[med-svn] r17714 - in trunk/packages/autodocksuite/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Aug 13 06:14:57 UTC 2014
Author: tille
Date: 2014-08-13 06:14:56 +0000 (Wed, 13 Aug 2014)
New Revision: 17714
Added:
trunk/packages/autodocksuite/trunk/debian/patches/create_fake_autoreconf_files.patch
Removed:
trunk/packages/autodocksuite/trunk/debian/README.source
trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_1.patch
trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_2.patch
trunk/packages/autodocksuite/trunk/debian/patches/fix_test_outputdir.patch
trunk/packages/autodocksuite/trunk/debian/patches/make.patch
Modified:
trunk/packages/autodocksuite/trunk/debian/changelog
trunk/packages/autodocksuite/trunk/debian/patches/series
Log:
Adapt patches
Deleted: trunk/packages/autodocksuite/trunk/debian/README.source
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/README.source 2014-08-13 05:47:48 UTC (rev 17713)
+++ trunk/packages/autodocksuite/trunk/debian/README.source 2014-08-13 06:14:56 UTC (rev 17714)
@@ -1 +0,0 @@
-The folder structure was simplified, i.e. /src renamed to autodock-<version> .
Modified: trunk/packages/autodocksuite/trunk/debian/changelog
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/changelog 2014-08-13 05:47:48 UTC (rev 17713)
+++ trunk/packages/autodocksuite/trunk/debian/changelog 2014-08-13 06:14:56 UTC (rev 17714)
@@ -1,6 +1,6 @@
autodocksuite (4.2.6-1) UNRELEASED; urgency=medium
- * New upstream version
+ * New upstream version (adapt patches)
* d/copyright: DEP5
-- Andreas Tille <tille at debian.org> Wed, 13 Aug 2014 07:37:23 +0200
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_1.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_1.patch 2014-08-13 05:47:48 UTC (rev 17713)
+++ trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_1.patch 2014-08-13 06:14:56 UTC (rev 17714)
@@ -1,92 +0,0 @@
-Index: autodocksuite-4.2.5.1/autodock/eval.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/eval.cc
-+++ autodocksuite-4.2.5.1/autodock/eval.cc
-@@ -63,7 +63,7 @@
- tor 1, ..., tor N are the ntor torsion angles
- */
-
--void make_state_from_rep(const Representation *const *const rep, /* not const */ State *const stateNow, const int outlev, FILE *logFile) /* not a member function */
-+void make_state_from_rep(const Representation *const *const rep, /* not const */ State *const stateNow, const int outlev, FILE *const logFile) /* not a member function */
- /*
- This routine modifies the various components of stateNow to correspond
- to the chromosome.
-@@ -252,7 +252,7 @@
- }
-
- int Eval::write(const Representation *const *const rep,
-- const int true_ligand_atoms, const int outlev, FILE *logFile)
-+ const int true_ligand_atoms, const int outlev, FILE *const logFile)
- {
- int i=0, retval=0;
- //char rec14[14];
-@@ -272,14 +272,14 @@
- }
-
- #if defined(USING_COLINY) // {
--double Eval::operator()(const double* const vec, const int len, const int outlev, FILE *logFile)
-+double Eval::operator()(const double* const vec, const int len, const int outlev, FILE *const logFile)
- {
- make_state_from_rep(vec, len, &stateNow, outlev, logFile);
- return eval();
- }
-
-
--void make_state_from_rep(const double *const rep, const int n, /* not const */ State *const now, const int outlev, FILE *logFile)
-+void make_state_from_rep(const double *const rep, const int n, /* not const */ State *const now, const int outlev, FILE *const logFile)
- {
- # ifdef DEBUG
- (void)fprintf(logFile, "eval.cc/make_state_from_rep(double *rep, int n, State *now)\n");
-Index: autodocksuite-4.2.5.1/autodock/eval.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/eval.h
-+++ autodocksuite-4.2.5.1/autodock/eval.h
-@@ -49,7 +49,7 @@
- void make_state_from_rep(const double *const x, const int n, State *const now);
- #endif
-
--void make_state_from_rep(const Representation *const *const rep, State *const stateNow, int outlev, FILE *logFile);
-+void make_state_from_rep(const Representation *const *const rep, State *const stateNow, int outlev, FILE *const logFile);
-
- class Eval
- {
-@@ -120,7 +120,7 @@
- const Boole init_B_have_flexible_residues,
- int init_true_ligand_atoms,
- int init_outlev,
-- FILE *init_logFile
-+ FILE *const init_logFile
- );
- void update_crds( Real init_crd[MAX_ATOMS][SPACE],
- Real init_vt[MAX_TORS][SPACE] );
-@@ -134,7 +134,7 @@
- double eval(const int); // GMM - allows calculation of a particular term of the total energy
- UnsignedFourByteLong evals(void);
- void reset(void);
-- int write(const Representation *const *const rep, const int true_ligand_atoms, const int outlev, FILE *logFile);
-+ int write(const Representation *const *const rep, const int true_ligand_atoms, const int outlev, FILE *const logFile);
- void compute_intermol_energy(const Boole init_B_compute_intermol_energy); // for computing unbound state
- };
-
-@@ -182,7 +182,7 @@
