[120407] trunk/dports/science/pymol

ryandesign at macports.org ryandesign at macports.org
Tue May 27 12:53:33 PDT 2014


Revision: 120407
          https://trac.macports.org/changeset/120407
Author:   ryandesign at macports.org
Date:     2014-05-27 12:53:32 -0700 (Tue, 27 May 2014)
Log Message:
-----------
pymol: maintainer update to 1.7.1.1 (#43824)

Modified Paths:
--------------
    trunk/dports/science/pymol/Portfile
    trunk/dports/science/pymol/files/pymol-clang.diff
    trunk/dports/science/pymol/files/setup_py.diff

Modified: trunk/dports/science/pymol/Portfile
===================================================================
--- 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)
@@ -6,8 +6,7 @@
 PortGroup           active_variants 1.1
 
 name                pymol
-version             1.6.0
-revision            1
+version             1.7.1.1
 categories          science chemistry
 license             GPL
 maintainers         bromo.med.uc.edu:howarth
@@ -23,7 +22,7 @@
 master_sites        sourceforge
 fetch.type          svn
 svn.url             https://svn.code.sf.net/p/pymol/code/trunk/pymol
-svn.revision        4039
+svn.revision        4074
 worksrcdir          pymol
 
 python.default_version 27
@@ -56,6 +55,7 @@
     reinplace  "s|@PREFIX@|${prefix}|g" ${worksrcpath}/setup.py
     reinplace  "s|@@PYTHON_PKGDIR@@|${python.pkgd}|g" ${worksrcpath}/setup/pymol_macports
     reinplace  "s|@@PYTHON_BINARY@@|${python.bin}|g" ${worksrcpath}/setup/pymol_macports
+    reinplace  "s|\"-O3\",|\"-O3\", \"-g\",|g" ${worksrcpath}/setup.py
 }
 
 use_parallel_build yes

Modified: trunk/dports/science/pymol/files/pymol-clang.diff
===================================================================
--- 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)
@@ -1,8 +1,8 @@
 Index: layer0/ShaderMgr.c
 ===================================================================
---- layer0/ShaderMgr.c	(revision 4039)
+--- layer0/ShaderMgr.c	(revision 4074)
 +++ layer0/ShaderMgr.c	(working copy)
-@@ -150,7 +150,7 @@ void CShaderPrg_ReplaceStringsInPlace(Py
+@@ -151,7 +151,7 @@
      while (replaceStrings[i]){
        slen = strlen(replaceStrings[i]);
        rlen = strlen(replaceStrings[i+1]);
@@ -11,7 +11,7 @@
  	strcpy(tmp_line, rstr + slen);
  	strcpy(rstr, replaceStrings[i+1]);
  	strcpy(rstr+rlen, tmp_line);
-@@ -488,15 +488,15 @@ void CShaderPrg_BindAttribLocations(PyMO
+@@ -499,15 +499,15 @@
    if (I){
      GLenum err ;
      glBindAttribLocation(I->id, VERTEX_POS, "a_Vertex");
@@ -30,7 +30,7 @@
        PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Color: %d\n", err ENDFB(G);
      }
      CShaderPrg_Link(I);
-@@ -510,19 +510,19 @@ void CShaderPrg_BindCylinderAttribLocati
+@@ -538,19 +538,19 @@
    if (I){
      GLenum err ;
      glBindAttribLocation(I->id, CYLINDER_ORIGIN, "attr_origin");
@@ -54,7 +54,7 @@
        PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: attr_color2: %d\n", err ENDFB(G);
      }
      CShaderPrg_Link(I);	  
-@@ -842,11 +842,11 @@ void ShaderMgrConfig(PyMOLGlobals * G) {
+@@ -873,11 +873,11 @@
      if (indicatorShader){
        GLenum err ;
        glBindAttribLocation(indicatorShader->id, VERTEX_POS, "a_Vertex");
@@ -68,25 +68,11 @@
  	PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Color: %d\n", err ENDFB(G);
        }
        CShaderPrg_Link(indicatorShader);	
-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) {
 Index: layer0/Map.c
 ===================================================================
---- layer0/Map.c	(revision 4039)
+--- layer0/Map.c	(revision 4074)
 +++ layer0/Map.c	(working copy)
-@@ -588,7 +588,7 @@ int MapSetupExpress(MapType * I)
+@@ -588,7 +588,7 @@
    register int *link = I->Link;
    register int st, flag;
    register int *i_ptr3, *i_ptr4, *i_ptr5;
@@ -97,9 +83,9 @@
    register int group_id = I->group_id;
 Index: layer1/Basis.c
 ===================================================================
---- layer1/Basis.c	(revision 4039)
+--- layer1/Basis.c	(revision 4074)
 +++ layer1/Basis.c	(working copy)
-@@ -2868,11 +2868,11 @@ int BasisMakeMap(CBasis * I, int *vert2p
+@@ -2868,11 +2868,11 @@
    float ll;
    CPrimitive *prm;
    register int i;
@@ -116,9 +102,9 @@
                                   * than one voxel, so we have to worry about populating
 Index: layer1/CGO.c
 ===================================================================
---- layer1/CGO.c	(revision 4039)
+--- layer1/CGO.c	(revision 4074)
 +++ layer1/CGO.c	(working copy)
-@@ -47,7 +47,7 @@ Z* -------------------------------------
+@@ -47,7 +47,7 @@
  #define CLIP_NORMAL_VALUE(cv)  ((cv>1.f) ? 127 :  (cv < -1.f) ? -128 : pymol_roundf(((cv + 1.f)/2.f) * 255) - 128 )
  
