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<title>[120407] trunk/dports/science/pymol</title>
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<dl class="meta">
<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/120407">120407</a></dd>
<dt>Author</dt> <dd>ryandesign@macports.org</dd>
<dt>Date</dt> <dd>2014-05-27 12:53:32 -0700 (Tue, 27 May 2014)</dd>
</dl>
<h3>Log Message</h3>
<pre>pymol: maintainer update to 1.7.1.1 (#43824)</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportssciencepymolPortfile">trunk/dports/science/pymol/Portfile</a></li>
<li><a href="#trunkdportssciencepymolfilespymolclangdiff">trunk/dports/science/pymol/files/pymol-clang.diff</a></li>
<li><a href="#trunkdportssciencepymolfilessetup_pydiff">trunk/dports/science/pymol/files/setup_py.diff</a></li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportssciencepymolPortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/pymol/Portfile (120406 => 120407)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/Portfile 2014-05-27 19:49:21 UTC (rev 120406)
+++ trunk/dports/science/pymol/Portfile 2014-05-27 19:53:32 UTC (rev 120407)
</span><span class="lines">@@ -6,8 +6,7 @@
</span><span class="cx"> PortGroup active_variants 1.1
</span><span class="cx">
</span><span class="cx"> name pymol
</span><del>-version 1.6.0
-revision 1
</del><ins>+version 1.7.1.1
</ins><span class="cx"> categories science chemistry
</span><span class="cx"> license GPL
</span><span class="cx"> maintainers bromo.med.uc.edu:howarth
</span><span class="lines">@@ -23,7 +22,7 @@
</span><span class="cx"> master_sites sourceforge
</span><span class="cx"> fetch.type svn
</span><span class="cx"> svn.url https://svn.code.sf.net/p/pymol/code/trunk/pymol
</span><del>-svn.revision 4039
</del><ins>+svn.revision 4074
</ins><span class="cx"> worksrcdir pymol
</span><span class="cx">
</span><span class="cx"> python.default_version 27
</span><span class="lines">@@ -56,6 +55,7 @@
</span><span class="cx"> reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/setup.py
</span><span class="cx"> reinplace "s|@@PYTHON_PKGDIR@@|${python.pkgd}|g" ${worksrcpath}/setup/pymol_macports
</span><span class="cx"> reinplace "s|@@PYTHON_BINARY@@|${python.bin}|g" ${worksrcpath}/setup/pymol_macports
</span><ins>+ reinplace "s|\"-O3\",|\"-O3\", \"-g\",|g" ${worksrcpath}/setup.py
</ins><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> use_parallel_build yes
</span></span></pre></div>
<a id="trunkdportssciencepymolfilespymolclangdiff"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/pymol/files/pymol-clang.diff (120406 => 120407)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/files/pymol-clang.diff 2014-05-27 19:49:21 UTC (rev 120406)
+++ trunk/dports/science/pymol/files/pymol-clang.diff 2014-05-27 19:53:32 UTC (rev 120407)
</span><span class="lines">@@ -1,8 +1,8 @@
</span><span class="cx"> Index: layer0/ShaderMgr.c
</span><span class="cx"> ===================================================================
</span><del>---- layer0/ShaderMgr.c (revision 4039)
</del><ins>+--- layer0/ShaderMgr.c (revision 4074)
</ins><span class="cx"> +++ layer0/ShaderMgr.c (working copy)
</span><del>-@@ -150,7 +150,7 @@ void CShaderPrg_ReplaceStringsInPlace(Py
</del><ins>+@@ -151,7 +151,7 @@
</ins><span class="cx"> while (replaceStrings[i]){
</span><span class="cx"> slen = strlen(replaceStrings[i]);
</span><span class="cx"> rlen = strlen(replaceStrings[i+1]);
</span><span class="lines">@@ -11,7 +11,7 @@
</span><span class="cx"> strcpy(tmp_line, rstr + slen);
</span><span class="cx"> strcpy(rstr, replaceStrings[i+1]);
</span><span class="cx"> strcpy(rstr+rlen, tmp_line);
</span><del>-@@ -488,15 +488,15 @@ void CShaderPrg_BindAttribLocations(PyMO
</del><ins>+@@ -499,15 +499,15 @@
</ins><span class="cx"> if (I){
</span><span class="cx"> GLenum err ;
</span><span class="cx"> glBindAttribLocation(I->id, VERTEX_POS, "a_Vertex");
</span><span class="lines">@@ -30,7 +30,7 @@
</span><span class="cx"> PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Color: %d\n", err ENDFB(G);
</span><span class="cx"> }
</span><span class="cx"> CShaderPrg_Link(I);
</span><del>-@@ -510,19 +510,19 @@ void CShaderPrg_BindCylinderAttribLocati
</del><ins>+@@ -538,19 +538,19 @@
</ins><span class="cx"> if (I){
</span><span class="cx"> GLenum err ;
</span><span class="cx"> glBindAttribLocation(I->id, CYLINDER_ORIGIN, "attr_origin");
</span><span class="lines">@@ -54,7 +54,7 @@
</span><span class="cx"> PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: attr_color2: %d\n", err ENDFB(G);
</span><span class="cx"> }
</span><span class="cx"> CShaderPrg_Link(I);
</span><del>-@@ -842,11 +842,11 @@ void ShaderMgrConfig(PyMOLGlobals * G) {
</del><ins>+@@ -873,11 +873,11 @@
</ins><span class="cx"> if (indicatorShader){
</span><span class="cx"> GLenum err ;
</span><span class="cx"> glBindAttribLocation(indicatorShader->id, VERTEX_POS, "a_Vertex");
</span><span class="lines">@@ -68,25 +68,11 @@
</span><span class="cx"> PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Color: %d\n", err ENDFB(G);
</span><span class="cx"> }
</span><span class="cx"> CShaderPrg_Link(indicatorShader);
</span><del>-Index: layer0/Tetsurf.c
-===================================================================
