Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv28582
Modified Files:
ccp4.patch
Log Message:
update to build on 10.9
Index: ccp4.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/ccp4.patch,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- ccp4.patch 18 Sep 2012 18:14:03 -0000 1.3
+++ ccp4.patch 2 Aug 2013 17:53:36 -0000 1.4
@@ -50,7 +50,7 @@
FFTW_LIBS="-L${prefix}/lib -lrfftw -lfftw"
FFTW_CXXFLAGS="-I${prefix}/lib/fftw/fftw -I${prefix}/lib/fftw/rfftw
-I${prefix}/include"
- export CFLAGS
-+ FLIBS="-L@PREFIX@/lib/gcc4.7/lib -lgfortran"
++ FLIBS="@PREFIX@/lib/gcc4.8/lib/libgfortran.dylib"
+ export CFLAGS FLIBS
# must use --enable-float
xopts="--enable-float"
@@ -3447,3 +3447,486 @@
1305 IF (ANM4(I,1).EQ.REXELIN(13:16)) THEN
READ (REXELIN(31:54),1126) XC(I),YC(I),ZC(I)
+---
ccp4-6.3.0/src/rapper/gc7.0//libatomic_ops-1.2/src/atomic_ops/sysdeps/gcc/x86_64.h.orig
2013-07-31 19:45:46.000000000 -0400
++++
ccp4-6.3.0/src/rapper/gc7.0//libatomic_ops-1.2/src/atomic_ops/sysdeps/gcc/x86_64.h
2013-07-31 19:47:49.000000000 -0400
+@@ -124,7 +124,7 @@
+ /* Note: the "xchg" instruction does not need a "lock" prefix */
+ __asm__ __volatile__("xchgb %0, %1"
+ : "=q"(oldval), "=m"(*addr)
+- : "0"(0xff), "m"(*addr) : "memory");
++ : "0"((unsigned char)0xff), "m"(*addr) : "memory");
+ return (AO_TS_VAL_t)oldval;
+ }
+
+---
ccp4-6.3.0/src/rapper/gc7.0//libatomic_ops-1.2/src/atomic_ops/sysdeps/gcc/x86.h.orig
2013-07-31 19:48:06.000000000 -0400
++++
ccp4-6.3.0/src/rapper/gc7.0//libatomic_ops-1.2/src/atomic_ops/sysdeps/gcc/x86.h
2013-07-31 19:49:01.000000000 -0400
+@@ -113,7 +113,7 @@
+ /* Note: the "xchg" instruction does not need a "lock" prefix */
+ __asm__ __volatile__("xchgb %0, %1"
+ : "=q"(oldval), "=m"(*addr)
+- : "0"(0xff), "m"(*addr) : "memory");
++ : "0"((unsigned char)0xff), "m"(*addr) : "memory");
+ return (AO_TS_VAL_t)oldval;
+ }
+
+--- ccp4-6.3.0/src/clipper_progs/src/ctruncate/ctruncate_analyse.cpp.orig
2013-08-01 09:19:32.000000000 -0400
++++ ccp4-6.3.0/src/clipper_progs/src/ctruncate/ctruncate_analyse.cpp
2013-08-01 09:26:36.000000000 -0400
+@@ -867,7 +867,7 @@
+
+ //want a point, but use Coord_orth for now
+ template <class T> clipper::Coord_orth
AnisoPlot<T>::point(clipper::ftype offsetx, clipper::ftype offsety,
clipper::ftype sigmau,
+-
clipper::ftype sigmav,
clipper::ftype angleuv, clipper::ftype theta, clipper::ftype frac=1.0/1.17741)
++
clipper::ftype sigmav,
clipper::ftype angleuv, clipper::ftype theta, clipper::ftype frac)
+ {
+ clipper::ftype f = std::sqrt(2*std::log(1.0/frac));
+ clipper::ftype sinuv = std::sin(angleuv);
+@@ -883,7 +883,7 @@
+
+ // plot at frac of height
+ template <class T> std::vector<clipper::Coord_orth>
AnisoPlot<T>::isoline(clipper::ftype offsetx, clipper::ftype offsety,
clipper::ftype sigmau,
+-
clipper::ftype sigmav, clipper::ftype angleuv,
clipper::ftype frac=1.0/1.17741, int steps=60)
++
clipper::ftype sigmav, clipper::ftype angleuv,
clipper::ftype frac, int steps)
+ {
+ std::vector<clipper::Coord_orth> points(steps);
+ clipper::ftype f = std::sqrt(2*std::log(1.0/frac));
+--- ccp4-6.3.0/src/clipper_progs/src/ctruncate/ctruncate_analyse.h.orig