  #define CHECK_GL_ERROR_OK(printstr)	\
@@ -127,7 +113,7 @@
       PRINTFB(I->G, FB_CGO, FB_Errors) printstr, err ENDFB(I->G);	   \
    }
  
-@@ -2279,7 +2279,7 @@ void CGOCountNumVerticesForScreen(CGO *I
+@@ -2310,7 +2310,7 @@
    *num_total_vertices = 0;
    *num_total_indexes = 0;
  
@@ -136,7 +122,7 @@
      save_pc = pc;
      err = 0;
      switch (op) {
-@@ -4339,7 +4339,7 @@ CGO *CGOOptimizeGLSLCylindersToVBOIndexe
+@@ -4368,7 +4368,7 @@
      GL_C_INT_TYPE *indexVals = 0;
      int tot = 4 * 4 * 3 * num_total_cylinders;
      short copyToLeftOver, copyColorToLeftOver, copyPickColorToLeftOver, copyAlphaToLeftOver, copyToReturnCGO ;
@@ -145,7 +131,7 @@
      float *org_axisVals;
      float *org_colorVals;
      float *org_color2Vals = NULL;
-@@ -7101,7 +7101,7 @@ static void CGO_gl_draw_label(CCGORender
+@@ -7135,7 +7135,7 @@
    int  texture_id = CGO_get_int(*pc);
    float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
    CShaderPrg * shaderPrg;
@@ -154,7 +140,7 @@
    copy3f(*pc, worldPos);  worldPos[3] = 1.f;
    copy3f(*pc+3, screenMin);
    copy3f(*pc+6, screenMax);
-@@ -7142,7 +7142,7 @@ static void CGO_gl_draw_texture(CCGORend
+@@ -7176,7 +7176,7 @@
    int  texture_id = CGO_get_int(*pc);
    float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
    CShaderPrg * shaderPrg;
@@ -163,7 +149,7 @@
    copy3f(*pc, worldPos);  worldPos[3] = 1.f;
    copy3f(*pc+3, screenMin);
    copy3f(*pc+6, screenMax);
-@@ -9528,7 +9528,7 @@ int CGOCountNumberCustomCylinders(CGO *I
+@@ -9564,7 +9564,7 @@
  int CGOChangeShadersTo(CGO *I, int frommode, int tomode){
    register float *pc = I->op;
    int op = 0, totops = 0;
@@ -174,9 +160,9 @@
      case CGO_ENABLE:
 Index: layer1/Ortho.c
 ===================================================================
---- layer1/Ortho.c	(revision 4039)
+--- layer1/Ortho.c	(revision 4074)
 +++ layer1/Ortho.c	(working copy)
-@@ -1014,7 +1014,7 @@ void OrthoKey(PyMOLGlobals * G, unsigned
+@@ -1020,7 +1020,7 @@
          curLine = I->CurLine & OrthoSaveLines;
          if(I->PromptChar) {
            strcpy(buffer, I->Line[curLine]);
@@ -185,7 +171,7 @@
          }
        }
        break;
-@@ -1394,7 +1394,7 @@ void bg_grad(PyMOLGlobals * G) {
+@@ -1400,7 +1400,7 @@
  