---- layer0/Tetsurf.c (revision 4039)
-+++ layer0/Tetsurf.c (working copy)
-@@ -679,8 +679,7 @@ static void TetsurfPurge(CTetsurf * II)
- if(I->Tri) {
- VLAFreeP(I->Tri);
- }
-- if(I->PtLink);
-- {
-+ if(I->PtLink) {
- VLAFreeP(I->PtLink);
- }
- if(I->VertexCodes) {
</del><span class="cx"> Index: layer0/Map.c
</span><span class="cx"> ===================================================================
</span><del>---- layer0/Map.c (revision 4039)
</del><ins>+--- layer0/Map.c (revision 4074)
</ins><span class="cx"> +++ layer0/Map.c (working copy)
</span><del>-@@ -588,7 +588,7 @@ int MapSetupExpress(MapType * I)
</del><ins>+@@ -588,7 +588,7 @@
</ins><span class="cx"> register int *link = I->Link;
</span><span class="cx"> register int st, flag;
</span><span class="cx"> register int *i_ptr3, *i_ptr4, *i_ptr5;
</span><span class="lines">@@ -97,9 +83,9 @@
</span><span class="cx"> register int group_id = I->group_id;
</span><span class="cx"> Index: layer1/Basis.c
</span><span class="cx"> ===================================================================
</span><del>---- layer1/Basis.c (revision 4039)
</del><ins>+--- layer1/Basis.c (revision 4074)
</ins><span class="cx"> +++ layer1/Basis.c (working copy)
</span><del>-@@ -2868,11 +2868,11 @@ int BasisMakeMap(CBasis * I, int *vert2p
</del><ins>+@@ -2868,11 +2868,11 @@
</ins><span class="cx"> float ll;
</span><span class="cx"> CPrimitive *prm;
</span><span class="cx"> register int i;
</span><span class="lines">@@ -116,9 +102,9 @@
</span><span class="cx"> * than one voxel, so we have to worry about populating
</span><span class="cx"> Index: layer1/CGO.c
</span><span class="cx"> ===================================================================
</span><del>---- layer1/CGO.c (revision 4039)
</del><ins>+--- layer1/CGO.c (revision 4074)
</ins><span class="cx"> +++ layer1/CGO.c (working copy)
</span><del>-@@ -47,7 +47,7 @@ Z* -------------------------------------
</del><ins>+@@ -47,7 +47,7 @@
</ins><span class="cx"> #define CLIP_NORMAL_VALUE(cv) ((cv>1.f) ? 127 : (cv < -1.f) ? -128 : pymol_roundf(((cv + 1.f)/2.f) * 255) - 128 )
</span><span class="cx">
</span><span class="cx"> #define CHECK_GL_ERROR_OK(printstr) \
</span><span class="lines">@@ -127,7 +113,7 @@
</span><span class="cx"> PRINTFB(I->G, FB_CGO, FB_Errors) printstr, err ENDFB(I->G); \
</span><span class="cx"> }
</span><span class="cx">
</span><del>-@@ -2279,7 +2279,7 @@ void CGOCountNumVerticesForScreen(CGO *I
</del><ins>+@@ -2310,7 +2310,7 @@
</ins><span class="cx"> *num_total_vertices = 0;
</span><span class="cx"> *num_total_indexes = 0;
</span><span class="cx">
</span><span class="lines">@@ -136,7 +122,7 @@
</span><span class="cx"> save_pc = pc;
</span><span class="cx"> err = 0;
</span><span class="cx"> switch (op) {
</span><del>-@@ -4339,7 +4339,7 @@ CGO *CGOOptimizeGLSLCylindersToVBOIndexe
</del><ins>+@@ -4368,7 +4368,7 @@
</ins><span class="cx"> GL_C_INT_TYPE *indexVals = 0;
</span><span class="cx"> int tot = 4 * 4 * 3 * num_total_cylinders;
</span><span class="cx"> short copyToLeftOver, copyColorToLeftOver, copyPickColorToLeftOver, copyAlphaToLeftOver, copyToReturnCGO ;
</span><span class="lines">@@ -145,7 +131,7 @@
</span><span class="cx"> float *org_axisVals;
</span><span class="cx"> float *org_colorVals;
</span><span class="cx"> float *org_color2Vals = NULL;
</span><del>-@@ -7101,7 +7101,7 @@ static void CGO_gl_draw_label(CCGORender
</del><ins>+@@ -7135,7 +7135,7 @@
</ins><span class="cx"> int texture_id = CGO_get_int(*pc);
</span><span class="cx"> float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
</span><span class="cx"> CShaderPrg * shaderPrg;
</span><span class="lines">@@ -154,7 +140,7 @@
</span><span class="cx"> copy3f(*pc, worldPos); worldPos[3] = 1.f;
</span><span class="cx"> copy3f(*pc+3, screenMin);
</span><span class="cx"> copy3f(*pc+6, screenMax);
</span><del>-@@ -7142,7 +7142,7 @@ static void CGO_gl_draw_texture(CCGORend
</del><ins>+@@ -7176,7 +7176,7 @@
</ins><span class="cx"> int texture_id = CGO_get_int(*pc);
</span><span class="cx"> float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
</span><span class="cx"> CShaderPrg * shaderPrg;
</span><span class="lines">@@ -163,7 +149,7 @@
</span><span class="cx"> copy3f(*pc, worldPos); worldPos[3] = 1.f;
</span><span class="cx"> copy3f(*pc+3, screenMin);
</span><span class="cx"> copy3f(*pc+6, screenMax);
</span><del>-@@ -9528,7 +9528,7 @@ int CGOCountNumberCustomCylinders(CGO *I
</del><ins>+@@ -9564,7 +9564,7 @@
</ins><span class="cx"> int CGOChangeShadersTo(CGO *I, int frommode, int tomode){
</span><span class="cx"> register float *pc = I->op;
</span><span class="cx"> int op = 0, totops = 0;
</span><span class="lines">@@ -174,9 +160,9 @@
</span><span class="cx"> case CGO_ENABLE:
</span><span class="cx"> Index: layer1/Ortho.c
</span><span class="cx"> ===================================================================
</span><del>---- layer1/Ortho.c (revision 4039)
</del><ins>+--- layer1/Ortho.c (revision 4074)
</ins><span class="cx"> +++ layer1/Ortho.c (working copy)
</span><del>-@@ -1014,7 +1014,7 @@ void OrthoKey(PyMOLGlobals * G, unsigned
</del><ins>+@@ -1020,7 +1020,7 @@
</ins><span class="cx"> curLine = I->CurLine & OrthoSaveLines;
</span><span class="cx"> if(I->PromptChar) {
