @@
int NPHIH, MPHIA, NHPARM, NPARM, NNB, NRES;
int NBONA, NTHETA, NPHIA, NUMBND, NUMANG, NPTRA;
int NATYP, NPHB, IFPERT, NBPER, NGPER, NDPER;
- int MBPER, MGPER, MDPER, IFBOX, NMXRS, IFCAP;
+ int MBPER, MGPER, MDPER, IFBOX = 0, NMXRS, IFCAP;
int NEXTRA, IPOL = 0;
int wid, col;
float BETA;
@@ -2018,7 +2018,7 @@
if(IFBOX > 0) {
- int IPTRES, NSPM, NSPSOL;
+ int IPTRES, NSPM = 0, NSPSOL;
if(amber7) {
p = findflag(G, buffer, "SOLVENT_POINTERS", "3I8");
@@ -10478,7 +10478,7 @@
rms = MatrixFitRMSTTTf(G, op->nvv1, op->vv1, vt, NULL,
op->ttt);
else
rms = MatrixGetRMS(G, op->nvv1, op->vv1, vt, NULL);
- if((op->i1 == 2)) {
+ if(op->i1 == 2) {
ObjectMoleculeTransformTTTf(I, op->ttt, b);
if(op->i3) {
--- pymol-1.5/layer2/ObjectMolecule2.c.orig 2013-06-07 19:47:12.000000000
-0400
+++ pymol-1.5/layer2/ObjectMolecule2.c 2013-06-07 19:47:49.000000000 -0400
@@ -3624,7 +3624,7 @@
#else
int ok = true;
ObjectMolecule *I = NULL;
- int discrete_flag;
+ int discrete_flag = 0;
int ll;
(*result) = NULL;
--- pymol-1.5/layer2/RepSurface.c.orig 2013-06-07 19:48:34.000000000 -0400
+++ pymol-1.5/layer2/RepSurface.c 2013-06-07 19:49:43.000000000 -0400
@@ -5653,7 +5653,7 @@
SurfaceJobAtomInfo *j_atom_info = atom_info + j;
if(j > a) /* only check if this is atom trails */
if((!present) || present[j]) {
- if((j_atom_info->vdw == a_atom_info->vdw)) { /*
handle singularities */
+ if(j_atom_info->vdw == a_atom_info->vdw) { /*
handle singularities */
float *v1 = coord + 3 * j;
if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] ==
v1[2]))
skip_flag = true;
@@ -5747,7 +5747,7 @@
SurfaceJobAtomInfo *j_atom_info = atom_info + j;
if(j > a) /* only check if this is atom trails */
if((!present) || present[j]) {
- if((j_atom_info->vdw == a_atom_info->vdw)) { /*
handle singularities */
+ if(j_atom_info->vdw == a_atom_info->vdw) { /*
handle singularities */
float *v2 = coord + 3 * j;
if((v0[0] == v2[0]) && (v0[1] == v2[1]) && (v0[2] ==
v2[2]))
skip_flag = true;
@@ -5917,7 +5917,7 @@
SurfaceJobAtomInfo *j_atom_info = atom_info + j;
if(j > a) /* only check if this is atom trails */
if((!present) || present[j]) {
- if((j_atom_info->vdw == a_atom_info->vdw)) { /*
handle singularities */
+ if(j_atom_info->vdw == a_atom_info->vdw) { /*
handle singularities */
float *v1 = coord + 3 * j;
if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] ==
v1[2]))
skip_flag = true;
--- pymol-1.5/modules/cealign/src/tnt/tnt_array1d.h.orig 2013-06-07
19:51:46.000000000 -0400
+++ pymol-1.5/modules/cealign/src/tnt/tnt_array1d.h 2013-06-07
19:52:08.000000000 -0400