    {
      if (!I->bgCGO) {
@@ -196,9 +182,54 @@
  	ok &= CGOVertex(cgo, -1.f, -1.f, 0.98f);
 Index: layer1/P.c
 ===================================================================
---- layer1/P.c	(revision 4039)
+--- layer1/P.c	(revision 4074)
 +++ layer1/P.c	(working copy)
-@@ -2613,7 +2613,7 @@ int PFlush(PyMOLGlobals * G)
+@@ -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 @@
        /* don't run if we're currently banned */
        char *buffer = 0;
        int size, curSize = 0;
@@ -207,7 +238,7 @@
  	if (!curSize){
  	  buffer = VLACalloc(char, size);
  	  curSize = size;
-@@ -2657,7 +2657,7 @@ int PFlushFast(PyMOLGlobals * G)
+@@ -2676,7 +2676,7 @@
    int did_work = false;
    char *buffer = 0;
    int size, curSize = 0;
@@ -216,11 +247,47 @@
      if (!curSize){
        buffer = VLACalloc(char, size);
        curSize = size;
+@@ -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 */
 Index: layer1/Extrude.c
 ===================================================================
---- layer1/Extrude.c	(revision 4039)
+--- layer1/Extrude.c	(revision 4074)
 +++ layer1/Extrude.c	(working copy)
-@@ -753,7 +753,7 @@ int ExtrudeCGOSurfaceTube(CExtrude * I, 
+@@ -687,7 +687,7 @@
    float *v;
    float *n;
    float *c;
@@ -229,7 +296,7 @@
    float v0[3];
    int start, stop;
    int ok = true;
-@@ -1683,7 +1683,7 @@ int ExtrudeCGOSurfacePolygon(CExtrude * 
+@@ -1387,7 +1387,7 @@
    float *v;
    float *n;
    float *c;
@@ -238,25 +305,7 @@
    float v0[3];
    int ok = true;
  
-@@ -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
+@@ -1705,7 +1705,7 @@
    float *v;
    float *n;
    float *c;
@@ -267,9 +316,9 @@
    int ok = true;
 Index: layer1/Scene.c
 ===================================================================
---- layer1/Scene.c	(revision 4039)
+--- layer1/Scene.c	(revision 4074)
 +++ layer1/Scene.c	(working copy)
-@@ -7640,7 +7640,7 @@ void SceneUpdate(PyMOLGlobals * G, int f
+@@ -7623,7 +7623,7 @@
        /* update all gadgets first (single-threaded since they're thread-unsafe) */
        rec = NULL;
        while(ListIterate(I->Obj, rec, next)) {
@@ -280,9 +329,9 @@
          }
 Index: layer1/Control.c
 ===================================================================
---- layer1/Control.c	(revision 4039)
+--- layer1/Control.c	(revision 4074)
 +++ layer1/Control.c	(working copy)
-@@ -637,7 +637,7 @@ static void ControlDraw(Block * block OR
+@@ -637,7 +637,7 @@
        but_bottom = y - (cControlBoxSize - 1);
        but_height = cControlBoxSize;
  