</span><span class="cx"> strcpy(buffer, I->Line[curLine]);
</span><span class="lines">@@ -185,7 +171,7 @@
</span><span class="cx"> }
</span><span class="cx"> }
</span><span class="cx"> break;
</span><del>-@@ -1394,7 +1394,7 @@ void bg_grad(PyMOLGlobals * G) {
</del><ins>+@@ -1400,7 +1400,7 @@
</ins><span class="cx">
</span><span class="cx"> {
</span><span class="cx"> if (!I->bgCGO) {
</span><span class="lines">@@ -196,9 +182,54 @@
</span><span class="cx"> ok &= CGOVertex(cgo, -1.f, -1.f, 0.98f);
</span><span class="cx"> Index: layer1/P.c
</span><span class="cx"> ===================================================================
</span><del>---- layer1/P.c (revision 4039)
</del><ins>+--- layer1/P.c (revision 4074)
</ins><span class="cx"> +++ layer1/P.c (working copy)
</span><del>-@@ -2613,7 +2613,7 @@ int PFlush(PyMOLGlobals * G)
</del><ins>+@@ -1464,7 +1464,7 @@
+ void PUnlockAPIAsGlut(PyMOLGlobals * G)
+ { /* must call with unblocked interpreter */
+ PRINTFD(G, FB_Threads)
+- " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident()
++ " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%lx\n", PyThread_get_thread_ident()
+ ENDFD;
+ PBlock(G);
+ PXDecRef(PyObject_CallFunction(G->P_inst->unlock, "iO", 0, G->P_inst->cmd)); /* NOTE this may flush the command buffer! */
+@@ -1478,7 +1478,7 @@
+ void PUnlockAPIAsGlutNoFlush(PyMOLGlobals * G)
+ { /* must call with unblocked interpreter */
+ PRINTFD(G, FB_Threads)
+- " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident()
++ " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%lx\n", PyThread_get_thread_ident()
+ ENDFD;
+ PBlock(G);
+ PXDecRef(PyObject_CallFunction(G->P_inst->unlock, "iO", -1, G->P_inst->cmd)); /* prevents flushing of the buffer */
+@@ -1529,7 +1529,7 @@
+ int PLockAPIAsGlut(PyMOLGlobals * G, int block_if_busy)
+ {
+ PRINTFD(G, FB_Threads)
+- "*PLockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident()
++ "*PLockAPIAsGlut-DEBUG: entered as thread 0x%lx\n", PyThread_get_thread_ident()
+ ENDFD;
+
+ PBlock(G);
+@@ -1541,7 +1541,7 @@
+ PUnlockStatus(G);
+
+ PRINTFD(G, FB_Threads)
+- "#PLockAPIAsGlut-DEBUG: acquiring lock as thread 0x%x\n", PyThread_get_thread_ident()
++ "#PLockAPIAsGlut-DEBUG: acquiring lock as thread 0x%lx\n", PyThread_get_thread_ident()
+ ENDFD;
+
+ if(!get_api_lock(G, block_if_busy)) {
+@@ -1559,7 +1559,7 @@
+ holding the API lock, therefore it is safe even through increment
+ isn't atomic. */
+ PRINTFD(G, FB_Threads)
+- "-PLockAPIAsGlut-DEBUG: glut_thread_keep_out 0x%x\n", PyThread_get_thread_ident()
++ "-PLockAPIAsGlut-DEBUG: glut_thread_keep_out 0x%lx\n", PyThread_get_thread_ident()
+ ENDFD;
+
+ PXDecRef(PyObject_CallFunction(G->P_inst->unlock, "iO", -1, G->P_inst->cmd)); /* prevent buffer flushing */
+@@ -2632,7 +2632,7 @@
</ins><span class="cx"> /* don't run if we're currently banned */
</span><span class="cx"> char *buffer = 0;
</span><span class="cx"> int size, curSize = 0;
</span><span class="lines">@@ -207,7 +238,7 @@
</span><span class="cx"> if (!curSize){
</span><span class="cx"> buffer = VLACalloc(char, size);
</span><span class="cx"> curSize = size;
</span><del>-@@ -2657,7 +2657,7 @@ int PFlushFast(PyMOLGlobals * G)
</del><ins>+@@ -2676,7 +2676,7 @@
</ins><span class="cx"> int did_work = false;
</span><span class="cx"> char *buffer = 0;
</span><span class="cx"> int size, curSize = 0;
</span><span class="lines">@@ -216,11 +247,47 @@
</span><span class="cx"> if (!curSize){
</span><span class="cx"> buffer = VLACalloc(char, size);
</span><span class="cx"> curSize = size;
</span><ins>+@@ -2688,7 +2688,7 @@
+ OrthoCommandNest(G, 1);
+ did_work = true;
+ PRINTFD(G, FB_Threads)
+- " PFlushFast-DEBUG: executing '%s' as thread 0x%x\n", buffer,
++ " PFlushFast-DEBUG: executing '%s' as thread 0x%lx\n", buffer,
+ PyThread_get_thread_ident()
+ ENDFD;
+ if(PyErr_Occurred()) {
+@@ -2784,7 +2784,7 @@
+ PXDecRef(PyObject_CallFunction(G->P_inst->unlock_c, "O", G->P_inst->cmd));
+
+ PRINTFD(G, FB_Threads)
+- " PAutoBlock-DEBUG: blocked 0x%x (0x%x, 0x%x, 0x%x)\n",
++ " PAutoBlock-DEBUG: blocked 0x%lx (0x%x, 0x%x, 0x%x)\n",
+ PyThread_get_thread_ident(), SavedThread[MAX_SAVED_THREAD - 1].id,
+ SavedThread[MAX_SAVED_THREAD - 2].id, SavedThread[MAX_SAVED_THREAD - 3].id ENDFD;
+
+@@ -2793,7 +2793,7 @@
+ a--;
+ }
+ PRINTFD(G, FB_Threads)
+- " PAutoBlock-DEBUG: 0x%x not found, thus already blocked.\n",
++ " PAutoBlock-DEBUG: 0x%lx not found, thus already blocked.\n",
+ PyThread_get_thread_ident()
+ ENDFD;
+ return 0;
+@@ -2814,7 +2814,7 @@
+ SavedThreadRec *SavedThread = G->P_inst->savedThread;
+ /* NOTE: ASSUMES a locked API */
+ PRINTFD(G, FB_Threads)
+- " PUnblock-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident()
++ " PUnblock-DEBUG: entered as thread 0x%lx\n", PyThread_get_thread_ident()
+ ENDFD;
+
+ /* reserve a space while we have a lock */
</ins><span class="cx"> Index: layer1/Extrude.c
</span><span class="cx"> ===================================================================
</span><del>---- layer1/Extrude.c (revision 4039)
</del><ins>+--- layer1/Extrude.c (revision 4074)
</ins><span class="cx"> +++ layer1/Extrude.c (working copy)
</span><del>-@@ -753,7 +753,7 @@ int ExtrudeCGOSurfaceTube(CExtrude * I,
</del><ins>+@@ -687,7 +687,7 @@
</ins><span class="cx"> float *v;
