Author: lkajan-guest Date: 2012-09-28 15:59:19 +0000 (Fri, 28 Sep 2012) New Revision: 12292
Added: trunk/packages/concavity/trunk/debian/ trunk/packages/concavity/trunk/debian/README.source trunk/packages/concavity/trunk/debian/changelog trunk/packages/concavity/trunk/debian/compat trunk/packages/concavity/trunk/debian/control trunk/packages/concavity/trunk/debian/copyright trunk/packages/concavity/trunk/debian/docs trunk/packages/concavity/trunk/debian/patches/ trunk/packages/concavity/trunk/debian/patches/CFLAGSasf trunk/packages/concavity/trunk/debian/patches/compiler_errors trunk/packages/concavity/trunk/debian/patches/default_target_all trunk/packages/concavity/trunk/debian/patches/freeglut trunk/packages/concavity/trunk/debian/patches/noopengllink trunk/packages/concavity/trunk/debian/patches/safe_recursive_make trunk/packages/concavity/trunk/debian/patches/series trunk/packages/concavity/trunk/debian/rules trunk/packages/concavity/trunk/debian/source/ trunk/packages/concavity/trunk/debian/source/format trunk/packages/concavity/trunk/debian/upstream Log: compiles but still no docs Property changes on: trunk/packages/concavity/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/concavity/trunk/debian/README.source =================================================================== --- trunk/packages/concavity/trunk/debian/README.source (rev 0) +++ trunk/packages/concavity/trunk/debian/README.source 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,20 @@ +concavity for Debian +==================== + +Repackaged Upstream Source +-------------------------- +The 'get-orig-source' target is provided to build the upstream tarball. +The problem with the upstream tarball is that it contains a copy of freeglut. In 'get-orig-source' this is deleted from the archive. + +Missing d/watch +--------------- +Upstream (as of 20120928) does not version the downloadable tarball. The version (v0.1) is mentioned on the home page, but the downloadable is simply concavity_distr.tar.gz . +A watch file will be created when upstream introduces version numbers to the name of the downloadable archive. + +Static linking to GAPS library +------------------------------ +These are the files in pkg/. In a personal communication the author (Thomas Funkhouser <[email protected]>) did not endorse the separate packaging of this library, although the license would allow this. +His argument is: +'The problem is that gaps is truly a research-oriented code base. It is highly dynamic, it is partially implemented (some functionality is very fleshed out and other is not at all depending on the needs of our research), and it is not easy to learn (there is no user manual). [...] If other people used the gaps, then they would surely stumble across aspects of the code they don't understand and/or aren't implemented and/or don't work. Unfortunately, I am not in a position to answer questions or to fix/complete the parts of the code not relevant to our research.' + +# vim:et:ts=2: Added: trunk/packages/concavity/trunk/debian/changelog =================================================================== --- trunk/packages/concavity/trunk/debian/changelog (rev 0) +++ trunk/packages/concavity/trunk/debian/changelog 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,6 @@ +concavity (0.1-1) UNRELEASED; urgency=low + + * Initial release (Closes: #689020) + + -- Laszlo Kajan <[email protected]> Fri, 28 Sep 2012 14:23:53 +0200 + Added: trunk/packages/concavity/trunk/debian/compat =================================================================== --- trunk/packages/concavity/trunk/debian/compat (rev 0) +++ trunk/packages/concavity/trunk/debian/compat 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1 @@ +8 Added: trunk/packages/concavity/trunk/debian/control =================================================================== --- trunk/packages/concavity/trunk/debian/control (rev 0) +++ trunk/packages/concavity/trunk/debian/control 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,44 @@ +Source: concavity +Section: science +Priority: extra +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Laszlo Kajan <[email protected]> +Build-Depends: debhelper (>= 8.0.0) +Standards-Version: 3.9.3 +Homepage: http://compbio.cs.princeton.edu/concavity/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/concavity/trunk/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/concavity/trunk/ +DM-Upload-Allowed: yes + +Package: concavity +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: predictor of protein ligand binding sites from structure and conservation + ConCavity predicts protein ligand binding sites by combining evolutionary + sequence conservation and 3D structure. + . + ConCavity takes as input a PDB format protein structure and (optionally) + files that characterize the evolutionary sequence conservation of the chains + in the structure file. + . + The following result files are produced (by default): + * residue ligand binding predictions for each chain (*.scores) + * residue ligand binding predictions in a PDB format file (residue + scores placed in the temp. factor field, *_residue.pdb + * pocket prediction locations in a DX format file (*.dx) + * PyMOL script to visualize the predictions (*.pml) + . + ConCavity has many features. The default run of concavity is equivalent to + ConCavity^L in the paper: + 'Capra JA, Laskowski RA, Thornton JM, Singh M, and Funkhouser TA(2009) + Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence + Conservation and 3D Structure. PLoS Comput Biol, 5(12).'