[Debian-med-packaging] patches for concavity
Laszlo Kajan
lkajan at rostlab.org
Fri Sep 28 20:10:19 UTC 2012
Dear Tom!
Please find attached the (quilt) patches I created during packaging.
Please let me know if you use some to create a new upstream, so that I can update the packaged version.
Best regards,
Laszlo
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default_target_all
safe_recursive_make
freeglut
CFLAGSasf
compiler_errors
noopengllink
spelling
-------------- next part --------------
Author: Laszlo Kajan <lkajan at rostlab.org>
Description: respect CFLAGS and alike from environment
CFLAGS CPPFLAGS LDFLAGS, to allow hardening flags to be passed
--- a/scripts/Makefile.apps
+++ b/scripts/Makefile.apps
@@ -42,7 +42,7 @@
BASE_LDFLAGS=$(USER_LDFLAGS) -L$(LIB_DIR)
DEBUG_LDFLAGS=$(BASE_LDFLAGS) -g
OPT_LDFLAGS=$(BASE_LDFLAGS) -O
-LDFLAGS=$(DEBUG_LDFLAGS)
+LDFLAGS:=$(DEBUG_LDFLAGS) $(LDFLAGS)
#
@@ -67,10 +67,10 @@
#
opt:
- $(MAKE) $(EXE) "CFLAGS=$(OPT_CFLAGS)" "LDFLAGS=$(OPT_LDFLAGS)"
+ $(MAKE) $(EXE) "CFLAGS=$(OPT_CFLAGS) $(CFLAGS)" "LDFLAGS=$(OPT_LDFLAGS) $(LDFLAGS)"
debug:
- $(MAKE) $(EXE) "CFLAGS=$(DEBUG_CFLAGS)" "LDFLAGS=$(DEBUG_LDFLAGS)"
+ $(MAKE) $(EXE) "CFLAGS=$(DEBUG_CFLAGS) $(CFLAGS)" "LDFLAGS=$(DEBUG_LDFLAGS) $(LDFLAGS)"
$(EXE): $(OBJS) $(LIBDIR)
mkdir -p $(EXE_DIR)
--- a/scripts/Makefile.pkgs
+++ b/scripts/Makefile.pkgs
@@ -39,10 +39,10 @@
#
opt:
- $(MAKE) $(LIB) "CFLAGS=$(OPT_CFLAGS)"
+ $(MAKE) $(LIB) "CFLAGS=$(OPT_CFLAGS) $(CFLAGS)"
debug:
- $(MAKE) $(LIB) "CFLAGS=$(DEBUG_CFLAGS)"
+ $(MAKE) $(LIB) "CFLAGS=$(DEBUG_CFLAGS) $(CFLAGS)"
$(LIB): $(CCSRCS) $(CSRCS) $(OSRCS) $(OBJS)
mkdir -p $(LIB_DIR)
--- a/scripts/Makefile.std
+++ b/scripts/Makefile.std
@@ -21,7 +21,7 @@
BASE_CFLAGS=$(USER_CFLAGS) -Wall -I. -I../../pkgs
DEBUG_CFLAGS=$(BASE_CFLAGS) -g
OPT_CFLAGS=$(BASE_CFLAGS) -O3 -DNDEBUG
-CFLAGS=$(DEBUG_CFLAGS)
+CFLAGS:=$(DEBUG_CFLAGS) $(CFLAGS)
@@ -52,8 +52,8 @@
.SUFFIXES: .c .C .o
.C.o:
- $(CC) $(CFLAGS) -c $<
+ $(CC) $(CPPFLAGS) $(CFLAGS) -c $<
.c.o:
- gcc $(CFLAGS) -c $<
+ gcc $(CPPFLAGS) $(CFLAGS) -c $<
--- a/scripts/MSVC/Makefile.apps
+++ b/scripts/MSVC/Makefile.apps
@@ -39,7 +39,7 @@
BASE_LDFLAGS=$(USER_LDFLAGS) /link /libpath:$(LIB_DIR)
DEBUG_LDFLAGS=$(BASE_LDFLAGS) -Zi
OPT_LDFLAGS=$(BASE_LDFLAGS) -Ox
-LDFLAGS=$(DEBUG_LDFLAGS)
+LDFLAGS:=$(DEBUG_LDFLAGS) $(LDFLAGS)
@@ -58,10 +58,10 @@
#
opt:
- $(MAKE) $(EXE) "CFLAGS=$(OPT_CFLAGS)" "LDFLAGS=$(OPT_LDFLAGS)"
+ $(MAKE) $(EXE) "CFLAGS=$(OPT_CFLAGS) $(CFLAGS)" "LDFLAGS=$(OPT_LDFLAGS) $(LDFLAGS)"
debug:
- $(MAKE) $(EXE) "CFLAGS=$(DEBUG_CFLAGS)" "LDFLAGS=$(DEBUG_LDFLAGS)"
+ $(MAKE) $(EXE) "CFLAGS=$(DEBUG_CFLAGS) $(CFLAGS)" "LDFLAGS=$(DEBUG_LDFLAGS) $(LDFLAGS)"