</span><span class="cx"> float *n;
</span><span class="cx"> float *c;
</span><span class="lines">@@ -229,7 +296,7 @@
</span><span class="cx"> float v0[3];
</span><span class="cx"> int start, stop;
</span><span class="cx"> int ok = true;
</span><del>-@@ -1683,7 +1683,7 @@ int ExtrudeCGOSurfacePolygon(CExtrude *
</del><ins>+@@ -1387,7 +1387,7 @@
</ins><span class="cx"> float *v;
</span><span class="cx"> float *n;
</span><span class="cx"> float *c;
</span><span class="lines">@@ -238,25 +305,7 @@
</span><span class="cx"> float v0[3];
</span><span class="cx"> int ok = true;
</span><span class="cx">
</span><del>-@@ -1737,7 +1737,7 @@ int ExtrudeCGOSurfacePolygon(CExtrude *
- for(b = 0; ok && b < I->Ns; b += 2) {
- #ifdef _PYMOL_CGO_DRAWARRAYS
- int nverts = 2*I->N, pl = 0, plc = 0, damode = CGO_VERTEX_ARRAY | CGO_NORMAL_ARRAY | CGO_PICK_COLOR_ARRAY, nxtn = 3;
-- float *vertexVals, *normalVals, *colorVals = 0, *nxtVals = 0, *tmp_ptr;
-+ float *vertexVals = NULL, *normalVals, *colorVals = 0, *nxtVals = 0, *tmp_ptr;
- float *pickColorVals;
- GLenum mode = GL_LINE_STRIP;
- if(SettingGetGlobal_i(I->G, cSetting_cartoon_debug) < 1.5)
-@@ -2048,7 +2048,7 @@ int ExtrudeCGOSurfacePolygonTaper(CExtru
- i = I->i;
- if (ok){
- int nverts = 2*I->N, pl = 0, plc = 0, damode = CGO_VERTEX_ARRAY | CGO_NORMAL_ARRAY | CGO_PICK_COLOR_ARRAY, nxtn = 3;
-- float *vertexVals, *normalVals, *colorVals = 0, *nxtVals = 0, *tmp_ptr;
-+ float *vertexVals = NULL, *normalVals, *colorVals = 0, *nxtVals = 0, *tmp_ptr;
- float *pickColorVals;
- if (color_override)
- ok &= CGOColorv(cgo, color_override);
-@@ -2156,7 +2156,7 @@ int ExtrudeCGOSurfaceStrand(CExtrude * I
</del><ins>+@@ -1705,7 +1705,7 @@
</ins><span class="cx"> float *v;
</span><span class="cx"> float *n;
</span><span class="cx"> float *c;
</span><span class="lines">@@ -267,9 +316,9 @@
</span><span class="cx"> int ok = true;
</span><span class="cx"> Index: layer1/Scene.c
</span><span class="cx"> ===================================================================
</span><del>---- layer1/Scene.c (revision 4039)
</del><ins>+--- layer1/Scene.c (revision 4074)
</ins><span class="cx"> +++ layer1/Scene.c (working copy)
</span><del>-@@ -7640,7 +7640,7 @@ void SceneUpdate(PyMOLGlobals * G, int f
</del><ins>+@@ -7623,7 +7623,7 @@
</ins><span class="cx"> /* update all gadgets first (single-threaded since they're thread-unsafe) */
</span><span class="cx"> rec = NULL;
</span><span class="cx"> while(ListIterate(I->Obj, rec, next)) {
</span><span class="lines">@@ -280,9 +329,9 @@
</span><span class="cx"> }
</span><span class="cx"> Index: layer1/Control.c
</span><span class="cx"> ===================================================================
</span><del>---- layer1/Control.c (revision 4039)
</del><ins>+--- layer1/Control.c (revision 4074)
</ins><span class="cx"> +++ layer1/Control.c (working copy)
</span><del>-@@ -637,7 +637,7 @@ static void ControlDraw(Block * block OR
</del><ins>+@@ -637,7 +637,7 @@
</ins><span class="cx"> but_bottom = y - (cControlBoxSize - 1);
</span><span class="cx"> but_height = cControlBoxSize;
</span><span class="cx">
</span><span class="lines">@@ -291,25 +340,12 @@
</span><span class="cx"> draw_button(but_left, but_bottom,
</span><span class="cx"> but_width, but_height, lightEdge, darkEdge, pushed ORTHOCGOARGVAR);
</span><span class="cx"> } else if(((but_num == 6) && (SettingGetGlobal_b(G, cSetting_seq_view))) ||
</span><del>-Index: layer2/RepCylBond.c
-===================================================================
---- layer2/RepCylBond.c (revision 4039)
-+++ layer2/RepCylBond.c (working copy)
-@@ -1998,7 +1998,7 @@ Rep *RepCylBondNew(CoordSet * cs, int st
- I->NSPC++;
- }
-
-- if(s2 && (!marked[b2]) && (!stick_ball_filter_single_atoms || (ord==1 || adjacent_atoms[a2] && adjacent_atoms[a2][0] > 1))) {
-+ if(s2 && (!marked[b2]) && (!stick_ball_filter_single_atoms || (ord==1 || (adjacent_atoms[a2] && adjacent_atoms[a2][0] > 1)))) {
- /* just once for each atom..., if stick_ball_filter is on, then only for atoms that have more than one adjacent atom */
- float vdw =
- stick_ball_ratio * ((ati2->protons == cAN_H) ? bd_radius : bd_radius_full);
</del><span class="cx"> Index: layer2/RepSphere.c
</span><span class="cx"> ===================================================================
</span><del>---- layer2/RepSphere.c (revision 4039)
</del><ins>+--- layer2/RepSphere.c (revision 4074)
</ins><span class="cx"> +++ layer2/RepSphere.c (working copy)
</span><del>-@@ -1991,8 +1991,8 @@ static void RepSphereRender(RepSphere *
- int a;
</del><ins>+@@ -2204,8 +2204,8 @@
+ int c = I->N;
</ins><span class="cx"> SphereRec *sp = I->SP;
</span><span class="cx"> float alpha;
</span><span class="cx"> - int n_quad_verts;
</span><span class="lines">@@ -321,9 +357,9 @@
</span><span class="cx"> SettingGetGlobal_b(G, cSetting_use_shaders);
</span><span class="cx"> Index: layer2/ObjectMolecule2.c
</span><span class="cx"> ===================================================================
</span><del>---- layer2/ObjectMolecule2.c (revision 4039)
</del><ins>+--- layer2/ObjectMolecule2.c (revision 4074)
</ins><span class="cx"> +++ layer2/ObjectMolecule2.c (working copy)
</span><del>-@@ -3678,7 +3678,7 @@ int ObjectMoleculeNewFromPyList(PyMOLGlo