2013-08-01 09:20:11.000000000 -0400
++++ ccp4-6.3.0/src/clipper_progs/src/ctruncate/ctruncate_analyse.h
2013-08-01 09:25:56.000000000 -0400
+@@ -113,10 +113,10 @@
+ std::vector<std::vector<clipper::Coord_orth> > _isoline3;
+
+ std::vector<clipper::Coord_orth> isoline(clipper::ftype
offsetx, clipper::ftype offsety, clipper::ftype sigmau,
+- clipper::ftype sigmav, clipper::ftype
angleuv, clipper::ftype frac, int steps);
++ clipper::ftype sigmav, clipper::ftype
angleuv, clipper::ftype frac=1.0/1.17741, int steps=60);
+
+ clipper::Coord_orth point(clipper::ftype offsetx,
clipper::ftype offsety, clipper::ftype sigmau,
+-
clipper::ftype sigmav, clipper::ftype angleuv, clipper::ftype theta,
clipper::ftype frac);
++
clipper::ftype sigmav, clipper::ftype angleuv, clipper::ftype theta,
clipper::ftype frac=1.0/1.17741);
+
+ void ellipse(clipper::ftype sig1, clipper::ftype sig2,
clipper::ftype cov,
+ clipper::ftype& angle, clipper::ftype&
sigmau, clipper::ftype& sigmav);
+--- ccp4-6.3.0/src/leiden/bp3lib/src/covmat.h.orig 2013-08-01
10:00:12.000000000 -0400
++++ ccp4-6.3.0/src/leiden/bp3lib/src/covmat.h 2013-08-01 10:01:51.000000000
-0400
+@@ -2014,7 +2014,7 @@
+
+
+ template <typename realnum>
+-void covar_matrix<realnum>::SetZeroRows( int r1=-1, int r2=-1, int r3=-1, int
r4=-1, int r5=-1, int r6=-1 )
++void covar_matrix<realnum>::SetZeroRows( int r1, int r2, int r3, int r4, int
r5, int r6 )
+ {
+ int r[6] = {r1,r2,r3,r4,r5,r6};
+ zero_cov_row_num=0;
+--- ccp4-6.3.0/src/leiden/bp3lib/src/pavol.C.orig 2013-08-01
10:04:52.000000000 -0400
++++ ccp4-6.3.0/src/leiden/bp3lib/src/pavol.C 2013-08-01 10:05:08.000000000
-0400
+@@ -368,7 +368,7 @@
+
+ multivar_llhood::likelihood<Type> l( N_meas, Num, 1, 1, targe.c_str(),
N_part, 25, 1, 1 );
+ if (target == "PSAD")
+- l.cov->SetZeroRows(4);
++ l.cov->SetZeroRows(4,-1,-1,-1,-1,-1);
+ l.checkOK = 1;
+ l.SetImproveInteg(0);
+ l.cov->no_imag = 1;
+--- ccp4-6.3.0/src/ccp4mapwish_/c_src/ccp4mapwish.h.orig 2013-08-01
10:36:23.000000000 -0400
++++ ccp4-6.3.0/src/ccp4mapwish_/c_src/ccp4mapwish.h 2013-08-01
10:36:45.000000000 -0400
+@@ -35,6 +35,12 @@
+ #include <tcl.h>
+ #include <tk.h>
+
++#if TCL_MAJOR_VERSION <=8 && TCL_MINOR_VERSION < 6
++#define Tcl_GetStringResult(x) x->result
++#define Tcl_GetErrorLine(x) x->errorLine
++#define Tcl_SetResult(x, y, z) x->result = y
++#endif
++
+ /* CCP4 CMap include file */
+ #include <ccp4/cmaplib.h>
+
+--- ccp4-6.3.0/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c.orig
2013-08-01 10:26:30.000000000 -0400
++++ ccp4-6.3.0/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c 2013-08-01
10:43:28.000000000 -0400
+@@ -297,7 +297,7 @@
+ puts("canvas_draw_line: about to evaluate the command...");
+ }
+ if (Tcl_Eval(interp,command) != TCL_OK) {
+- printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result);
++ printf("canvas_draw_line: error from Tcl_Eval:
%s",Tcl_GetStringResult(interp));
+ return 0;
+ }
+ if (CCP4MAPWISH_CANVAS_DIAG)
+@@ -432,7 +432,7 @@
+ puts("canvas_draw_rectangle: about to evaluate the command...");
+ }
+ if (Tcl_Eval(interp,command) != TCL_OK) {
+- printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result);