@@ -291,25 +340,12 @@
          draw_button(but_left, but_bottom,
                      but_width, but_height, lightEdge, darkEdge, pushed ORTHOCGOARGVAR);
        } else if(((but_num == 6) && (SettingGetGlobal_b(G, cSetting_seq_view))) ||
-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);
 Index: layer2/RepSphere.c
 ===================================================================
---- layer2/RepSphere.c	(revision 4039)
+--- layer2/RepSphere.c	(revision 4074)
 +++ layer2/RepSphere.c	(working copy)
-@@ -1991,8 +1991,8 @@ static void RepSphereRender(RepSphere * 
-   int a;
+@@ -2204,8 +2204,8 @@
+   int c = I->N;
    SphereRec *sp = I->SP;
    float alpha;
 -  int n_quad_verts;
@@ -321,9 +357,9 @@
                       SettingGetGlobal_b(G, cSetting_use_shaders);
 Index: layer2/ObjectMolecule2.c
 ===================================================================
---- layer2/ObjectMolecule2.c	(revision 4039)
+--- layer2/ObjectMolecule2.c	(revision 4074)
 +++ layer2/ObjectMolecule2.c	(working copy)
-@@ -3678,7 +3678,7 @@ int ObjectMoleculeNewFromPyList(PyMOLGlo
+@@ -3678,7 +3678,7 @@
  #else
    int ok = true;
    ObjectMolecule *I = NULL;
@@ -332,7 +368,7 @@
    int ll;
    (*result) = NULL;
  