</del><ins>+@@ -3678,7 +3678,7 @@
</ins><span class="cx"> #else
</span><span class="cx"> int ok = true;
</span><span class="cx"> ObjectMolecule *I = NULL;
</span><span class="lines">@@ -332,7 +368,7 @@
</span><span class="cx"> int ll;
</span><span class="cx"> (*result) = NULL;
</span><span class="cx">
</span><del>-@@ -4305,7 +4305,7 @@ int ObjectMoleculeSort(ObjectMolecule *
</del><ins>+@@ -4305,7 +4305,7 @@
</ins><span class="cx"> register int a, b;
</span><span class="cx"> CoordSet *cs, **dcs;
</span><span class="cx"> AtomInfoType *atInfo;
</span><span class="lines">@@ -343,9 +379,9 @@
</span><span class="cx"> int n_bytes = sizeof(int) * I->NAtom;
</span><span class="cx"> Index: layer2/RepDot.c
</span><span class="cx"> ===================================================================
</span><del>---- layer2/RepDot.c (revision 4039)
</del><ins>+--- layer2/RepDot.c (revision 4074)
</ins><span class="cx"> +++ layer2/RepDot.c (working copy)
</span><del>-@@ -192,7 +192,7 @@ static void RepDotRender(RepDot * I, Ren
</del><ins>+@@ -192,7 +192,7 @@
</ins><span class="cx"> ok &= CGOColorv(cgo, v);
</span><span class="cx"> v += 3;
</span><span class="cx"> }
</span><span class="lines">@@ -354,7 +390,7 @@
</span><span class="cx"> CGONormalv(cgo, v);*/
</span><span class="cx"> v += 3;
</span><span class="cx"> if (ok)
</span><del>-@@ -210,7 +210,7 @@ static void RepDotRender(RepDot * I, Ren
</del><ins>+@@ -210,7 +210,7 @@
</ins><span class="cx"> I->shaderCGO = CGOOptimizeSpheresToVBONonIndexed(cgo, CGO_BOUNDING_BOX_SZ + CGO_DRAW_SPHERE_BUFFERS_SZ);
</span><span class="cx"> CHECKOK(ok, I->shaderCGO);
</span><span class="cx"> } else {
</span><span class="lines">@@ -363,7 +399,7 @@
</span><span class="cx"> CHECKOK(ok, convertcgo);
</span><span class="cx"> if (ok)
</span><span class="cx"> tmpCGO = CGOOptimizeToVBONotIndexed(convertcgo, CGO_BOUNDING_BOX_SZ + I->N * 3 + 7);
</span><del>-@@ -344,7 +344,7 @@ Rep *RepDotDoNew(CoordSet * cs, int mode
</del><ins>+@@ -344,7 +344,7 @@
</ins><span class="cx"> float *countPtr = NULL;
</span><span class="cx"> int colorCnt, lastColor;
</span><span class="cx"> Vector3f v1;
</span><span class="lines">@@ -374,9 +410,9 @@
</span><span class="cx"> float max_vdw = MAX_VDW;
</span><span class="cx"> Index: layer2/RepSurface.c
</span><span class="cx"> ===================================================================
</span><del>---- layer2/RepSurface.c (revision 4039)
</del><ins>+--- layer2/RepSurface.c (revision 4074)
</ins><span class="cx"> +++ layer2/RepSurface.c (working copy)
</span><del>-@@ -3304,7 +3304,7 @@ static void RepSurfaceRender(RepSurface
</del><ins>+@@ -3304,7 +3304,7 @@
</ins><span class="cx"> if (ok)
</span><span class="cx"> convertcgo->use_shader = true;
</span><span class="cx"> } else if (I->Type == 2) {
</span><span class="lines">@@ -385,7 +421,7 @@
</span><span class="cx"> convertcgo2 = CGOConvertLinesToShaderCylinders(I->shaderCGO, 0);
</span><span class="cx"> CHECKOK(ok, convertcgo2);
</span><span class="cx"> if (ok)
</span><del>-@@ -4503,7 +4503,7 @@ static int SurfaceJobRun(PyMOLGlobals *
</del><ins>+@@ -4503,7 +4503,7 @@
</ins><span class="cx"> }
</span><span class="cx"> ok &= !G->Interrupt;
</span><span class="cx"> if(ok) {
</span><span class="lines">@@ -394,7 +430,7 @@
</span><span class="cx"> map = MapNewFlagged(G, I->maxVdw + probe_rad_more,
</span><span class="cx"> I->coord, VLAGetSize(I->coord) / 3, NULL, NULL);
</span><span class="cx"> CHECKOK(ok, map);
</span><del>-@@ -5747,7 +5747,7 @@ static SolventDot *SolventDotNew(PyMOLGl
</del><ins>+@@ -5747,7 +5747,7 @@
</ins><span class="cx"> SurfaceJobAtomInfo *j_atom_info = atom_info + j;
</span><span class="cx"> if(j > a) /* only check if this is atom trails */
</span><span class="cx"> if((!present) || present[j]) {
</span><span class="lines">@@ -403,7 +439,7 @@
</span><span class="cx"> float *v1 = coord + 3 * j;
</span><span class="cx"> if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] == v1[2]))
</span><span class="cx"> skip_flag = true;
</span><del>-@@ -5842,7 +5842,7 @@ static SolventDot *SolventDotNew(PyMOLGl
</del><ins>+@@ -5842,7 +5842,7 @@
</ins><span class="cx"> SurfaceJobAtomInfo *j_atom_info = atom_info + j;
</span><span class="cx"> if(j > a) /* only check if this is atom trails */
</span><span class="cx"> if((!present) || present[j]) {
</span><span class="lines">@@ -412,7 +448,7 @@
</span><span class="cx"> float *v2 = coord + 3 * j;
</span><span class="cx"> if((v0[0] == v2[0]) && (v0[1] == v2[1]) && (v0[2] == v2[2]))
</span><span class="cx"> skip_flag = true;
</span><del>-@@ -6002,7 +6002,7 @@ static SolventDot *SolventDotNew(PyMOLGl
</del><ins>+@@ -6002,7 +6002,7 @@
</ins><span class="cx"> SurfaceJobAtomInfo *j_atom_info = atom_info + j;
</span><span class="cx"> if(j > a) /* only check if this is atom trails */
</span><span class="cx"> if((!present) || present[j]) {
</span><span class="lines">@@ -423,9 +459,9 @@
</span><span class="cx"> skip_flag = true;
</span><span class="cx"> Index: layer2/RepCartoon.c
</span><span class="cx"> ===================================================================
</span><del>---- layer2/RepCartoon.c (revision 4039)
</del><ins>+--- layer2/RepCartoon.c (revision 4074)
</ins><span class="cx"> +++ layer2/RepCartoon.c (working copy)
