[med-svn] r16969 - trunk/packages/theseus/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Tue May 20 13:34:07 UTC 2014
Author: tille
Date: 2014-05-20 13:34:07 +0000 (Tue, 20 May 2014)
New Revision: 16969
Removed:
trunk/packages/theseus/trunk/debian/patches/20_hardening.patch
Modified:
trunk/packages/theseus/trunk/debian/patches/30_fix_gcc_options.patch
trunk/packages/theseus/trunk/debian/patches/series
Log:
Adapt patches to new upstream version
Deleted: trunk/packages/theseus/trunk/debian/patches/20_hardening.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/20_hardening.patch 2014-05-20 13:15:51 UTC (rev 16968)
+++ trunk/packages/theseus/trunk/debian/patches/20_hardening.patch 2014-05-20 13:34:07 UTC (rev 16969)
@@ -1,324 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Sat, 24 Mar 2012 07:48:57 +0100
-Description: Build with hardening flags
- When compiling with hardening flags variables that are set but not used
- [-Werror=unused-but-set-variable] all warnings being treated as errors
-
---- a/libdistfit/gamma_dist.c
-+++ b/libdistfit/gamma_dist.c
-@@ -547,7 +547,7 @@ gamma_fit(const double *data, const int
- void
- gamma_fit_no_stats(const double *data, const int num, double *b, double *c)
- {
-- double ave, /* var, */logterm, logdata, fx, dfx, fxdfx, guess_b, guess_c;
-+ double ave, /* var, */logterm, logdata, fx, dfx, fxdfx/*, guess_b, guess_c*/;
- int i, maxiter = 500;
- double tol = FLT_EPSILON;
-
-@@ -604,8 +604,8 @@ gamma_fit_no_stats(const double *data, c
- if (*c > FLT_MAX)
- *c = FLT_MAX;
-
-- guess_b = *b;
-- guess_c = *c;
-+ /* guess_b = *b; */
-+ /* guess_c = *c; */
- /* Maximum likelihood fit. */
- /* Use Newton-Raphson to find ML estimate of c
- Based on _Statistical Distributions_ 3rd ed. Evans, Hastings, and Peacock, p 41.
---- a/libdistfit/lognormal_dist.c
-+++ b/libdistfit/lognormal_dist.c
-@@ -128,7 +128,7 @@ lognormal_logL(const double zeta, const
- double
- lognormal_fit(const double *data, const int num, double *zeta, double *sigma, double *prob)
- {
-- double ave, avesqr, var, /* m, */ x, theta;
-+ double ave, avesqr, var, /* m, */ x/*, theta*/;
- int i;
-
- ave = avesqr = 0.0;
-@@ -165,7 +165,7 @@ lognormal_fit(const double *data, const
-
- *zeta = ave;
- *sigma = sqrt(var);
-- theta = 0.5*(sqrt(1.0 + 4.0*avesqr) - 1.0);
-+ /* theta = 0.5*(sqrt(1.0 + 4.0*avesqr) - 1.0); */
- /* printf(" LogNormal theta: %f %e\n", theta, theta*theta + theta - avesqr); */
- /* printf("\n LogNormal logL: %f", lognormal_logL(*zeta, *sigma)); */
-
---- a/libdssplite/dssplite.c
-+++ b/libdssplite/dssplite.c
-@@ -167,7 +167,7 @@ char
- int vlen) /* used to be that len = # of CA atoms, not full x vector length */
- {
- DSSP *dssp = NULL;
-- int Hbonds, len;
-+ int /*Hbonds, */len;
- char *summary;
-
- /* Setup DSSP structure */
-@@ -184,7 +184,7 @@ char
-
- /* do the DSSP algorithm, Doug-style */
- GetCONHCA(dssp);
-- Hbonds = FlagHBonds(dssp);