- const Boole init_B_have_flexible_residues,
- int init_true_ligand_atoms,
- int init_outlev,
-- FILE *init_logFile
-+ FILE *const init_logFile
- )
-
- {
-Index: autodocksuite-4.2.5.1/autodock/qmultiply.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/qmultiply.cc
-+++ autodocksuite-4.2.5.1/autodock/qmultiply.cc
-@@ -514,7 +514,7 @@
- ratioB = sin(t * halfTheta) / sinHalfTheta;
- } else {
- // qa and qb (qb_local) are very close, so we can do a linear interpolation
-- ratioA = 1 - t ;
-+ ratioA = 1. - t ;
- ratioB = t;
- }
- // Calculate final values
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_2.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_2.patch 2014-08-13 05:47:48 UTC (rev 17713)
+++ trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_2.patch 2014-08-13 06:14:56 UTC (rev 17714)
@@ -1,886 +0,0 @@
-Index: autodocksuite-4.2.5.1/autodock/rep.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/rep.cc
-+++ autodocksuite-4.2.5.1/autodock/rep.cc
-@@ -914,7 +914,7 @@
-
- //______________________________________________________________________________
- //
--void BitVector::write(const FourByteLong& value, const int gene)
-+void BitVector::write(const FourByteLong& value, const int gene)
- {
-
- #ifdef DEBUG
-Index: autodocksuite-4.2.5.1/autodock/conformation_sampler.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/conformation_sampler.cc
-+++ autodocksuite-4.2.5.1/autodock/conformation_sampler.cc
-@@ -71,7 +71,7 @@
- {ICO_Y, ICO_X, 0.}, {-ICO_Y, ICO_X, 0.}, {ICO_Y, -ICO_X, 0.}, {-ICO_Y, -ICO_X, 0.}};
-
- ConformationSampler::ConformationSampler(const State& init_state,
-- int true_ligand_atoms, int outlev, FILE *logFile) {
-+ const int true_ligand_atoms, const int outlev, FILE *const logFile) {
- base_state = init_state;
- base_ind = set_ind(info, init_state);
- base_point = base_ind.phenotyp;
-@@ -116,11 +116,11 @@
- }
- }
-
--void ConformationSampler::random_sample(int true_ligand_atoms, int outlev, FILE *logFile) {
-+void ConformationSampler::random_sample(const int true_ligand_atoms, const int outlev, FILE *const logFile) {
- random_sample(1, true_ligand_atoms, outlev, logFile);
- }
-
--void ConformationSampler::random_sample(const int num_samples, int true_ligand_atoms, int outlev, FILE *logFile) {
-+void ConformationSampler::random_sample(const int num_samples, const int true_ligand_atoms, const int outlev, FILE *const logFile) {
- Real multiplier;
-
- for (int sample=0; sample < num_samples; sample++) {
-@@ -152,7 +152,7 @@
-
- // NOTE: currently, the torsional free energy penalty is not included.
- // Since this is an entropic term, I believe we can ignore it in this analysis.
--Real ConformationSampler::current_energy(int true_ligand_atoms, int outlev, FILE *logFile) /* not const */ {
-+Real ConformationSampler::current_energy(const int true_ligand_atoms, const int outlev, FILE *const logFile) /* not const */ {
- evals++;
- Real energy = probe_point.evaluate(Normal_Eval);
- Real rmsd = current_rmsd(true_ligand_atoms, outlev, logFile);
-@@ -198,7 +198,7 @@
- }
-
- Real ConformationSampler::current_rmsd(
-- int true_ligand_atoms, int outlev, FILE *logFile) /* not const */ {
-+ const int true_ligand_atoms, const int outlev, FILE *const logFile) /* not const */ {
- probe_ind.phenotyp = probe_point;
- probe_ind.inverse_mapping();
- probe_state = probe_ind.state(base_state.ntor);
-@@ -245,7 +245,7 @@
- }
- }
-
--void ConformationSampler::systematic_search(const int index, int true_ligand_atoms, int outlev, FILE *logFile) {
-+void ConformationSampler::systematic_search(const int index, const int true_ligand_atoms, const int outlev, FILE *const logFile) {
-
- // for rotation axes, rotate using the pre-defined vertices
- if ( is_axis_index( index ) ) {
-@@ -369,7 +369,7 @@
- return RT_CONSTANT*log(Vtot*Vconf*Boltzmann_diff_sum);
- }
-
--void ConformationSampler::output_statistics(int outlev, FILE *logFile) const {
-+void ConformationSampler::output_statistics(const int outlev, FILE *const logFile) const {
- if(outlev<0) return;
- fprintf(logFile, "Conformation starting energy: %.3f\n", base_energy);
- fprintf(logFile, "RMSD from reference state: %.3f\n", reference_rmsd());
-@@ -391,7 +391,7 @@
- }
-
- void systematic_conformation_sampler(const State hist[MAX_RUNS], const int nconf, Real init_vt[MAX_TORS][SPACE], Real init_crdpdb[MAX_ATOMS][SPACE], int init_tlist[MAX_TORS+1][MAX_ATOMS], Real init_lig_center[SPACE], const int init_natom, int init_type[MAX_ATOMS], GridMapSetInfo *const init_info,
-- int true_ligand_atoms, int outlev, FILE *logFile) {
-+ const int true_ligand_atoms, const int outlev, FILE *const logFile) {
- vt = init_vt;
- crdpdb = init_crdpdb;
- tlist = init_tlist;
-@@ -415,7 +415,7 @@
- }
-