@@ -258,7 +258,7 @@
template <class T>
inline Array1D<T> Array1D<T>::subarray(int i0, int i1)
{
- if ((i0 >= 0) && (i1 < n_) || (i0 <= i1))
+ if (((i0 >= 0) && (i1 < n_)) || (i0 <= i1))
{
Array1D<T> X(*this); /* create a new instance of this array. */
X.n_ = i1-i0+1;
--- pymol-1.5/modules/cealign/src/tnt/tnt_fortran_array1d.h.orig
2013-06-07 19:53:25.000000000 -0400
+++ pymol-1.5/modules/cealign/src/tnt/tnt_fortran_array1d.h 2013-06-07
19:53:54.000000000 -0400
@@ -221,7 +221,7 @@
#ifdef TNT_DEBUG
std::cout << "entered subarray. \n";
#endif
- if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
+ if (((i0 > 0) && (i1 < n_)) || (i0 <= i1))
{
Fortran_Array1D<T> X(*this); /* create a new instance of this
array. */
X.n_ = i1-i0+1;
--- pymol-1.5/layer3/Executive.c.orig 2013-06-07 19:55:06.000000000 -0400
+++ pymol-1.5/layer3/Executive.c 2013-06-07 19:56:00.000000000 -0400
@@ -17137,7 +17137,7 @@
ExecutiveSpecSetVisibility(G, rec, true, mod, false);
I->LastChanged = rec;
}
- if((mod == (cOrthoSHIFT | cOrthoCTRL))) {
+ if(mod == (cOrthoSHIFT | cOrthoCTRL)) {
if(rec != I->LastZoomed)
ExecutiveWindowZoom(G, rec->name, 0.0F, -1, false,
-1.0F,
true);
--- pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c.orig
2013-06-07 19:57:24.000000000 -0400
+++ pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c
2013-06-07 19:57:54.000000000 -0400
@@ -375,7 +375,7 @@
const char *filetype, int *natoms) {
FILE *fd;
- qmdata_t *data;
+ qmdata_t *data = NULL;
gmsdata *gms;
/* open the input file */
--- pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c.orig
2013-06-07 19:59:19.000000000 -0400
+++ pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c
2013-06-07 19:59:37.000000000 -0400
@@ -99,7 +99,7 @@
const char *filetype,
int *natoms) {
FILE *fd;
- qmdata_t *data;
+ qmdata_t *data = NULL;
moldendata_t *moldendata;
char buffer[1024];
char keystring[20];
--- pymol-1.5/layer4/Cmd.c.orig 2013-06-07 20:01:48.000000000 -0400
+++ pymol-1.5/layer4/Cmd.c 2013-06-07 20:03:00.000000000 -0400
@@ -1881,7 +1881,7 @@
static PyObject *CmdGetRenderer(PyObject * self, PyObject * args)
{
PyMOLGlobals *G = NULL;
- char *vendor, *renderer, *version;
+ char *vendor = NULL, *renderer = NULL, *version = NULL;
int ok = false;
ok = PyArg_ParseTuple(args, "O", &self);
if(ok) {
--- pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp.orig
2013-06-07 20:04:28.000000000 -0400
+++ pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp
2013-06-07 20:04:44.000000000 -0400
@@ -104,7 +104,7 @@
///ojo aqui le quite el !