</span><del>-@@ -2615,7 +2615,7 @@ CGO *GenerateRepCartoonCGO(CoordSet *cs,
</del><ins>+@@ -2615,7 +2615,7 @@
</ins><span class="cx">
</span><span class="cx"> #ifdef _PYMOL_CGO_DRAWARRAYS
</span><span class="cx"> int nverts = nAt * 4, pl = 0;
</span><span class="lines">@@ -436,9 +472,9 @@
</span><span class="cx"> CHECKOK(ok, vertexVals);
</span><span class="cx"> Index: layer2/ObjectMolecule.c
</span><span class="cx"> ===================================================================
</span><del>---- layer2/ObjectMolecule.c (revision 4039)
</del><ins>+--- layer2/ObjectMolecule.c (revision 4074)
</ins><span class="cx"> +++ layer2/ObjectMolecule.c (working copy)
</span><del>-@@ -1448,7 +1448,7 @@ CoordSet *ObjectMoleculeTOPStr2CoordSet(
</del><ins>+@@ -1448,7 +1448,7 @@
</ins><span class="cx"> int NPHIH, MPHIA, NHPARM, NPARM, NNB, NRES;
</span><span class="cx"> int NBONA, NTHETA, NPHIA, NUMBND, NUMANG, NPTRA;
</span><span class="cx"> int NATYP, NPHB, IFPERT, NBPER, NGPER, NDPER;
</span><span class="lines">@@ -447,7 +483,7 @@
</span><span class="cx"> int NEXTRA, IPOL = 0;
</span><span class="cx"> int wid, col;
</span><span class="cx"> float BETA;
</span><del>-@@ -2076,7 +2076,7 @@ CoordSet *ObjectMoleculeTOPStr2CoordSet(
</del><ins>+@@ -2076,7 +2076,7 @@
</ins><span class="cx">
</span><span class="cx"> if(IFBOX > 0) {
</span><span class="cx">
</span><span class="lines">@@ -456,7 +492,7 @@
</span><span class="cx">
</span><span class="cx"> if(amber7) {
</span><span class="cx"> p = findflag(G, buffer, "SOLVENT_POINTERS", "3I8");
</span><del>-@@ -4431,7 +4431,7 @@ int ObjectMoleculeAttach(ObjectMolecule
</del><ins>+@@ -4431,7 +4431,7 @@
</ins><span class="cx"> AtomInfoType *ai;
</span><span class="cx"> int n, nn;
</span><span class="cx"> float v[3], v0[3], d;
</span><span class="lines">@@ -465,7 +501,7 @@
</span><span class="cx"> int ok = true;
</span><span class="cx">
</span><span class="cx"> ok &= ObjectMoleculeUpdateNeighbors(I);
</span><del>-@@ -9755,7 +9755,7 @@ int ObjectMoleculeMerge(ObjectMolecule *
</del><ins>+@@ -9767,7 +9767,7 @@
</ins><span class="cx"> CoordSet * cs, int bondSearchFlag, int aic_mask, int invalidate)
</span><span class="cx"> {
</span><span class="cx"> PyMOLGlobals *G = I->Obj.G;
</span><span class="lines">@@ -474,7 +510,7 @@
</span><span class="cx"> BondType *bond = NULL;
</span><span class="cx"> register int a, b, lb = 0, ac;
</span><span class="cx"> int c, nb, a1, a2;
</span><del>-@@ -10539,7 +10539,7 @@ void ObjectMoleculeSeleOp(ObjectMolecule
</del><ins>+@@ -10551,7 +10551,7 @@
</ins><span class="cx"> rms = MatrixFitRMSTTTf(G, op->nvv1, op->vv1, vt, NULL, op->ttt);
</span><span class="cx"> else
</span><span class="cx"> rms = MatrixGetRMS(G, op->nvv1, op->vv1, vt, NULL);
</span><span class="lines">@@ -485,9 +521,9 @@
</span><span class="cx"> if(op->i3) {
</span><span class="cx"> Index: layer3/Selector.c
</span><span class="cx"> ===================================================================
</span><del>---- layer3/Selector.c (revision 4039)
</del><ins>+--- layer3/Selector.c (revision 4074)
</ins><span class="cx"> +++ layer3/Selector.c (working copy)
</span><del>-@@ -8615,11 +8615,11 @@ static int SelectorSelect0(PyMOLGlobals
</del><ins>+@@ -8658,11 +8658,11 @@
</ins><span class="cx"> for(a = cNDummyAtoms; a < I->NAtom; a++) {
</span><span class="cx"> b = i_obj[i_table[a].model]->AtomInfo[i_table[a].atom].protons;
</span><span class="cx"> base[0].sele[a] = (
</span><span class="lines">@@ -506,9 +542,9 @@
</span><span class="cx"> break;
</span><span class="cx"> Index: layer3/Executive.c
</span><span class="cx"> ===================================================================
</span><del>---- layer3/Executive.c (revision 4039)
</del><ins>+--- layer3/Executive.c (revision 4074)
</ins><span class="cx"> +++ layer3/Executive.c (working copy)
</span><del>-@@ -15915,7 +15915,7 @@ static int ExecutiveDrag(Block * block,
</del><ins>+@@ -15928,7 +15928,7 @@
</ins><span class="cx"> ExecutiveSpecSetVisibility(G, rec, true, mod, false);
</span><span class="cx"> I->LastChanged = rec;
</span><span class="cx"> }
</span><span class="lines">@@ -519,9 +555,9 @@
</span><span class="cx"> true);
</span><span class="cx"> Index: layer3/PlugIOManager.c
</span><span class="cx"> ===================================================================
</span><del>---- layer3/PlugIOManager.c (revision 4039)
</del><ins>+--- layer3/PlugIOManager.c (revision 4074)
</ins><span class="cx"> +++ layer3/PlugIOManager.c (working copy)
</span><del>-@@ -225,7 +225,7 @@ int PlugIOManagerLoadTraj(PyMOLGlobals *
</del><ins>+@@ -229,7 +229,7 @@
</ins><span class="cx"> ENDFB(G);
</span><span class="cx"> }
</span><span class="cx">
</span><span class="lines">@@ -532,9 +568,45 @@
</span><span class="cx"> }
</span><span class="cx"> Index: layer4/Cmd.c
</span><span class="cx"> ===================================================================
</span><del>---- layer4/Cmd.c (revision 4039)
</del><ins>+--- layer4/Cmd.c (revision 4074)
</ins><span class="cx"> +++ layer4/Cmd.c (working copy)
</span><del>-@@ -1846,7 +1846,7 @@ static PyObject *CmdMapHalve(PyObject *
</del><ins>+@@ -128,7 +128,7 @@
+ static void APIEnter(PyMOLGlobals * G)
+ { /* assumes API is locked */
+ PRINTFD(G, FB_API)