- void random_conformation_sampler(const State hist[MAX_RUNS], const int nconf, /* not const */ int num_samples, Real init_vt[MAX_TORS][SPACE], Real init_crdpdb[MAX_ATOMS][SPACE], int init_tlist[MAX_TORS+1][MAX_ATOMS], Real init_lig_center[SPACE], const int init_natom, int init_type[MAX_ATOMS], GridMapSetInfo *const init_info,
-- int true_ligand_atoms, int outlev, FILE *logFile) {
-+ const int true_ligand_atoms, const int outlev, FILE *const logFile) {
- vt = init_vt;
- crdpdb = init_crdpdb;
- tlist = init_tlist;
-@@ -442,7 +442,7 @@
-
-
- /* copied (and slightly modified) from non-included code in call_glss.cc */
--Individual set_ind(GridMapSetInfo *const info, const State state)
-+Individual set_ind(const GridMapSetInfo *const info, const State& state) // ATTENTION: Steffen changed 2013 const State to const State &
- {
- Genotype temp_Gtype;
- Phenotype temp_Ptype;
-@@ -500,7 +500,7 @@
- Real angle_sin = sin(raa[3]);
- Real t = 1.0 - angle_cos;
-
-- // make sure that input vecotr is a unit vector
-+ // make sure that input vector is a unit vector
- Real length = hypotenuse(raa[0], raa[1], raa[2]);
- raa[0] /= length;
- raa[1] /= length;
-Index: autodocksuite-4.2.5.1/autodock/conformation_sampler.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/conformation_sampler.h
-+++ autodocksuite-4.2.5.1/autodock/conformation_sampler.h
-@@ -65,20 +65,20 @@
- Real bin_Boltzmann_sum[NUM_BINS];
-
- ConformationSampler(const State&,
-- int true_ligand_atoms, int outlev, FILE *logFile);
-+ const int true_ligand_atoms, const int outlev, FILE *const logFile);
- ~ConformationSampler(void);
-
-- void random_sample(int true_ligand_atoms, int outlev, FILE *logFile);
-- void random_sample(const int, int true_ligand_atoms, int outlev, FILE *logFile);
-- void systematic_search(const int index, int true_ligand_atoms, int outlev, FILE *logFile);
-- Real current_energy(int true_ligand_atoms, int outlev, FILE *logFile); /* not const */
-- Real current_rmsd(int true_ligand_atoms, int outlev, FILE *logFile); /* not const */
-+ void random_sample(const int true_ligand_atoms, const int outlev, FILE *const logFile);
-+ void random_sample(const int, const int true_ligand_atoms, const int outlev, FILE *const logFile);
-+ void systematic_search(const int index, const int true_ligand_atoms, const int outlev, FILE *const logFile);
-+ Real current_energy(const int true_ligand_atoms, const int outlev, FILE *const logFile); /* not const */
-+ Real current_rmsd(const int true_ligand_atoms, const int outlev, FILE *const logFile); /* not const */
- Real reference_rmsd(void) const;
- Real fraction_favorable(void) const;
- Real average_favorable_energy(void) const;
- Real energy_volume(void) const;
- Real RK_entropy(void) const;
-- void output_statistics(int outlev, FILE *logFile) const;
-+ void output_statistics(const int outlev, FILE *const logFile) const;
- Real partition_function(void) const;
- Real partition_function(int bin) const;
- Real entropy_estimate(void) const;
-@@ -93,16 +93,16 @@
- const int nconf, Real init_vt[MAX_TORS][SPACE], Real init_crdpdb[MAX_ATOMS][SPACE],
- int init_tlist[MAX_TORS+1][MAX_ATOMS], Real init_lig_center[SPACE],
- const int init_natom, int init_type[MAX_ATOMS], GridMapSetInfo *const init_info,
-- int true_ligand_atoms, int outlev, FILE *logFile);
-+ const int true_ligand_atoms, const int outlev, FILE *const logFile);
-
- void random_conformation_sampler(const State hist[MAX_RUNS], const int nconf,
- /* const */ int num_samples, Real init_vt[MAX_TORS][SPACE],
- Real init_crdpdb[MAX_ATOMS][SPACE], int init_tlist[MAX_TORS+1][MAX_ATOMS],
- Real init_lig_center[SPACE], const int init_natom, int init_type[MAX_ATOMS],
- GridMapSetInfo *const init_info,
-- int true_ligand_atoms, int outlev, FILE *logFile);
-+ const int true_ligand_atoms, const int outlev, FILE *const logFile);
-
--Individual set_ind(GridMapSetInfo *const info, const State state);
-+Individual set_ind(const GridMapSetInfo *const info, const State& state); // Attention, newly changed const State to State&
- void raaEuler(const Real raa[4], /* not const */ Real euler[3]);
- void testMatrix(void);
- void raaMatrix(Real raa[4], Real matrix[3][3]);
-Index: autodocksuite-4.2.5.1/autodock/eintcal.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/eintcal.cc
-+++ autodocksuite-4.2.5.1/autodock/eintcal.cc
-@@ -55,7 +55,7 @@
- const Boole B_use_non_bond_cutoff,
- const Boole B_have_flexible_residues, // if the receptor has flexibile residues, this will be set to TRUE
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- )
-
- #else
-@@ -80,7 +80,7 @@
- const int type[],
- char const atom_type_name[MAX_MAPS][3],
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- )
- // eintcalPrint ]
-
-Index: autodocksuite-4.2.5.1/autodock/eintcal.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/eintcal.h
-+++ autodocksuite-4.2.5.1/autodock/eintcal.h
-@@ -46,6 +46,6 @@
- const Boole B_use_non_bond_cutoff,
- const Boole B_have_flexible_residues,
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