$(EXE): $(OBJS) $(LIBDIR)
mkdir -p $(EXE_DIR)
--- a/scripts/MSVC/Makefile.pkgs
+++ b/scripts/MSVC/Makefile.pkgs
@@ -39,10 +39,10 @@
#
opt:
- $(MAKE) $(LIB) "CFLAGS=$(OPT_CFLAGS)"
+ $(MAKE) $(LIB) "CFLAGS=$(OPT_CFLAGS) $(CFLAGS)"
debug:
- $(MAKE) $(LIB) "CFLAGS=$(DEBUG_CFLAGS)"
+ $(MAKE) $(LIB) "CFLAGS=$(DEBUG_CFLAGS) $(CFLAGS)"
$(LIB): $(CCSRCS) $(CSRCS) $(OSRCS) $(OBJS)
mkdir -p $(LIB_DIR)
--- a/scripts/MSVC/Makefile.std
+++ b/scripts/MSVC/Makefile.std
@@ -21,7 +21,7 @@
BASE_CFLAGS=$(USER_CFLAGS) /TP /W3 -I. -I../../pkgs
DEBUG_CFLAGS=-Zi $(BASE_CFLAGS)
OPT_CFLAGS=-Ox -DNDEBUG $(BASE_CFLAGS)
-CFLAGS=$(DEBUG_CFLAGS)
+CFLAGS:=$(DEBUG_CFLAGS) $(CFLAGS)
@@ -42,9 +42,9 @@
.SUFFIXES: .c .C .obj
.C.obj:
- $(CC) $(CFLAGS) -c $<
+ $(CC) $(CPPFLAGS) $(CFLAGS) -c $<
.c.obj:
- $(CC) $(CFLAGS) -c $<
+ $(CC) $(CPPFLAGS) $(CFLAGS) -c $<
-------------- next part --------------
Author: Laszlo Kajan <lkajan at rostlab.org>
Description: fix compiler errors and warnings
--- a/pkgs/PDB/PDBFile.C
+++ b/pkgs/PDB/PDBFile.C
@@ -396,7 +396,7 @@
{
// Write all header lines
for (int i = 0; i < headers.NEntries(); i++) {
- fprintf(fp, headers.Kth(i));
+ fprintf(fp, "%s", headers.Kth(i));
}
// Write all models
@@ -444,7 +444,7 @@
// Write all trailing lines
for (int i = 0; i < trailers.NEntries(); i++) {
- fprintf(fp, trailers.Kth(i));
+ fprintf(fp, "%s", trailers.Kth(i));
}
// Return number of models written
@@ -1355,7 +1355,7 @@
}
// Check jsd files for chain A if chain name is "-" or " " ???
- if (translate_unnamed_chains && !strcmp(chain_name, "-") || !strcmp(chain_name, " ")) {
+ if (translate_unnamed_chains && ( !strcmp(chain_name, "-") || !strcmp(chain_name, " ") ) ) {
// Get chain jsd filename
strcpy(chain_filename, jsd_basename);
strcat(chain_filename, "_");
-------------- next part --------------
Author: Laszlo Kajan <lkajan at rostlab.org>
Description: make default target 'all'
--- a/Makefile
+++ b/Makefile
@@ -2,6 +2,9 @@
# Makefile for GAPS
#
+.PHONY: all opt
+all: opt
+
opt:
$(MAKE) target "TARGET=$@"
-------------- next part --------------
Author: Laszlo Kajan <lkajan at rostlab.org>
Description: do not make freeglut, this is packaged separately
--- a/pkgs/Makefile
+++ b/pkgs/Makefile
@@ -33,7 +33,7 @@
cd R3Shapes && $(MAKE) $(TARGET)
cd R3Graphics && $(MAKE) $(TARGET)
cd PDB && $(MAKE) $(TARGET)
- cd freeglut && $(MAKE) $(TARGET)
+ #cd freeglut && $(MAKE) $(TARGET)
endif
-------------- next part --------------
Author: Laszlo Kajan <lkajan at rostlab.org>
Description: do not require linking with opengl
None of the affected methods are used by the application.