+- " APIEnter-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident()
++ " APIEnter-DEBUG: as thread 0x%lx.\n", PyThread_get_thread_ident()
+ ENDFD;
+
+ if(G->Terminating) { /* try to bail */
+@@ -163,7 +163,7 @@
+ { /* assumes API is locked */
+
+ PRINTFD(G, FB_API)
+- " APIEnterBlocked-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident()
++ " APIEnterBlocked-DEBUG: as thread 0x%lx.\n", PyThread_get_thread_ident()
+ ENDFD;
+
+ if(G->Terminating) { /* try to bail */
+@@ -199,7 +199,7 @@
+ if(!PIsGlutThread())
+ G->P_inst->glut_thread_keep_out--;
+ PRINTFD(G, FB_API)
+- " APIExit-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident()
++ " APIExit-DEBUG: as thread 0x%lx.\n", PyThread_get_thread_ident()
+ ENDFD;
+ }
+
+@@ -209,7 +209,7 @@
+ if(!PIsGlutThread())
+ G->P_inst->glut_thread_keep_out--;
+ PRINTFD(G, FB_API)
+- " APIExitBlocked-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident()
++ " APIExitBlocked-DEBUG: as thread 0x%lx.\n", PyThread_get_thread_ident()
+ ENDFD;
+ }
+
+@@ -1853,7 +1853,7 @@
</ins><span class="cx"> static PyObject *CmdGetRenderer(PyObject * self, PyObject * args)
</span><span class="cx"> {
</span><span class="cx"> PyMOLGlobals *G = NULL;
</span><span class="lines">@@ -545,9 +617,9 @@
</span><span class="cx"> if(ok) {
</span><span class="cx"> Index: contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp
</span><span class="cx"> ===================================================================
</span><del>---- contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp (revision 4039)
</del><ins>+--- contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp (revision 4074)
</ins><span class="cx"> +++ contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp (working copy)
</span><del>-@@ -259,7 +259,7 @@ static int read_pbeq_data(void *v, int s
</del><ins>+@@ -259,7 +259,7 @@
</ins><span class="cx"> int addr = z*nclx*ncly + y*nclx + x;
</span><span class="cx"> if (fread(datablock + addr, 4, 1, fd) != 1) {
</span><span class="cx"> printf("pbeqplugin) Error reading potential map cell: %d,%d,%d\n", x, y, z);
</span><span class="lines">@@ -556,11 +628,51 @@
</span><span class="cx"> return MOLFILE_ERROR;
</span><span class="cx"> }
</span><span class="cx"> count++;
</span><ins>+Index: contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp
+===================================================================
+--- contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp (revision 4074)
++++ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp (working copy)
+@@ -484,7 +484,7 @@
+ /* constant frame size */
+ if (keys[i].size() != m_framesize) {
+ fprintf(stderr, "non-constant framesize at frame %ld\n", i);
+- printf("size %d framesize %d\n\n",
++ printf("size %lld framesize %lld\n\n",
+ keys[i].size(), m_framesize);
+ return true;
+ }
+@@ -1298,7 +1298,7 @@
+ }
+ Blob pos=blobs["POSITION"];
+ if (pos.count != 3*natoms) {
+- fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n",
++ fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %lld\n",
+ 3*natoms, pos.count);
+ return MOLFILE_ERROR;
+ }
+@@ -1307,7 +1307,7 @@
+ if (with_velocity && ts->velocities && blobs.find("VELOCITY")!=blobs.end()) {
+ Blob vel=blobs["VELOCITY"];
+ if (vel.count != 3*natoms) {
+- fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n",
++ fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %lld\n",
+ 3*natoms, vel.count);
+ return MOLFILE_ERROR;
+ }
+@@ -1569,7 +1569,7 @@
+ // if required, get velocities
+ if (ts->velocities && velblob.count > 0) {
+ if (velblob.count != 3*natoms) {
+- fprintf(stderr, "VELOCITY field has %ld values; expected %d\n",
++ fprintf(stderr, "VELOCITY field has %lld values; expected %d\n",
+ velblob.count, 3*natoms);
+ return MOLFILE_ERROR;
+ }
</ins><span class="cx"> Index: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c
</span><span class="cx"> ===================================================================
</span><del>---- contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c (revision 4039)
</del><ins>+--- contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c (revision 4074)
</ins><span class="cx"> +++ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c (working copy)
</span><del>-@@ -99,7 +99,7 @@ static void *open_molden_read(const char
</del><ins>+@@ -99,7 +99,7 @@
</ins><span class="cx"> const char *filetype,
</span><span class="cx"> int *natoms) {
</span><span class="cx"> FILE *fd;
</span><span class="lines">@@ -569,11 +681,78 @@
</span><span class="cx"> moldendata_t *moldendata;
</span><span class="cx"> char buffer[1024];
</span><span class="cx"> char keystring[20];
</span><ins>+Index: contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c
+===================================================================
+--- contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c (revision 4074)
++++ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c (working copy)
+@@ -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;
+ }
</ins><span class="cx"> Index: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c
</span><span class="cx"> ===================================================================
</span><del>---- contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c (revision 4039)