-
- #endif /*!EINTCAL*/
-Index: autodocksuite-4.2.5.1/autodock/intnbtable.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/intnbtable.cc
-+++ autodocksuite-4.2.5.1/autodock/intnbtable.cc
-@@ -51,8 +51,8 @@
- #endif
-
- extern int debug;
--static void printminvalue( char *label, const Real e_vdW_Hb[NEINT][MAX_ATOM_TYPES][MAX_ATOM_TYPES],
-- const int neint, const int a1, const int a2, FILE *logFile); // see end of this file
-+static void printminvalue(const char *const label, const Real e_vdW_Hb[NEINT][MAX_ATOM_TYPES][MAX_ATOM_TYPES],
-+ const int neint, const int a1, const int a2, FILE *const logFile); // see end of this file
-
-
- void intnbtable( Boole *const P_B_havenbp,
-@@ -69,7 +69,7 @@
- ConstDouble sigma,
- /* not const */ EnergyTables *const ad_tables,
- const Boole B_is_unbound_calculation,
-- FILE *logFile,
-+ FILE *const logFile,
- const int outlev)
- {
- /* Local variables: */
-@@ -260,7 +260,7 @@
- /* end of intnbtable */
-
-
--void setup_distdepdiel( FILE *logFile,
-+void setup_distdepdiel( FILE *const logFile,
- const int outlev,
- EnergyTables *const ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
- )
-@@ -291,8 +291,8 @@
- }
- /* end of setup_distdepdiel */
-
--static void printminvalue( char *label, const Real e_vdW_Hb[NEINT][MAX_ATOM_TYPES][MAX_ATOM_TYPES],
-- const int neint, const int a1, const int a2, FILE *logFile)
-+static void printminvalue(const char *const label, const Real e_vdW_Hb[NEINT][MAX_ATOM_TYPES][MAX_ATOM_TYPES],
-+ const int neint, const int a1, const int a2, FILE *const logFile)
- {
- /* report distance range over which minimum value appears - a 'smoothing' debug tool mostly */
- int i;
-Index: autodocksuite-4.2.5.1/autodock/intnbtable.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/intnbtable.h
-+++ autodocksuite-4.2.5.1/autodock/intnbtable.h
-@@ -44,6 +44,6 @@
- ConstDouble sigma,
- /* not const */ EnergyTables *const ad_tables,
- const Boole B_is_unbound_calculation,
-- FILE *logFile,
-+ FILE *const logFile,
- const int outlev);
- #endif
-Index: autodocksuite-4.2.5.1/autodock/mkNewState.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/mkNewState.cc
-+++ autodocksuite-4.2.5.1/autodock/mkNewState.cc
-@@ -50,7 +50,7 @@
- const int N_con[MAX_TORS],
- const int true_ligand_atoms,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
- // Create a new state, based on the current state
- {
- register int i;
-Index: autodocksuite-4.2.5.1/autodock/mkNewState.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/mkNewState.h
-+++ autodocksuite-4.2.5.1/autodock/mkNewState.h
-@@ -55,5 +55,5 @@
- const int N_con[MAX_TORS],
- const int true_ligand_atoms,
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
- #endif
-Index: autodocksuite-4.2.5.1/autodock/mkRandomState.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/mkRandomState.cc
-+++ autodocksuite-4.2.5.1/autodock/mkRandomState.cc
-@@ -34,10 +34,10 @@
- #include "mkRandomState.h"
-
-
--State mkRandomState( int ntor,
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS],
-- GridMapSetInfo *info)
-+State mkRandomState( const int ntor,
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS],
-+ const GridMapSetInfo *const info)
-
- {
- State now;
-Index: autodocksuite-4.2.5.1/autodock/mkRandomState.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/mkRandomState.h
-+++ autodocksuite-4.2.5.1/autodock/mkRandomState.h
-@@ -29,8 +29,8 @@
-
- #include "constants.h"
-
--State mkRandomState( int ntor,
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS],
-- GridMapSetInfo *info);
-+State mkRandomState( const int ntor,
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS],
-+ const GridMapSetInfo *const info);
- #endif
-Index: autodocksuite-4.2.5.1/autodock/mkTorTree.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/mkTorTree.cc
-+++ autodocksuite-4.2.5.1/autodock/mkTorTree.cc
-@@ -58,9 +58,9 @@
- /* not const */ Real *const P_squpper,
- /* not const */ int *const P_ntorsdof,
- /* not const */ int ignore_inter[MAX_ATOMS],
-- int true_ligand_atoms,
-- int outlev,
-- FILE *logFile)
-+ const int true_ligand_atoms,
-+ const int outlev,
-+ FILE *const logFile)
-
- {
-
-Index: autodocksuite-4.2.5.1/autodock/mkTorTree.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/mkTorTree.h
-+++ autodocksuite-4.2.5.1/autodock/mkTorTree.h
-@@ -46,7 +46,7 @@
- Real *const P_squpper,
- int *const P_ntorsdof,
- int ignore_inter[MAX_ATOMS],
-- int true_ligand_atoms,
-- int outlev,
-- FILE *logFile);
-+ const int true_ligand_atoms,
-+ const int outlev,
-+ FILE *const logFile);
- #endif
-Index: autodocksuite-4.2.5.1/autodock/nonbonds.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/nonbonds.cc
-+++ autodocksuite-4.2.5.1/autodock/nonbonds.cc
-@@ -50,9 +50,9 @@
- const int bonded[MAX_ATOMS][MAX_NBONDS],
- const int debug,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
- {