if ((grassp->flag)!=POTENTIALS) {
- if (index >=0 && index <= 4)
+ if (index <= 4)
printf("graspplugin) No data available for '%s' option\n", name[index]);
else
printf("graspplugin) out of range property, flag: %d index: %d\n",
grassp->flag, index);
--- pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp.orig
2013-06-07 20:09:26.000000000 -0400
+++ pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
2013-06-07 20:09:56.000000000 -0400
@@ -1983,7 +1983,7 @@
}
}
catch (std::exception &e) {
- fprintf(stderr, e.what());
+ fprintf(stderr, "%s", e.what());
return MOLFILE_ERROR;
}
return MOLFILE_SUCCESS;
--- pymol-1.5/contrib/pyopengl/openglutil.c.orig 2013-06-07
20:11:42.000000000 -0400
+++ pymol-1.5/contrib/pyopengl/openglutil.c 2013-06-07 20:12:18.000000000
-0400
@@ -278,7 +278,7 @@
if (pix > 127.0)
bitpixel |= 0x01;
- fprintf(fp, "%02hx", bitpixel);
+ fprintf(fp, "%02hhx", bitpixel);
if (++pos >= 40) {
fprintf(fp, "\n%%");
pos = 0;
@@ -320,7 +320,7 @@
curpix = (unsigned char *) pixels;
pos = 0;
for (i = width * height * components; i > 0; i--) {
- fprintf(fp, "%02hx", *curpix++);
+ fprintf(fp, "%02hhx", *curpix++);
if (++pos >= 40) {
fprintf(fp, "\n");
pos = 0;
--- pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp.orig
2013-06-07 20:21:43.000000000 -0400
+++ pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp
2013-06-07 20:22:02.000000000 -0400
@@ -259,7 +259,7 @@
int addr = z*nclx*ncly + y*nclx + x;
if (fread(datablock + addr, 4, 1, fd) != 1) {
printf("pbeqplugin) Error reading potential map cell: %d,%d,%d\n",
x, y, z);
- printf("pbeqplugin) offset: %d\n", ftell(fd));
+ printf("pbeqplugin) offset: %ld\n", ftell(fd));
return MOLFILE_ERROR;
}
count++;
--- pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c.orig
2013-06-07 20:26:11.000000000 -0400
+++ pymol-1.5/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c
2013-06-07 20:37:17.000000000 -0400
@@ -231,7 +231,7 @@
switch (tolower(keyword[0])) {
case 'n': {
/* name */
- if (sscanf(s, "%16s %n", &atom.name, &n) < 1) {
+ if (sscanf(s, "%16s %n", (char *) &atom.name, &n) < 1) {
vtf_error("could not get name in atom record", line);
return MOLFILE_ERROR;
}
@@ -240,7 +240,7 @@
}
case 't': {
/* type */
- if (sscanf(s, "%16s %n", &atom.type, &n) < 1) {
+ if (sscanf(s, "%16s %n", (char *) &atom.type, &n) < 1) {
vtf_error("could not get type in atom record", line);
return MOLFILE_ERROR;
}
@@ -266,7 +266,7 @@
} else if (strcmp(keyword, "res") == 0 ||
strcmp(keyword, "resname") == 0) {
/* resname */
- if (sscanf(s, "%8s %n", &atom.resname, &n) < 1) {
+ if (sscanf(s, "%8s %n", (char *) &atom.resname, &n) < 1) {
vtf_error("could not get resname in atom record", line);
return MOLFILE_ERROR;
}
@@ -281,7 +281,7 @@
}
case 's': {
/* segid */
- if (sscanf(s, "%8s %n", &atom.segid, &n) < 1) {
+ if (sscanf(s, "%8s %n", (char *) &atom.segid, &n) < 1) {
vtf_error("could not get segid in atom record", line);
return MOLFILE_ERROR;
}
@@ -290,7 +290,7 @@
}
case 'i': {
/* insertion */
- if (sscanf(s, "%2s %n", &atom.insertion, &n) < 1) {
+ if (sscanf(s, "%2s %n", (char *) &atom.insertion, &n) < 1) {
vtf_error("could not get insertion in atom record", line);
return MOLFILE_ERROR;
}
@@ -302,7 +302,7 @@
/* chain, charge */
if (strlen(keyword) == 1 ||
strcmp(keyword, "chain") == 0) {
- if (sscanf(s, "%2s %n", &atom.chain, &n) < 1) {
+ if (sscanf(s, "%2s %n", (char *) &atom.chain, &n) < 1) {
vtf_error("could not get chain in atom record", line);
return MOLFILE_ERROR;
}
@@ -336,7 +336,7 @@
}
d->optflags |= MOLFILE_ATOMICNUMBER;
} else if (strcmp(keyword, "altloc")) {
- if (sscanf(s, "%2s %n", &atom.altloc, &n) < 1) {
+ if (sscanf(s, "%2s %n", (char *) &atom.altloc, &n) < 1) {
vtf_error("could not get altloc in atom record", line);
return MOLFILE_ERROR;
}
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