++ printf("canvas_draw_rectangle: error from Tcl_Eval:
%s",Tcl_GetStringResult(interp));
+ printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor =
\"%s\"\nunits = \"%c\"\n",canvas,tags,color,units);
+ return 0;
+ }
+@@ -536,7 +536,7 @@
+ /* Execute the command which draws the label */
+ if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is:
%s\n",command);
+ if (Tcl_Eval(interp,command) != TCL_OK) {
+- printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result);
++ printf("canvas_draw_label: error from Tcl_Eval:
%s\n",Tcl_GetStringResult(interp));
+ return 0;
+ }
+
+@@ -617,7 +617,7 @@
+ /* Execute the command which scales the canvas */
+ if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is:
%s\n",command);
+ if (Tcl_Eval(interp,command) != TCL_OK) {
+- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
++ printf("canvas_scale_canvas: error from Tcl_Eval:
%s\n",Tcl_GetStringResult(interp));
+ return 0;
+ }
+
+@@ -706,7 +706,7 @@
+ /* Execute the command which resizes the canvas */
+ if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is:
%s\n",command);
+ if (Tcl_Eval(interp,command) != TCL_OK) {
+- printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result);
++ printf("canvas_shift_canvas: error from Tcl_Eval:
%s\n",Tcl_GetStringResult(interp));
+ return 0;
+ }
+
+@@ -789,7 +789,7 @@
+ /* Execute the command which resizes the canvas */
+ if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is:
%s\n",command);
+ if (Tcl_Eval(interp,command) != TCL_OK) {
+- printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result);
++ printf("canvas_shift_element: error from Tcl_Eval:
%s\n",Tcl_GetStringResult(interp));
+ return 0;
+ }
+
+@@ -861,7 +861,7 @@
+ /* Execute the command which deletes the tagged items */
+ if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is:
%s\n",command);
+ if (Tcl_Eval(interp,command) != TCL_OK) {
+- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
++ printf("canvas_scale_canvas: error from Tcl_Eval:
%s\n",Tcl_GetStringResult(interp));
+ return 0;
+ }
+
+@@ -892,15 +892,15 @@
+
+ sprintf(tmpstr,"winfo exists %s",canvas);
+ if (Tcl_Eval(interp,tmpstr) != TCL_OK) {
+- printf("canvas_exists: error from Tcl_Eval: %s",interp->result);
++ printf("canvas_exists: error from Tcl_Eval:
%s",Tcl_GetStringResult(interp));
+ return 0;
+ }
+ /* Extract a long int using strtol
+ If no conversion takes place then "endptr" will be equal
+ to "result" */
+- istatus = (int) strtol(interp->result,&endptr,10);
+- if (strcmp(interp->result,endptr) == 0) {
+- printf("canvas_exists: bad return status from winfo command
\"%s\"\n",interp->result);
++ istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10);
++ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
++ printf("canvas_exists: bad return status from winfo command
\"%s\"\n",Tcl_GetStringResult(interp));
+ return 0;
+ }
+ if (!istatus) {
+@@ -930,13 +930,13 @@
+
+ /* Execute the tk scaling command */
+ if (Tcl_Eval(interp,"tk scaling") != TCL_OK) {
+- printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result);
++ printf("canvas_get_tk_scaling: error from Tcl_Eval:
%s",Tcl_GetStringResult(interp));