-- int i,j,k,l;
-+ int i,j,k,l;
- int nonbond_type;
- int errorcode = 0;
-
-@@ -137,7 +137,7 @@
- /* not const */ int bonded[MAX_ATOMS][MAX_NBONDS],
- const int debug,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- )
- {
- int i,j;
-@@ -240,7 +240,7 @@
- /*----------------------------------------------------------------------------*/
-
- void printbonds(const int natom, const int nbonds[MAX_ATOMS], const int bonded[MAX_ATOMS][MAX_NBONDS], const char *message, const int B_print_all_bonds,
--const int outlev, FILE *logFile)
-+const int outlev, FILE *const logFile)
- {
- pr(logFile, "%s", message);
- for (int i = 0; i<natom; i++) { // loop over atoms, "i", from 1 to natom
-@@ -256,7 +256,7 @@
-
- /*----------------------------------------------------------------------------*/
-
--void print_1_4_message(const Boole B_include_1_4_interactions, const Real scale_1_4, const int outlev, FILE *logFile)
-+void print_1_4_message(const Boole B_include_1_4_interactions, const Real scale_1_4, const int outlev, FILE *const logFile)
- {
- if (B_include_1_4_interactions == FALSE) {
- if(outlev >= LOGBASIC)
-Index: autodocksuite-4.2.5.1/autodock/nonbonds.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/nonbonds.h
-+++ autodocksuite-4.2.5.1/autodock/nonbonds.h
-@@ -37,7 +37,7 @@
- const int bonded[MAX_ATOMS][MAX_NBONDS],
- const int debug,
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
- #endif
-
- #ifndef GETBONDS
-@@ -52,13 +52,13 @@
- /* not const */ int bonded[MAX_ATOMS][MAX_NBONDS],
- const int debug,
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
- #endif
-
- #ifndef PRINTBONDS
- #define PRINTBONDS
- #include "constants.h"
--void printbonds(const int natom, const int nbonds[MAX_ATOMS], const int bonded[MAX_ATOMS][MAX_NBONDS], const char *message, const int B_print_all_bonds, const int outlev, FILE *logFile);
-+void printbonds(const int natom, const int nbonds[MAX_ATOMS], const int bonded[MAX_ATOMS][MAX_NBONDS], const char *message, const int B_print_all_bonds, const int outlev, FILE *const logFile);
- #endif
-
- #ifndef PRINT14
-@@ -66,5 +66,5 @@
- #include "constants.h"
- #include <stdio.h>
- void print_1_4_message(Boole B_include_1_4_interactions, Real scale_1_4,
--const int outlev, FILE *logFile);
-+const int outlev, FILE *const logFile);
- #endif
-Index: autodocksuite-4.2.5.1/autodock/readPDBQT.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/readPDBQT.cc
-+++ autodocksuite-4.2.5.1/autodock/readPDBQT.cc
-@@ -96,7 +96,7 @@
- /* not const */ int end_of_branch[MAX_TORS],
- const int debug,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- )
-
- {
-@@ -667,7 +667,7 @@
- Real *const ptr_q,
- ParameterEntry *const this_parameter_entry,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
- /*----------------------------------------------------------------------------*/
- {
- char char8[9];
-Index: autodocksuite-4.2.5.1/autodock/readPDBQT.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/readPDBQT.h
-+++ autodocksuite-4.2.5.1/autodock/readPDBQT.h
-@@ -46,7 +46,7 @@
- Real *const P_q,
- ParameterEntry *thisparm,
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
-
- Molecule readPDBQT( char line[LINE_LEN],
-
-@@ -98,6 +98,6 @@
- /* not const */ int end_of_branch[MAX_TORS],
- const int debug,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- );
- #endif
-Index: autodocksuite-4.2.5.1/autodock/torNorVec.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/torNorVec.cc
-+++ autodocksuite-4.2.5.1/autodock/torNorVec.cc
-@@ -41,7 +41,7 @@
- const int tlist[MAX_TORS][MAX_ATOMS],
- /* not const */ Real vt[MAX_TORS][SPACE],
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
- {
-
- register int xyz = 0;
-@@ -99,7 +99,7 @@
- /* not const */ Molecule *ligand,
- const int debug,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
- { // Update the unit vectors for the torsion rotations
- register int i=0, j=0;
- if (debug > 0) {
-Index: autodocksuite-4.2.5.1/autodock/torNorVec.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/torNorVec.h
-+++ autodocksuite-4.2.5.1/autodock/torNorVec.h
-@@ -36,7 +36,7 @@
- const int tlist[MAX_TORS+1][MAX_ATOMS],
- /* not const */ Real vt[MAX_TORS][SPACE],
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
-
- void update_torsion_vectors( const Real crdpdb[MAX_ATOMS][SPACE],
- const int ntor,
-@@ -45,6 +45,6 @@
- /* not const */ Molecule *ligand,
- const int debug,
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
-
- #endif
-Index: autodocksuite-4.2.5.1/autodock/weedbonds.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/weedbonds.cc
-+++ autodocksuite-4.2.5.1/autodock/weedbonds.cc
-@@ -48,7 +48,7 @@
- const int type[MAX_ATOMS],
- const int debug,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
-
- {
- int a11=0;
-@@ -246,7 +246,7 @@
- const NonbondParam *const nonbondlist,
- const int type[MAX_ATOMS],