-@@ -4305,7 +4305,7 @@ int ObjectMoleculeSort(ObjectMolecule * 
+@@ -4305,7 +4305,7 @@
    register int a, b;
    CoordSet *cs, **dcs;
    AtomInfoType *atInfo;
@@ -343,9 +379,9 @@
      int n_bytes = sizeof(int) * I->NAtom;
 Index: layer2/RepDot.c
 ===================================================================
---- layer2/RepDot.c	(revision 4039)
+--- layer2/RepDot.c	(revision 4074)
 +++ layer2/RepDot.c	(working copy)
-@@ -192,7 +192,7 @@ static void RepDotRender(RepDot * I, Ren
+@@ -192,7 +192,7 @@
  	      ok &= CGOColorv(cgo, v);
  	      v += 3;
  	    }
@@ -354,7 +390,7 @@
                     CGONormalv(cgo, v);*/
  	    v += 3;
  	    if (ok)
-@@ -210,7 +210,7 @@ static void RepDotRender(RepDot * I, Ren
+@@ -210,7 +210,7 @@
  	    I->shaderCGO = CGOOptimizeSpheresToVBONonIndexed(cgo, CGO_BOUNDING_BOX_SZ + CGO_DRAW_SPHERE_BUFFERS_SZ);
  	    CHECKOK(ok, I->shaderCGO);
  	  } else {
@@ -363,7 +399,7 @@
  	    CHECKOK(ok, convertcgo);
  	    if (ok)
  	      tmpCGO = CGOOptimizeToVBONotIndexed(convertcgo, CGO_BOUNDING_BOX_SZ + I->N * 3 + 7);
-@@ -344,7 +344,7 @@ Rep *RepDotDoNew(CoordSet * cs, int mode
+@@ -344,7 +344,7 @@
    float *countPtr = NULL;
    int colorCnt, lastColor;
    Vector3f v1;
@@ -374,9 +410,9 @@
    float max_vdw = MAX_VDW;
 Index: layer2/RepSurface.c
 ===================================================================
---- layer2/RepSurface.c	(revision 4039)
+--- layer2/RepSurface.c	(revision 4074)
 +++ layer2/RepSurface.c	(working copy)
-@@ -3304,7 +3304,7 @@ static void RepSurfaceRender(RepSurface 
+@@ -3304,7 +3304,7 @@
  	    if (ok)
  	      convertcgo->use_shader = true;
  	  } else if (I->Type == 2) {
@@ -385,7 +421,7 @@
  	    convertcgo2 = CGOConvertLinesToShaderCylinders(I->shaderCGO, 0);
  	    CHECKOK(ok, convertcgo2);
  	    if (ok)
-@@ -4503,7 +4503,7 @@ static int SurfaceJobRun(PyMOLGlobals * 
+@@ -4503,7 +4503,7 @@
          }
  	ok &= !G->Interrupt;
          if(ok) {
@@ -394,7 +430,7 @@
            map = MapNewFlagged(G, I->maxVdw + probe_rad_more,
                                I->coord, VLAGetSize(I->coord) / 3, NULL, NULL);
  	  CHECKOK(ok, map);
-@@ -5747,7 +5747,7 @@ static SolventDot *SolventDotNew(PyMOLGl
+@@ -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]) {
@@ -403,7 +439,7 @@
                        float *v1 = coord + 3 * j;
                        if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] == v1[2]))
                          skip_flag = true;
-@@ -5842,7 +5842,7 @@ static SolventDot *SolventDotNew(PyMOLGl
+@@ -5842,7 +5842,7 @@
                    SurfaceJobAtomInfo *j_atom_info = atom_info + j;
                    if(j > a)     /* only check if this is atom trails */
                      if((!present) || present[j]) {
@@ -412,7 +448,7 @@
                          float *v2 = coord + 3 * j;
                          if((v0[0] == v2[0]) && (v0[1] == v2[1]) && (v0[2] == v2[2]))
                            skip_flag = true;
-@@ -6002,7 +6002,7 @@ static SolventDot *SolventDotNew(PyMOLGl
+@@ -6002,7 +6002,7 @@
                    SurfaceJobAtomInfo *j_atom_info = atom_info + j;
                    if(j > a)       /* only check if this is atom trails */
                      if((!present) || present[j]) {
@@ -423,9 +459,9 @@
                            skip_flag = true;
 Index: layer2/RepCartoon.c
 ===================================================================
---- layer2/RepCartoon.c	(revision 4039)
+--- layer2/RepCartoon.c	(revision 4074)
 +++ layer2/RepCartoon.c	(working copy)
-@@ -2615,7 +2615,7 @@ CGO *GenerateRepCartoonCGO(CoordSet *cs,
+@@ -2615,7 +2615,7 @@
  
  #ifdef _PYMOL_CGO_DRAWARRAYS
  	int nverts = nAt * 4, pl = 0;
@@ -436,9 +472,9 @@
  	CHECKOK(ok, vertexVals);
 Index: layer2/ObjectMolecule.c
 ===================================================================
---- layer2/ObjectMolecule.c	(revision 4039)
+--- layer2/ObjectMolecule.c	(revision 4074)
 +++ layer2/ObjectMolecule.c	(working copy)
-@@ -1448,7 +1448,7 @@ CoordSet *ObjectMoleculeTOPStr2CoordSet(
+@@ -1448,7 +1448,7 @@
    int NPHIH, MPHIA, NHPARM, NPARM, NNB, NRES;
    int NBONA, NTHETA, NPHIA, NUMBND, NUMANG, NPTRA;
    int NATYP, NPHB, IFPERT, NBPER, NGPER, NDPER;
@@ -447,7 +483,7 @@
    int NEXTRA, IPOL = 0;
    int wid, col;
    float BETA;
-@@ -2076,7 +2076,7 @@ CoordSet *ObjectMoleculeTOPStr2CoordSet(
+@@ -2076,7 +2076,7 @@
  
      if(IFBOX > 0) {
  
@@ -456,7 +492,7 @@
  
        if(amber7) {
          p = findflag(G, buffer, "SOLVENT_POINTERS", "3I8");
-@@ -4431,7 +4431,7 @@ int ObjectMoleculeAttach(ObjectMolecule 
+@@ -4431,7 +4431,7 @@
    AtomInfoType *ai;
    int n, nn;
    float v[3], v0[3], d;
@@ -465,7 +501,7 @@
    int ok = true;
  