--- a/scripts/Makefile.apps
+++ b/scripts/Makefile.apps
@@ -58,7 +58,7 @@
OPENGL_LIBS=-lglut32 -lglu32 -lopengl32
endif
-LIBS=$(USER_LIBS) $(PKG_LIBS) $(OPENGL_LIBS)
+LIBS=$(USER_LIBS) $(PKG_LIBS)
--- a/pkgs/Makefile
+++ b/pkgs/Makefile
@@ -31,7 +31,7 @@
cd RNBasics && $(MAKE) $(TARGET)
cd R2Shapes && $(MAKE) $(TARGET)
cd R3Shapes && $(MAKE) $(TARGET)
- cd R3Graphics && $(MAKE) $(TARGET)
+ #cd R3Graphics && $(MAKE) $(TARGET)
cd PDB && $(MAKE) $(TARGET)
#cd freeglut && $(MAKE) $(TARGET)
endif
--- a/pkgs/RNBasics/RNCompat.h
+++ b/pkgs/RNBasics/RNCompat.h
@@ -57,9 +57,6 @@
# ifdef RN_USE_OPENGL
# define RN_2D_GRFX RN_OPENGL
# define RN_3D_GRFX RN_OPENGL
-# else
-# define RN_2D_GRFX RN_OPENGL
-# define RN_3D_GRFX RN_OPENGL
# endif
#endif
--- a/pkgs/R3Shapes/R3Mesh.C
+++ b/pkgs/R3Shapes/R3Mesh.C
@@ -1561,6 +1561,7 @@
////////////////////////////////////////////////////////////////////////
// DRAW FUNCTIONS
////////////////////////////////////////////////////////////////////////
+#ifdef RN_3D_GRFX
void R3Mesh::
DrawVertices(void) const
@@ -1681,7 +1682,7 @@
}
-
+#endif
////////////////////////////////////////////////////////////////////////
// INTERSECTION FUNCTIONS
////////////////////////////////////////////////////////////////////////
--- a/pkgs/R3Shapes/R3Mesh.h
+++ b/pkgs/R3Shapes/R3Mesh.h
@@ -403,6 +403,7 @@
virtual R3MeshFace *SubdivideFace(R3MeshFace *face);
// Splits face into four by subdividing each edge at midpoint (returns middle face)
+#ifdef RN_3D_GRFX
// DRAW FUNCTIONS
virtual void Draw(void) const;
// Draws the faces
@@ -424,6 +425,7 @@
// Draws one edge
virtual void DrawFace(R3MeshFace *face) const;
// Draws one face
+#endif
// INTERSECT FUNCTIONS
R3MeshType Intersection(const R3Ray& ray, R3MeshIntersection *intersection = NULL) const;
@@ -1426,6 +1428,7 @@
////////////////////////////////////////////////////////////////////////
// DRAW FUNCTIONS
////////////////////////////////////////////////////////////////////////
+#ifdef RN_3D_GRFX
inline void R3Mesh::
Draw(void) const
@@ -1433,6 +1436,7 @@
// Draw the mesh
DrawFaces();
}
+#endif
--- a/pkgs/R3Shapes/R3Grid.C
+++ b/pkgs/R3Shapes/R3Grid.C
@@ -3414,6 +3414,7 @@
+#ifdef RN_3D_GRFX
void R3Grid::
DrawIsoSurface(RNScalar isolevel) const
{
@@ -3526,3 +3527,4 @@
// Reset OpenGL modes
glDisable(GL_TEXTURE_2D);
}
+#endif
--- a/pkgs/R3Shapes/R3Grid.h
+++ b/pkgs/R3Shapes/R3Grid.h
@@ -146,8 +146,10 @@
int WriteDX(FILE *fp = NULL) const;
// Visualization functions
+#ifdef RN_3D_GRFX
void DrawIsoSurface(RNScalar isolevel) const;
void DrawSlice(int dim, int coord) const;
+#endif
// Utility functions
int ConnectedComponents(RNScalar isolevel = 0, int max_components = 0, int *seeds = NULL, int *sizes = NULL, int *grid_components = NULL);
--- a/pkgs/R2Shapes/R2Grid.C
+++ b/pkgs/R2Shapes/R2Grid.C
@@ -1643,6 +1643,7 @@
+#ifdef RN_2D_GRFX
void R2Grid::
Capture(void)
{
@@ -1727,6 +1728,7 @@
glMatrixMode(GL_MODELVIEW);
glPopMatrix();
}
+#endif
--- a/pkgs/R2Shapes/R2Grid.h
+++ b/pkgs/R2Shapes/R2Grid.h
@@ -149,12 +149,16 @@
int WriteGRD(const char *filename) const;