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
-
- {
- register int i = 0;
-Index: autodocksuite-4.2.5.1/autodock/weedbonds.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/weedbonds.h
-+++ autodocksuite-4.2.5.1/autodock/weedbonds.h
-@@ -44,7 +44,7 @@
- const int type[MAX_ATOMS],
- const int debug,
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
- #endif
-
-
-@@ -66,6 +66,6 @@
- const NonbondParam *nonbondlist,
- const int type[MAX_ATOMS],
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
- #endif
-
-Index: autodocksuite-4.2.5.1/autodock/analysis.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/analysis.cc
-+++ autodocksuite-4.2.5.1/autodock/analysis.cc
-@@ -102,7 +102,7 @@
- const Boole B_rms_heavy_atoms_only,
- const int h_index,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
-
- )
-
-Index: autodocksuite-4.2.5.1/autodock/analysis.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/analysis.h
-+++ autodocksuite-4.2.5.1/autodock/analysis.h
-@@ -87,6 +87,6 @@
- const Boole B_rms_heavy_atoms_only,
- const int h_index,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- );
- #endif
-Index: autodocksuite-4.2.5.1/autodock/calculateEnergies.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/calculateEnergies.cc
-+++ autodocksuite-4.2.5.1/autodock/calculateEnergies.cc
-@@ -72,7 +72,7 @@
- const Real qsp_abs_charge[MAX_ATOMS], // input q-solvation parameters
- const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
-
- )
-
-@@ -189,7 +189,7 @@
- const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
- const Unbound_Model ad4_unbound_model,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
-
- )
-
-Index: autodocksuite-4.2.5.1/autodock/calculateEnergies.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/calculateEnergies.h
-+++ autodocksuite-4.2.5.1/autodock/calculateEnergies.h
-@@ -61,7 +61,7 @@
- const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
- const Unbound_Model ad4_unbound_model,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
-
- );
-
-@@ -103,7 +103,7 @@
- const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
- const Unbound_Model ad4_unbound_model,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
-
- );
-
-Index: autodocksuite-4.2.5.1/autodock/call_gs.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/call_gs.cc
-+++ autodocksuite-4.2.5.1/autodock/call_gs.cc
-@@ -47,11 +47,11 @@
-
- extern Eval evaluate;
-
--State call_gs(Global_Search *global_method, State& now, unsigned int num_evals, unsigned int pop_size,
-- Molecule *mol,
-- Output_pop_stats& extOutput_pop_stats,
-- GridMapSetInfo *info,
-- int end_of_branch[MAX_TORS], int outlev, FILE * logFile)
-+State call_gs(Global_Search *const global_method, const State& now, const unsigned int num_evals, const unsigned int pop_size,
-+ Molecule *const mol,
-+ const Output_pop_stats& extOutput_pop_stats,
-+ const GridMapSetInfo *const info,
-+ const int end_of_branch[MAX_TORS], const int outlev, FILE *const logFile)
- {
- register unsigned int i;
-
-Index: autodocksuite-4.2.5.1/autodock/clmode.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/clmode.cc
-+++ autodocksuite-4.2.5.1/autodock/clmode.cc
-@@ -55,7 +55,7 @@
- const Boole B_rms_heavy_atoms_only,
- const int h_index,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
-
- {
- FILE *clusFile;
-Index: autodocksuite-4.2.5.1/autodock/clmode.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/clmode.h
-+++ autodocksuite-4.2.5.1/autodock/clmode.h
-@@ -54,6 +54,6 @@
- const Boole B_rms_heavy_atoms_only,
- const int h_index,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- );
- #endif
-Index: autodocksuite-4.2.5.1/autodock/cnv_state_to_coords.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/cnv_state_to_coords.cc
-+++ autodocksuite-4.2.5.1/autodock/cnv_state_to_coords.cc
-@@ -50,7 +50,7 @@
- const int natom,
- const int true_ligand_atoms,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
-
- {
- #ifdef DEBUG
-Index: autodocksuite-4.2.5.1/autodock/getInitialState.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/getInitialState.cc
-+++ autodocksuite-4.2.5.1/autodock/getInitialState.cc
-@@ -99,7 +99,7 @@
- const Boole B_have_flexible_residues,
- const Unbound_Model ad4_unbound_model,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- )
-
- {
-Index: autodocksuite-4.2.5.1/autodock/getInitialState.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/getInitialState.h
-+++ autodocksuite-4.2.5.1/autodock/getInitialState.h
-@@ -92,7 +92,7 @@
- const Boole B_have_flexible_residues,
- const Unbound_Model ad4_unbound_model,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- );
-
- #endif
-Index: autodocksuite-4.2.5.1/autodock/gs.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/gs.cc
-+++ autodocksuite-4.2.5.1/autodock/gs.cc
-@@ -1415,7 +1415,7 @@
- //
- // This is where the action is... SEARCH!