. + +Package: concavity-dbg +Architecture: any +Depends: concavity (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends} +Description: predictor of protein ligand binding sites from structure and conservation (debug) + ConCavity predicts protein ligand binding sites by combining evolutionary + sequence conservation and 3D structure. + . + This package contains the debugging symbols. Added: trunk/packages/concavity/trunk/debian/copyright =================================================================== --- trunk/packages/concavity/trunk/debian/copyright (rev 0) +++ trunk/packages/concavity/trunk/debian/copyright 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,31 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: concavity +Upstream-Contact: Thomas Funkhouser <[email protected]> + John A. Capra <[email protected]> +Source: http://compbio.cs.princeton.edu/concavity/ + +Files: debian/* +Copyright: 2012 Laszlo Kajan <[email protected]> +License: GPL-3.0+ + +Files: * +Copyright: 2009 John A. Capra and Thomas Funkhouser +License: GPL-3.0+ + +License: GPL-3.0+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + On Debian systems, the complete text of the GNU General + Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". + Added: trunk/packages/concavity/trunk/debian/docs =================================================================== --- trunk/packages/concavity/trunk/debian/docs (rev 0) +++ trunk/packages/concavity/trunk/debian/docs 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1 @@ +README.txt Added: trunk/packages/concavity/trunk/debian/patches/CFLAGSasf =================================================================== --- trunk/packages/concavity/trunk/debian/patches/CFLAGSasf (rev 0) +++ trunk/packages/concavity/trunk/debian/patches/CFLAGSasf 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,123 @@ +--- 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 $< + + Added: trunk/packages/concavity/trunk/debian/patches/compiler_errors =================================================================== --- trunk/packages/concavity/trunk/debian/patches/compiler_errors (rev 0) +++ trunk/packages/concavity/trunk/debian/patches/compiler_errors 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,29 @@ +--- 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, "_"); Added: trunk/packages/concavity/trunk/debian/patches/default_target_all =================================================================== --- trunk/packages/concavity/trunk/debian/patches/default_target_all (rev 0) +++ trunk/packages/concavity/trunk/debian/patches/default_target_all 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,12 @@ +--- a/Makefile ++++ b/Makefile +@@ -2,6 +2,9 @@ + # Makefile for GAPS + # + ++.PHONY: all opt ++all: opt ++ + opt: + $(MAKE) target "TARGET=$@" + Added: trunk/packages/concavity/trunk/debian/patches/freeglut =================================================================== --- trunk/packages/concavity/trunk/debian/patches/freeglut (rev 0) +++ trunk/packages/concavity/trunk/debian/patches/freeglut 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,11 @@ +--- 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) $(TARGET) + endif + + Added: trunk/packages/concavity/trunk/debian/patches/noopengllink =================================================================== --- trunk/packages/concavity/trunk/debian/patches/noopengllink (rev 0) +++ trunk/packages/concavity/trunk/debian/patches/noopengllink 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,202 @@ +--- a/scripts/Makefile.apps ++++ b/scripts/Makefile.apps +@@ -58,7 +58,7 @@ + OPENGL_LIBS=-lglut32 -lglu32 -lopengl32 + endif + +-LIBS=$(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; Added: trunk/packages/concavity/trunk/debian/patches/safe_recursive_make =================================================================== --- trunk/packages/concavity/trunk/debian/patches/safe_recursive_make (rev 0) +++ trunk/packages/concavity/trunk/debian/patches/safe_recursive_make 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,57 @@ +--- 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) $(TARGET) + endif + + Added: trunk/packages/concavity/trunk/debian/patches/series =================================================================== --- trunk/packages/concavity/trunk/debian/patches/series (rev 0) +++ trunk/packages/concavity/trunk/debian/patches/series 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,6 @@ +default_target_all +safe_recursive_make +freeglut +CFLAGSasf +compiler_errors +noopengllink Added: trunk/packages/concavity/trunk/debian/rules =================================================================== --- trunk/packages/concavity/trunk/debian/rules (rev 0) +++ trunk/packages/concavity/trunk/debian/rules 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,30 @@ +#!/usr/bin/make -f +#export DH_VERBOSE=1 + +export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) +export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) +export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) +export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) + +export USER_CFLAGS:="-Wno-write-strings" + +.PHONY: get-orig-source +get-orig-source: + set -e; \ + t=$$(mktemp -d) || exit 1; \ + trap "rm -rf -- '$$t'" EXIT; \ + pwd; \ + wget -O $$t/concavity-0.1.tar.gz --quiet http://compbio.cs.princeton.edu/concavity/concavity_distr.tar.gz; \ + ( cd "$$t"; \ + gunzip *.tar.gz; \ + tar --owner=root --group=root --mode=a+rX --delete -f *.tar --wildcards 'concavity_distr/pkgs/freeglut'; \ + xz --best *.tar; \ + ); \ + mv $$t/*.tar.xz ./ + +%: + dh $@ --parallel + +.PHONY: override_dh_strip +override_dh_strip: + dh_strip --dbg-package=concavity-dbg Property changes on: trunk/packages/concavity/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/concavity/trunk/debian/source/format =================================================================== --- trunk/packages/concavity/trunk/debian/source/format (rev 0) +++ trunk/packages/concavity/trunk/debian/source/format 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/concavity/trunk/debian/upstream =================================================================== --- trunk/packages/concavity/trunk/debian/upstream (rev 0) +++ trunk/packages/concavity/trunk/debian/upstream 2012-09-28 15:59:19 UTC (rev 12292) @@ -0,0 +1,14 @@ +Name: ConCavity +Contact: http://compbio.cs.princeton.edu/concavity/ +Homepage: http://compbio.cs.princeton.edu/concavity/ +Reference: + - Author: John A. Capra and Roman A. Laskowski and Janet M. Thornton and Mona Singh and Thomas A. Funkhouser + Title: Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure + Journal: PLoS Computational Biology + Volume: 5 + Number: 12 + Pages: e1000585 + Year: 2009 + URL: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000585 + DOI: 10.1371/journal.pcbi.1000585 + PMID: 19997483 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