int WriteImage(const char *filename) const;
int Print(FILE *fp = NULL) const;
+#ifdef RN_2D_GRFX
void Capture(void);
+#endif
+#ifdef RN_2D_GRFX
// Draw functions
void Draw(void) const;
void DrawMesh(void) const;
void DrawImage(int x = 0, int y = 0) const;
+#endif
// Utility functions
RNScalar GridValue(RNCoord x, RNCoord y, RNLength sigma) const;
@@ -681,12 +685,14 @@
+#ifdef RN_2D_GRFX
inline void R2Grid::
Draw(void) const
{
// Draw image
DrawImage();
}
+#endif
--- a/pkgs/R2Shapes/R2Image.C
+++ b/pkgs/R2Shapes/R2Image.C
@@ -215,6 +215,7 @@
+#ifdef RN_2D_GRFX
void R2Image::
Capture(void)
{
@@ -270,6 +271,7 @@
glMatrixMode(GL_MODELVIEW);
glPopMatrix();
}
+#endif
int R2Image::
--- a/pkgs/R2Shapes/R2Image.h
+++ b/pkgs/R2Shapes/R2Image.h
@@ -46,10 +46,14 @@
int WriteRAW(const char *filename) const;
int WriteJPEG(const char *filename) const;
int WriteTIFF(const char *filename) const;
+#ifdef RN_2D_GRFX
void Capture(void);
+#endif
+#ifdef RN_2D_GRFX
// Draw functions
void Draw(int x = 0, int y = 0) const;
+#endif
private:
int width;
-------------- next part --------------
Author: Laszlo Kajan <lkajan at rostlab.org>
Description: safer recursive make calls
--- a/apps/Makefile
+++ b/apps/Makefile
@@ -17,7 +17,7 @@
$(MAKE) target "TARGET=$@"
target:
- cd concavity; $(MAKE) $(TARGET)
+ cd concavity && $(MAKE) $(TARGET)
--- a/Makefile
+++ b/Makefile
@@ -20,8 +20,8 @@
$(MAKE) target "TARGET=$@"
target:
- cd pkgs; $(MAKE) $(TARGET)
- cd apps; $(MAKE) $(TARGET)
+ cd pkgs && $(MAKE) $(TARGET)
+ cd apps && $(MAKE) $(TARGET)
--- a/pkgs/Makefile
+++ b/pkgs/Makefile
@@ -21,19 +21,19 @@
ifeq ("$(KERN)","Darwin")
target:
- cd RNBasics; $(MAKE) $(TARGET)
- cd R2Shapes; $(MAKE) $(TARGET)
- cd R3Shapes; $(MAKE) $(TARGET)
- cd R3Graphics; $(MAKE) $(TARGET)
- cd PDB; $(MAKE) $(TARGET)
+ cd RNBasics && $(MAKE) $(TARGET)
+ cd R2Shapes && $(MAKE) $(TARGET)
+ cd R3Shapes && $(MAKE) $(TARGET)
+ cd R3Graphics && $(MAKE) $(TARGET)
+ cd PDB && $(MAKE) $(TARGET)
else
target:
- cd RNBasics; $(MAKE) $(TARGET)
- cd R2Shapes; $(MAKE) $(TARGET)
- cd R3Shapes; $(MAKE) $(TARGET)
- cd R3Graphics; $(MAKE) $(TARGET)
- cd PDB; $(MAKE) $(TARGET)
- cd freeglut; $(MAKE) $(TARGET)
+ cd RNBasics && $(MAKE) $(TARGET)
+ cd R2Shapes && $(MAKE) $(TARGET)
+ cd R3Shapes && $(MAKE) $(TARGET)
+ cd R3Graphics && $(MAKE) $(TARGET)
+ cd PDB && $(MAKE) $(TARGET)
+ cd freeglut && $(MAKE) $(TARGET)
endif
-------------- next part --------------
Author: Laszlo Kajan <lkajan at rostlab.org>
Description: fix spelling error
--- a/apps/concavity/pocket_extraction.C
+++ b/apps/concavity/pocket_extraction.C
@@ -1028,7 +1028,7 @@
printf(" Minimum cavity radius = %g\n", min_cavity_radius);
printf(" Minimum cavity volume = %g\n", min_cavity_volume);
printf(" Max cavities = %d\n", max_cavities);
- printf(" Grid treshold = %g\n", threshold_range.Mid());
+ printf(" Grid threshold = %g\n", threshold_range.Mid());
printf(" Cardinality = %d\n", mask->Cardinality());
printf(" Volume = %g\n", mask->Volume());
RNInterval grid_range = mask->Range();
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