- //
--int Genetic_Algorithm::search(Population &solutions, int outlev, FILE *logFile)
-+int Genetic_Algorithm::search(Population &solutions, const int outlev, FILE *const logFile)
- {
- register unsigned int i;
-
-@@ -1516,8 +1516,8 @@
- }
- return(0);
- }
--int Genetic_Algorithm::localsearch(Population &thisPop, Local_Search *local_method,
-- int outlev, FILE *logFile)
-+int Genetic_Algorithm::localsearch(Population &thisPop, Local_Search *const local_method,
-+ const int outlev, FILE *const logFile)
- {
- // apply local search (if not NULL) to population with
- // frequency search_freq
-Index: autodocksuite-4.2.5.1/autodock/gs.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/gs.h
-+++ autodocksuite-4.2.5.1/autodock/gs.h
-@@ -46,8 +46,8 @@
- public:
- Global_Search(unsigned int init_max_evals, unsigned int init_max_generations);
- virtual ~Global_Search(void);
-- virtual int search(Population &, int, FILE *) = 0;
-- virtual int localsearch(Population &, Local_Search *, int, FILE *) = 0;
-+ virtual int search(Population &, const int, FILE *const) = 0;
-+ virtual int localsearch(Population &, Local_Search *const, int, FILE *) = 0;
- virtual int terminate(void) = 0;
- virtual void reset(void) = 0;
- virtual void reset(const Output_pop_stats&) = 0;
-@@ -137,8 +137,8 @@
- char * shortname(void);
- char * longname(void);
- int terminate(void);
-- int search(Population &, int, FILE *);
-- int localsearch(Population &, Local_Search *, int, FILE *);
-+ int search(Population &, const int, FILE *const);
-+ int localsearch(Population &, Local_Search *, const int, FILE *const);
- int set_linear_ranking_selection_probability_ratio(ConstReal );
-
- };
-Index: autodocksuite-4.2.5.1/autodock/investigate.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/investigate.cc
-+++ autodocksuite-4.2.5.1/autodock/investigate.cc
-@@ -94,7 +94,7 @@
- const int h_index,
- const int true_ligand_atoms,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
-
- {
- Boole B_outside = FALSE;
-Index: autodocksuite-4.2.5.1/autodock/pso.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/pso.cc
-+++ autodocksuite-4.2.5.1/autodock/pso.cc
-@@ -35,7 +35,7 @@
- * Caution: do not reorder the Pop array outside of these functions. MP/RH
- * Packaged algorithm options into a structure to simplify signatures.
- ***********************************************************************/
--int ParticleSwarmGS::search(Population &Pop, int outlev, FILE * logFile)
-+int ParticleSwarmGS::search(Population &Pop, const int outlev, FILE *const logFile)
- {
- int j;
- double curVal;
-@@ -371,7 +371,7 @@
- return (0);
- }
-
--int ParticleSwarmGS::localsearch(Population &Pop, Local_Search *local_method, int outlev, FILE * logFile)
-+int ParticleSwarmGS::localsearch(Population &Pop, Local_Search *const local_method, const int outlev, FILE *const logFile)
- {
- // does local search (unconditonally) on "best" (index) indiv, which may not be historic best
-
-Index: autodocksuite-4.2.5.1/autodock/pso.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/pso.h
-+++ autodocksuite-4.2.5.1/autodock/pso.h
-@@ -92,8 +92,8 @@
- void reset(void);
- void reset(const Output_pop_stats&);
- int terminate(void);
-- int search(Population &, int outlev, FILE * logFile);
-- int localsearch(Population &, Local_Search *, int outlev, FILE * logFile);
-+ int search(Population &, const int outlev, FILE *const logFile);
-+ int localsearch(Population &, Local_Search *const, const int outlev, FILE *const logFile);
- };
-
- inline char * ParticleSwarmGS::shortname(void)
-Index: autodocksuite-4.2.5.1/autodock/read_parameter_library.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/read_parameter_library.cc
-+++ autodocksuite-4.2.5.1/autodock/read_parameter_library.cc
-@@ -48,7 +48,7 @@
- static char parameter_library[MAX_CHARS];
-
- void read_parameter_library(
-- FILE *logFile,
-+ FILE *const logFile,
- const int outlev,
- const char *const FN_parameter_library,
- Linear_FE_Model *AD4
-Index: autodocksuite-4.2.5.1/autodock/readfield.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/readfield.cc
-+++ autodocksuite-4.2.5.1/autodock/readfield.cc
-@@ -41,7 +41,7 @@
- const Clock& jobStart,
- const struct tms& tms_jobStart,
- const int outlev,
-- FILE *logFile)
-+ FILE *const logFile)
- {
- FILE *fldFile;
- char rec9[9], inputline[LINE_LEN];
-Index: autodocksuite-4.2.5.1/autodock/readfield.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/readfield.h
-+++ autodocksuite-4.2.5.1/autodock/readfield.h
-@@ -37,7 +37,7 @@
- const Clock& jobStart,
- const struct tms& tms_jobStart,
- const int outlev,
-- FILE *logFile);
-+ FILE *const logFile);
-
-
- #endif
-Index: autodocksuite-4.2.5.1/autodock/simanneal.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/simanneal.cc
-+++ autodocksuite-4.2.5.1/autodock/simanneal.cc
-@@ -145,7 +145,7 @@
- const char PDBQT_record[MAX_RECORDS][LINE_LEN],
- const Unbound_Model ad4_unbound_model,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- )
-
- {
-Index: autodocksuite-4.2.5.1/autodock/writePDBQT.cc
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/writePDBQT.cc
-+++ autodocksuite-4.2.5.1/autodock/writePDBQT.cc
-@@ -84,7 +84,7 @@