+ return (float) 0.0;
+ }
+
+ /* Extract a float from the result */
+- tkscale = ((float) strtod(interp->result,&endptr));
+- if (strcmp(interp->result,endptr) == 0) {
++ tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr));
++ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
+ printf("canvas_get_tk_scaling: couldn't extract scale factor\n");
+ return (float) 0.0;
+ }
+@@ -1021,19 +1021,19 @@
+
+ /* Evaluate the command */
+ if (Tcl_Eval(interp,command) != TCL_OK) {
+- printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result);
++ printf("canvas_get_limits: error from Tcl_Eval:
%s\n",Tcl_GetStringResult(interp));
+ return 0;
+ }
+
+ /* Process the result - it should consist of 4 integers */
+ /* Use strtok which can split the string based on tokens
+ set by the programmer - in this case a space */
+- if (!interp->result) {
++ if (!Tcl_GetStringResult(interp)) {
+ puts("canvas_get_limits: failed to fetch canvas limits");
+ return TCL_ERROR;
+ }
+ i = 0;
+- p = strtok(interp->result," ");
++ p = strtok(Tcl_GetStringResult(interp)," ");
+ if (p == NULL) {
+ return 0;
+ }
+--- ccp4-6.3.0/lib/cctbx/cctbx_sources/tntbx/include/tnt_array1d.h.orig
2013-08-01 11:44:47.000000000 -0400
++++ ccp4-6.3.0/lib/cctbx/cctbx_sources/tntbx/include/tnt_array1d.h
2013-08-01 11:45:44.000000000 -0400
+@@ -71,7 +71,9 @@
+ Array1D copy() const;
+ Array1D & inject(const Array1D & A);
+ inline T& operator[](int i);
++ inline T& operator()(int i);
+ inline const T& operator[](int i) const;
++ inline const T& operator()(int i) const;
+ inline int dim1() const;
+ inline int dim() const;
+ ~Array1D();
+@@ -100,7 +102,6 @@
+
+ }
+
+-
+ template <class T>
+ Array1D<T>::Array1D(int n) : v_(n), n_(n), data_(v_.begin())
+ {
+@@ -163,6 +164,28 @@
+ }
+
+
++
++template <class T>
++inline T& Array1D<T>::operator()(int i)
++{
++#ifdef TNT_BOUNDS_CHECK
++ assert(i>= 0);
++ assert(i < n_);
++#endif
++ return data_[i-1];
++}
++
++template <class T>
++inline const T& Array1D<T>::operator()(int i) const
++{
++#ifdef TNT_BOUNDS_CHECK
++ assert(i>= 0);
++ assert(i < n_);
++#endif
++ return data_[i-1];
++}
++
++
+
+
+ template <class T>
+@@ -235,7 +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;
+--- ccp4-6.3.0/src/prosmart/src/tnt_jama/tnt_array1d.h.orig 2013-08-01
14:19:40.000000000 -0400
++++ ccp4-6.3.0/src/prosmart/src/tnt_jama/tnt_array1d.h 2013-08-01
14:30:34.000000000 -0400
+@@ -62,6 +62,7 @@
+ explicit Array1D(int n);
+ Array1D(int n, const T &a);
+ Array1D(int n, T *a);
++ inline Array1D(int n, const T *a);
+ inline Array1D(const Array1D &A);
+ inline operator T*();
+ inline operator const T*();
+@@ -129,6 +130,14 @@
+ }
+
+ template <class T>
++inline Array1D<T>::Array1D(int n, const T *a) : v_(a), n_(n) ,
data_(v_.begin())
++{
++#ifdef TNT_DEBUG
++ std::cout << "Created Array1D(int n, T* a) \n";
++#endif
++}
++
++template <class T>
+ inline Array1D<T>::operator T*()
+ {
+ return &(v_[0]);
+---
ccp4-6.3.0/lib/cctbx/cctbx_sources/cctbx_project/mmtbx/bulk_solvent/bulk_solvent.h.orig
2013-08-01 16:22:29.000000000 -0400
++++
ccp4-6.3.0/lib/cctbx/cctbx_sources/cctbx_project/mmtbx/bulk_solvent/bulk_solvent.h