</del><ins>+--- contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c (revision 4074)
</ins><span class="cx"> +++ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c (working copy)
</span><del>-@@ -375,7 +375,7 @@ static void *open_gamess_read(const char
</del><ins>+@@ -375,7 +375,7 @@
</ins><span class="cx"> const char *filetype, int *natoms) {
</span><span class="cx">
</span><span class="cx"> FILE *fd;
</span><span class="lines">@@ -584,9 +763,9 @@
</span><span class="cx"> /* open the input file */
</span><span class="cx"> Index: contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
</span><span class="cx"> ===================================================================
</span><del>---- contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp (revision 4039)
</del><ins>+--- contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp (revision 4074)
</ins><span class="cx"> +++ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp (working copy)
</span><del>-@@ -1983,7 +1983,7 @@ namespace {
</del><ins>+@@ -1983,7 +1983,7 @@
</ins><span class="cx"> }
</span><span class="cx"> }
</span><span class="cx"> catch (std::exception &e) {
</span><span class="lines">@@ -597,9 +776,9 @@
</span><span class="cx"> return MOLFILE_SUCCESS;
</span><span class="cx"> Index: contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp
</span><span class="cx"> ===================================================================
</span><del>---- contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp (revision 4039)
</del><ins>+--- contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp (revision 4074)
</ins><span class="cx"> +++ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp (working copy)
</span><del>-@@ -104,7 +104,7 @@ void Get_Property_Values(GRASSP *grassp,
</del><ins>+@@ -104,7 +104,7 @@
</ins><span class="cx">
</span><span class="cx"> ///ojo aqui le quite el !
</span><span class="cx"> if ((grassp->flag)!=POTENTIALS) {
</span><span class="lines">@@ -610,9 +789,9 @@
</span><span class="cx"> printf("graspplugin) out of range property, flag: %d index: %d\n", grassp->flag, index);
</span><span class="cx"> Index: modules/cealign/src/tnt/tnt_fortran_array1d.h
</span><span class="cx"> ===================================================================
</span><del>---- modules/cealign/src/tnt/tnt_fortran_array1d.h (revision 4039)
</del><ins>+--- modules/cealign/src/tnt/tnt_fortran_array1d.h (revision 4074)
</ins><span class="cx"> +++ modules/cealign/src/tnt/tnt_fortran_array1d.h (working copy)
</span><del>-@@ -221,7 +221,7 @@ inline Fortran_Array1D<T> Fortran_Array1
</del><ins>+@@ -221,7 +221,7 @@
</ins><span class="cx"> #ifdef TNT_DEBUG
</span><span class="cx"> std::cout << "entered subarray. \n";
</span><span class="cx"> #endif
</span><span class="lines">@@ -623,9 +802,9 @@
</span><span class="cx"> X.n_ = i1-i0+1;
</span><span class="cx"> Index: modules/cealign/src/tnt/tnt_array1d.h
</span><span class="cx"> ===================================================================
</span><del>---- modules/cealign/src/tnt/tnt_array1d.h (revision 4039)
</del><ins>+--- modules/cealign/src/tnt/tnt_array1d.h (revision 4074)
</ins><span class="cx"> +++ modules/cealign/src/tnt/tnt_array1d.h (working copy)
</span><del>-@@ -258,7 +258,7 @@ inline int Array1D<T>::ref_count() const
</del><ins>+@@ -258,7 +258,7 @@
</ins><span class="cx"> template <class T>
</span><span class="cx"> inline Array1D<T> Array1D<T>::subarray(int i0, int i1)
</span><span class="cx"> {
</span></span></pre></div>
<a id="trunkdportssciencepymolfilessetup_pydiff"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/pymol/files/setup_py.diff (120406 => 120407)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/files/setup_py.diff 2014-05-27 19:49:21 UTC (rev 120406)
+++ trunk/dports/science/pymol/files/setup_py.diff 2014-05-27 19:53:32 UTC (rev 120407)
</span><span class="lines">@@ -1,5 +1,5 @@
</span><del>---- setup.py.orig
-+++ setup.py
</del><ins>+--- setup.py.orig 2014-05-24 16:55:05.000000000 -0400
++++ setup.py 2014-05-24 17:00:43.000000000 -0400
</ins><span class="cx"> @@ -47,18 +47,6 @@
</span><span class="cx"> pmap(_single_compile, objects)
</span><span class="cx"> return objects
</span><span class="lines">@@ -12,14 +12,14 @@
</span><span class="cx"> - import argparse
</span><span class="cx"> - parser = argparse.ArgumentParser()
</span><span class="cx"> - parser.add_argument('--osx-frameworks', action="store_true")
</span><del>-- options, sys.argv = parser.parse_known_args(namespace=options)
</del><ins>+- options, sys.argv[1:] = parser.parse_known_args(namespace=options)
</ins><span class="cx"> -except ImportError:
</span><span class="cx"> - print "argparse not available"
</span><span class="cx"> -
</span><span class="cx"> jobs = int(os.getenv('JOBS', 0))
</span><span class="cx"> pmap = map if jobs == 1 else multiprocessing.pool.ThreadPool(jobs or None).map
</span><span class="cx">
</span><del>-@@ -246,22 +234,17 @@
</del><ins>+@@ -242,22 +230,17 @@
</ins><span class="cx"> try:
</span><span class="cx"> prefix_path = os.environ['PREFIX_PATH'].split(os.pathsep)
</span><span class="cx"> except KeyError:
</span></span></pre>
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