    ok &= ObjectMoleculeUpdateNeighbors(I);
-@@ -9755,7 +9755,7 @@ int ObjectMoleculeMerge(ObjectMolecule *
+@@ -9767,7 +9767,7 @@
  			CoordSet * cs, int bondSearchFlag, int aic_mask, int invalidate)
  {
    PyMOLGlobals *G = I->Obj.G;
@@ -474,7 +510,7 @@
    BondType *bond = NULL;
    register int a, b, lb = 0, ac;
    int c, nb, a1, a2;
-@@ -10539,7 +10539,7 @@ void ObjectMoleculeSeleOp(ObjectMolecule
+@@ -10551,7 +10551,7 @@
                  rms = MatrixFitRMSTTTf(G, op->nvv1, op->vv1, vt, NULL, op->ttt);
                else
                  rms = MatrixGetRMS(G, op->nvv1, op->vv1, vt, NULL);
@@ -485,9 +521,9 @@
                  if(op->i3) {
 Index: layer3/Selector.c
 ===================================================================
---- layer3/Selector.c	(revision 4039)
+--- layer3/Selector.c	(revision 4074)
 +++ layer3/Selector.c	(working copy)
-@@ -8615,11 +8615,11 @@ static int SelectorSelect0(PyMOLGlobals 
+@@ -8658,11 +8658,11 @@
      for(a = cNDummyAtoms; a < I->NAtom; a++) {
        b = i_obj[i_table[a].model]->AtomInfo[i_table[a].atom].protons;
        base[0].sele[a] = (
@@ -506,9 +542,9 @@
      break;
 Index: layer3/Executive.c
 ===================================================================
---- layer3/Executive.c	(revision 4039)
+--- layer3/Executive.c	(revision 4074)
 +++ layer3/Executive.c	(working copy)
-@@ -15915,7 +15915,7 @@ static int ExecutiveDrag(Block * block, 
+@@ -15928,7 +15928,7 @@
                            ExecutiveSpecSetVisibility(G, rec, true, mod, false);
                            I->LastChanged = rec;
                          }
@@ -519,9 +555,9 @@
                                                  true);
 Index: layer3/PlugIOManager.c
 ===================================================================
---- layer3/PlugIOManager.c	(revision 4039)
+--- layer3/PlugIOManager.c	(revision 4074)
 +++ layer3/PlugIOManager.c	(working copy)
-@@ -225,7 +225,7 @@ int PlugIOManagerLoadTraj(PyMOLGlobals *
+@@ -229,7 +229,7 @@
                        ENDFB(G);
                    }
  
@@ -532,9 +568,45 @@
                    }
 Index: layer4/Cmd.c
 ===================================================================
---- layer4/Cmd.c	(revision 4039)
+--- layer4/Cmd.c	(revision 4074)
 +++ layer4/Cmd.c	(working copy)
-@@ -1846,7 +1846,7 @@ static PyObject *CmdMapHalve(PyObject * 
+@@ -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 @@
  static PyObject *CmdGetRenderer(PyObject * self, PyObject * args)
  {
    PyMOLGlobals *G = NULL;
@@ -545,9 +617,9 @@
    if(ok) {
 Index: contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp
 ===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp	(revision 4039)
+--- contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp	(revision 4074)
 +++ contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp	(working copy)
-@@ -259,7 +259,7 @@ static int read_pbeq_data(void *v, int s
+@@ -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);
@@ -556,11 +628,51 @@
            return MOLFILE_ERROR;
          }
          count++;
+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;
+     }
 Index: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c
 ===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c	(revision 4039)
+--- contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c	(revision 4074)
 +++ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c	(working copy)
-@@ -99,7 +99,7 @@ static void *open_molden_read(const char
+@@ -99,7 +99,7 @@
                                const char *filetype,
                                int *natoms) {
    FILE *fd;
@@ -569,11 +681,78 @@
    moldendata_t *moldendata;
    char buffer[1024];
    char keystring[20];
+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;
+ 	}
 Index: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c
 ===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c	(revision 4039)
+--- contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c	(revision 4074)
 +++ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c	(working copy)
-@@ -375,7 +375,7 @@ static void *open_gamess_read(const char
+@@ -375,7 +375,7 @@
                    const char *filetype, int *natoms) {
  