2013-08-01 16:29:12.000000000 -0400
+@@ -615,72 +615,6 @@
+ }
+ };
+
+-template <typename FloatType, typename ComplexType>
+- af::shared<FloatType>
+- ksol_bsol_grid_search(
+- af::const_ref<FloatType> const& f_obs,
+- af::const_ref<ComplexType> const& f_calc,
+- af::const_ref<ComplexType> const& f_mask,
+- af::const_ref<FloatType> const& k_sol_range,
+- af::const_ref<FloatType> const& b_sol_range,
+- af::const_ref<FloatType> const& ss,
+- FloatType const& scalar_scale,
+- af::const_ref<FloatType> const& overall_scale,
+- af::const_ref<FloatType> const& overall_anisotropic_scale,
+- FloatType const& r_ref)
+- {
+- MMTBX_ASSERT(f_mask.size() == f_obs.size());
+- MMTBX_ASSERT(f_obs.size() == f_calc.size());
+- MMTBX_ASSERT(ss.size() == f_calc.size());
+- MMTBX_ASSERT(overall_scale.size() == f_calc.size());
+- MMTBX_ASSERT(overall_anisotropic_scale.size() == f_calc.size());
+- FloatType k_best = 0.0;
+- FloatType b_best = 0.0;
+- FloatType r_best = r_ref;
+- af::shared<ComplexType> f_model(ss.size());
+- af::shared<FloatType> bulk_solvent_scale(f_obs.size());
+- for(std::size_t i=0; i < k_sol_range.size(); i++) {
+- FloatType ks = k_sol_range[i];
+- for(std::size_t j=0; j < b_sol_range.size(); j++) {
+- FloatType mbs = -b_sol_range[j];
+- for(std::size_t k=0; k < f_obs.size(); k++) {
+- FloatType kbs = ks * std::exp(mbs * ss[k]);
+- f_model[k] = scalar_scale * overall_scale[k] *
+- overall_anisotropic_scale[k] * (f_calc[k] + kbs * f_mask[k]);
+- }
+- FloatType r = r_factor(f_obs, f_model.const_ref());
+- if(r < r_best) {
+- k_best = k_sol_range[i];
+- b_best = b_sol_range[j];
+- r_best = r;
+- }
+- }
+- }
+- for(std::size_t k=0; k < f_obs.size(); k++) {
+- bulk_solvent_scale[k] = k_best * std::exp(-b_best * ss[k]);
+- }
+- return bulk_solvent_scale;
+- };
+-
+-template <typename FloatType>
+- af::shared<FloatType>
+- set_k_mask_to_cubic_polynom(
+- af::const_ref<FloatType> const& ss,
+- FloatType const& ss_cutoff,
+- af::tiny<FloatType, 4> const& coeffs)
+- {
+- af::shared<FloatType> k_mask(ss.size());
+- for(std::size_t i=0; i < ss.size(); i++) {
+- FloatType x = ss[i];
+- FloatType f = coeffs[0] + coeffs[1]*x + coeffs[2]*x*x + coeffs[3]*x*x*x;
+- if(f<0) f = 0;
+- if(x<ss_cutoff) k_mask[i] = f;
+- else k_mask[i] = 0;
+- }
+- return k_mask;
+- };
+-
+-
+
//------------------------------------------------------------------------------
+ template <typename FloatType, typename ComplexType>
+ FloatType
+@@ -835,6 +769,73 @@
+
+
//------------------------------------------------------------------------------
+
++template <typename FloatType, typename ComplexType>
++ af::shared<FloatType>
++ ksol_bsol_grid_search(
++ af::const_ref<FloatType> const& f_obs,
++ af::const_ref<ComplexType> const& f_calc,
++ af::const_ref<ComplexType> const& f_mask,
++ af::const_ref<FloatType> const& k_sol_range,
++ af::const_ref<FloatType> const& b_sol_range,
++ af::const_ref<FloatType> const& ss,
++ FloatType const& scalar_scale,
++ af::const_ref<FloatType> const& overall_scale,
++ af::const_ref<FloatType> const& overall_anisotropic_scale,
++ FloatType const& r_ref)
++ {
++ MMTBX_ASSERT(f_mask.size() == f_obs.size());