- const Boole B_have_flexible_residues,
- const Unbound_Model ad4_unbound_model,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- )
-
- {
-Index: autodocksuite-4.2.5.1/autodock/writePDBQT.h
-===================================================================
---- autodocksuite-4.2.5.1.orig/autodock/writePDBQT.h
-+++ autodocksuite-4.2.5.1/autodock/writePDBQT.h
-@@ -75,7 +75,7 @@
- const Boole B_have_flexible_residues,
- const Unbound_Model ad4_unbound_model,
- const int outlev,
-- FILE *logFile
-+ FILE *const logFile
- );
-
- void print_PDBQT( FILE *const logFile,
Added: trunk/packages/autodocksuite/trunk/debian/patches/create_fake_autoreconf_files.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/create_fake_autoreconf_files.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/create_fake_autoreconf_files.patch 2014-08-13 06:14:56 UTC (rev 17714)
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 13 Aug 2014 07:37:23 +0200
+Description: Since we are using autoreconf the files NEWS and ChangeLog
+ are required. Just faking these with this simple patch
+
+--- /dev/null
++++ b/autodock/ChangeLog
+@@ -0,0 +1,2 @@
++
++
+--- /dev/null
++++ b/autodock/NEWS
+@@ -0,0 +1,2 @@
++
++
+--- /dev/null
++++ b/autogrid/ChangeLog
+@@ -0,0 +1,2 @@
++
++
+--- /dev/null
++++ b/autogrid/NEWS
+@@ -0,0 +1,2 @@
++
++
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/fix_test_outputdir.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/fix_test_outputdir.patch 2014-08-13 05:47:48 UTC (rev 17713)
+++ trunk/packages/autodocksuite/trunk/debian/patches/fix_test_outputdir.patch 2014-08-13 06:14:56 UTC (rev 17714)
@@ -1,46 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 15 Apr 2014 18:01:38 +0200
-Description: Make sure the test suite deals properly with its used directories
-
---- a/autodock/Makefile.am
-+++ b/autodock/Makefile.am
-@@ -439,7 +439,8 @@ test : autodock4 $(srcdir)/Tests/test_au
- @echo " "
- @echo "Running the Python test_autodock4.py unit-tests on autodock4"
- @echo " "
-- outputdir=`pwd` ;\
-+ outputdir=$(srcdir)/../autodock_testresults ;\
-+ mkdir -p $$outputdir ;\
- umask 0 ;\
- test -d $$outputdir/Tests || mkdir $$outputdir/Tests ;\
- rm -f $$outputdir/Tests/test_autodock4.py;\
-@@ -449,7 +450,7 @@ test : autodock4 $(srcdir)/Tests/test_au
- cp $(srcdir)/Tests/*.dpf $$outputdir/Tests;\
- cp $(srcdir)/Tests/*.pdbqt $$outputdir/Tests;\
- cp $(srcdir)/Tests/*.map* $$outputdir/Tests;\
-- cd Tests ; python ./test_autodock4.py -d . -e ../autodock4$(EXEEXT) -o .
-+ cd $$outputdir/Tests ; python ./test_autodock4.py -d . -e ../../autodock/autodock4$(EXEEXT) -o .
- #else
- # @echo " "
- # @echo "Python version 2.1 or higher needed for 'make check', but not found."
---- a/autogrid/Makefile.am
-+++ b/autogrid/Makefile.am
-@@ -130,7 +130,8 @@ test : autogrid4 $(srcdir)/Tests/test_au
- # for technical reasons, autogrid must be run in the Tests
- # directory because it writes its maps into its current directory
- # and expects to find AD4.1_bound.dat in that same directory.
-- outputdir=`pwd` ;\
-+ outputdir=$(srcdir)/../autogrid_testresults ;\
-+ mkdir -p $$outputdir ;\
- umask 0 ;\
- test -d $$outputdir/Tests || mkdir $$outputdir/Tests ;\
- chmod a+w $$outputdir/Tests/*;\
-@@ -141,7 +142,7 @@ test : autogrid4 $(srcdir)/Tests/test_au
- cp $(srcdir)/Tests/*.map* $$outputdir/Tests;\
- chmod a+w $$outputdir/Tests/*;\
- cd $$outputdir/Tests;\
-- python ./test_autogrid4.py -d . -e ../autogrid4$(EXEEXT) -o .
-+ python ./test_autogrid4.py -d . -e ../../autogrid/autogrid4$(EXEEXT) -o .
- #else
- # @echo " "
- # @echo "Python version 2.1 or higher needed for 'make test', but not found."
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/make.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/make.patch 2014-08-13 05:47:48 UTC (rev 17713)
+++ trunk/packages/autodocksuite/trunk/debian/patches/make.patch 2014-08-13 06:14:56 UTC (rev 17714)
@@ -1,15 +0,0 @@
-Description: adapt make process to Debian build environment
-Author: Thorsten Alteholz <debian at alteholz.de>
-Last-Update: 2013-02-16
---- a/autogrid/Makefile.am
-+++ b/autogrid/Makefile.am
-@@ -155,7 +155,8 @@ main.o : $(srcdir)/../autodock/autocomm.
- default_parameters.h : $(srcdir)/../autodock/paramdat2h.csh $(srcdir)/../autodock/AD4_parameters.dat $(srcdir)/../autodock/AD4.1_bound.dat
- rm -f $@
- csh $(srcdir)/../autodock/paramdat2h.csh $(srcdir)/../autodock/AD4_parameters.dat $(srcdir)/../autodock/AD4.1_bound.dat > $@
-- sh ../copyfilesfromAD -b # copying from build dir , not source dir
-+# sh ./copyfilesfromAD -b # copying from build dir , not source dir
-+ sh ./copyfilesfromAD # copying from src dir , not build dir
-
- # 2007-04-30 MP & GMM: this line is necessary to be able to compile read_parameter_library.o
- read_parameter_library.o : default_parameters.h
Modified: trunk/packages/autodocksuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/series 2014-08-13 05:47:48 UTC (rev 17713)
+++ trunk/packages/autodocksuite/trunk/debian/patches/series 2014-08-13 06:14:56 UTC (rev 17714)
@@ -1,2 +1 @@
-make.patch
-fix_test_outputdir.patch
+create_fake_autoreconf_files.patch
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