    FILE *fd;
@@ -584,9 +763,9 @@
    /* open the input file */
 Index: contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
 ===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp	(revision 4039)
+--- contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp	(revision 4074)
 +++ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp	(working copy)
-@@ -1983,7 +1983,7 @@ namespace {
+@@ -1983,7 +1983,7 @@
        }
      }
      catch (std::exception &e) {
@@ -597,9 +776,9 @@
      return MOLFILE_SUCCESS;
 Index: contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp
 ===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp	(revision 4039)
+--- contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp	(revision 4074)
 +++ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp	(working copy)
-@@ -104,7 +104,7 @@ void Get_Property_Values(GRASSP *grassp,
+@@ -104,7 +104,7 @@
  
    ///ojo aqui le quite el  !
    if ((grassp->flag)!=POTENTIALS) {
@@ -610,9 +789,9 @@
        printf("graspplugin) out of range property, flag: %d index: %d\n", grassp->flag, index);
 Index: modules/cealign/src/tnt/tnt_fortran_array1d.h
 ===================================================================
---- modules/cealign/src/tnt/tnt_fortran_array1d.h	(revision 4039)
+--- modules/cealign/src/tnt/tnt_fortran_array1d.h	(revision 4074)
 +++ modules/cealign/src/tnt/tnt_fortran_array1d.h	(working copy)
-@@ -221,7 +221,7 @@ inline Fortran_Array1D<T> Fortran_Array1
+@@ -221,7 +221,7 @@
  #ifdef TNT_DEBUG
  		std::cout << "entered subarray. \n";
  #endif
@@ -623,9 +802,9 @@
  		X.n_ = i1-i0+1;
 Index: modules/cealign/src/tnt/tnt_array1d.h
 ===================================================================
---- modules/cealign/src/tnt/tnt_array1d.h	(revision 4039)
+--- modules/cealign/src/tnt/tnt_array1d.h	(revision 4074)
 +++ modules/cealign/src/tnt/tnt_array1d.h	(working copy)
-@@ -258,7 +258,7 @@ inline int Array1D<T>::ref_count() const
+@@ -258,7 +258,7 @@
  template <class T>
  inline Array1D<T> Array1D<T>::subarray(int i0, int i1)
  {

Modified: trunk/dports/science/pymol/files/setup_py.diff
===================================================================
--- 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)
@@ -1,5 +1,5 @@
---- setup.py.orig
-+++ setup.py
+--- setup.py.orig	2014-05-24 16:55:05.000000000 -0400
++++ setup.py	2014-05-24 17:00:43.000000000 -0400
 @@ -47,18 +47,6 @@
      pmap(_single_compile, objects)
      return objects
@@ -12,14 +12,14 @@
 -    import argparse
 -    parser = argparse.ArgumentParser()
 -    parser.add_argument('--osx-frameworks', action="store_true")
--    options, sys.argv = parser.parse_known_args(namespace=options)
+-    options, sys.argv[1:] = parser.parse_known_args(namespace=options)
 -except ImportError:
 -    print "argparse not available"
 -
  jobs = int(os.getenv('JOBS', 0))
  pmap = map if jobs == 1 else multiprocessing.pool.ThreadPool(jobs or None).map
  
-@@ -246,22 +234,17 @@
+@@ -242,22 +230,17 @@
      try:
          prefix_path = os.environ['PREFIX_PATH'].split(os.pathsep)
      except KeyError:
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