++ MMTBX_ASSERT(f_obs.size() == f_calc.size());
++ MMTBX_ASSERT(ss.size() == f_calc.size());
++ MMTBX_ASSERT(overall_scale.size() == f_calc.size());
++ MMTBX_ASSERT(overall_anisotropic_scale.size() == f_calc.size());
++ FloatType k_best = 0.0;
++ FloatType b_best = 0.0;
++ FloatType r_best = r_ref;
++ af::shared<ComplexType> f_model(ss.size());
++ af::shared<FloatType> bulk_solvent_scale(f_obs.size());
++ for(std::size_t i=0; i < k_sol_range.size(); i++) {
++ FloatType ks = k_sol_range[i];
++ for(std::size_t j=0; j < b_sol_range.size(); j++) {
++ FloatType mbs = -b_sol_range[j];
++ for(std::size_t k=0; k < f_obs.size(); k++) {
++ FloatType kbs = ks * std::exp(mbs * ss[k]);
++ f_model[k] = scalar_scale * overall_scale[k] *
++ overall_anisotropic_scale[k] * (f_calc[k] + kbs * f_mask[k]);
++ }
++ FloatType r = r_factor(f_obs, f_model.const_ref());
++ if(r < r_best) {
++ k_best = k_sol_range[i];
++ b_best = b_sol_range[j];
++ r_best = r;
++ }
++ }
++ }
++ for(std::size_t k=0; k < f_obs.size(); k++) {
++ bulk_solvent_scale[k] = k_best * std::exp(-b_best * ss[k]);
++ }
++ return bulk_solvent_scale;
++ };
++
++template <typename FloatType>
++ af::shared<FloatType>
++ set_k_mask_to_cubic_polynom(
++ af::const_ref<FloatType> const& ss,
++ FloatType const& ss_cutoff,
++ af::tiny<FloatType, 4> const& coeffs)
++ {
++ af::shared<FloatType> k_mask(ss.size());
++ for(std::size_t i=0; i < ss.size(); i++) {
++ FloatType x = ss[i];
++ FloatType f = coeffs[0] + coeffs[1]*x + coeffs[2]*x*x + coeffs[3]*x*x*x;
++ if(f<0) f = 0;
++ if(x<ss_cutoff) k_mask[i] = f;
++ else k_mask[i] = 0;
++ }
++ return k_mask;
++ };
++
++
++
+ template <typename DataType, typename TagType>
+ void
+ symmetrize_mask(
+--- ccp4-6.3.0/configure.orig 2013-08-01 16:40:51.000000000 -0400
++++ ccp4-6.3.0/configure 2013-08-01 16:41:22.000000000 -0400
+@@ -3868,7 +3868,7 @@
+ cat > testlink.c <<EOF
+ #define MAXBMT 2
+
+-int main(int argc, char *argv) {
++int main(int argc, char *argv[]) {
+ /* A bit of scala code to test the linking */
+ float bf[3], bnorm;
+ double B[MAXBMT][MAXBMT], eigval[MAXBMT],
+--- ccp4-6.3.0/x-windows/RasMol/src/wbrotate.c.orig 2013-08-01
16:49:08.000000000 -0400
++++ ccp4-6.3.0/x-windows/RasMol/src/wbrotate.c 2013-08-01 16:49:25.000000000
-0400
+@@ -249,7 +249,7 @@
+ if( nsrc == ndst )
+ { InvalidateCmndLine();
+ WriteString("Error: Duplicate atom serial numbers!\n");
+- return;
++ return 0;
+ }
+
+ done = False;
+---
ccp4-6.3.0/lib/cctbx/cctbx_sources/boost/boost/math/special_functions/detail/bessel_jy.hpp.orig
2013-08-01 19:00:44.000000000 -0400
++++
ccp4-6.3.0/lib/cctbx/cctbx_sources/boost/boost/math/special_functions/detail/bessel_jy.hpp
2013-08-01 19:01:05.000000000 -0400
+@@ -21,6 +21,7 @@
+ #include <boost/math/policies/error_handling.hpp>
+ #include <boost/mpl/if.hpp>
+ #include <boost/type_traits/is_floating_point.hpp>
++#include <boost/math/special_functions/detail/bessel_jy_series.hpp>
+ #include <complex>
+
+ // Bessel functions of the first and second kind of fractional order
------------------------------------------------------------------------------
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