-+ /*Hbonds =*/ FlagHBonds(dssp);
-
- FlagBends(dssp);
- FlagTurns(dssp);
---- a/Embed.c
-+++ b/Embed.c
-@@ -856,7 +856,7 @@ int FastCalcRMSDAndRotation(double *rot,
- double oldg = 0.0;
- double b, a, delta, ms;
- double q1, q2, q3, q4, normq;
-- double d11, d12, d13, d14, d21, d22, d23, d24;
-+ double /*d11, d12, */d13, d14, d21, d22, d23, d24;
- double d31, d32, d33, d34, d41, d42, d43, d44;
- double a2, x2, y2, z2;
- double xy, az, zx, ay, yz, ax;
-@@ -932,7 +932,7 @@ int FastCalcRMSDAndRotation(double *rot,
- }
- }
-
-- d11 = SxxpSyy + Szz-mxEigenV; d12 = SyzmSzy; d13 = - SxzmSzx; d14 = SxymSyx;
-+ /*d11 = SxxpSyy + Szz-mxEigenV; d12 = SyzmSzy; */ d13 = - SxzmSzx; d14 = SxymSyx;
- d21 = SyzmSzy; d22 = SxxmSyy - Szz-mxEigenV; d23 = SxypSyx; d24= SxzpSzx;
- d31 = d13; d32 = d23; d33 = Syy-Sxx-Szz - mxEigenV; d34 = SyzpSzy;
- d41 = d14; d42 = d24; d43 = d34; d44 = Szz - SxxpSyy - mxEigenV;
---- a/HierarchVars.c
-+++ b/HierarchVars.c
-@@ -650,7 +650,7 @@ InvGammaFitEvals(CdsArray *cdsA, int ite
- double **evecs = NULL;
- double precision = cdsA->algo->precision;
- const int vlen = cdsA->vlen, cnum = cdsA->cnum;
-- double nd, oldb, oldc, b, c, chi2 = DBL_MAX, logL, harmave, mode;
-+ double nd, oldb, oldc, b, c, chi2 = DBL_MAX, logL, harmave/*, mode*/;
- int i, count, newlen;
-
- newvar = malloc(vlen * sizeof(double));
-@@ -754,7 +754,7 @@ InvGammaFitEvals(CdsArray *cdsA, int ite
- newvar[i] = (nd*variance[i] + 2.0*b) / (nd + 2.0*(1.0 + c));
-
- /* the mode of an inv gamma dist */
-- mode = b / (c+1.0);
-+ /* mode = b / (c+1.0); */
-
- /* for (i = 0; i < vlen - newlen; ++i) */
- /* newvar[i] = mode; */
-@@ -820,7 +820,7 @@ InvGammaFitEvalsNoN(CdsArray *cdsA, int
- double **evecs = NULL;
- double precision = cdsA->algo->precision;
- const int vlen = cdsA->vlen, cnum = cdsA->cnum;
-- double nd, oldb, oldc, b, c, chi2 = DBL_MAX, logL, harmave, mode;
-+ double nd, oldb, oldc, b, c, chi2 = DBL_MAX, logL, harmave/*, mode*/;
- int i, count, newlen;
-
- newvar = malloc(vlen * sizeof(double));
-@@ -924,7 +924,7 @@ InvGammaFitEvalsNoN(CdsArray *cdsA, int
- newvar[i] = (nd*variance[i] + 2.0*b) / (nd + 2.0*(1.0 + c));
-
- /* the mode of an inv gamma dist */
-- mode = b / (c+1.0);
-+ /* mode = b / (c+1.0); */
-
- /* for (i = 0; i < vlen - newlen; ++i) */
- /* newvar[i] = mode; */
-@@ -1178,7 +1178,7 @@ InvGammaBayesFitEvals(CdsArray *cdsA, in
- double **evecs = NULL;
- double precision = cdsA->algo->precision;
- const int vlen = cdsA->vlen, cnum = cdsA->cnum;
-- double nd, oldb, oldc, b, c, chi2 = DBL_MAX, logL, harmave, mode;
-+ double nd, oldb, oldc, b, c, chi2 = DBL_MAX, logL, harmave/*, mode*/;
- int i, count, newlen;
-
- newvar = malloc(vlen * sizeof(double));
-@@ -1282,7 +1282,7 @@ InvGammaBayesFitEvals(CdsArray *cdsA, in
- newvar[i] = (nd*variance[i] + 2.0*b) / (nd + 2.0*(1.0 + c));
-
- /* the mode of an inv gamma dist */
-- mode = b / (c+1.0);
-+ /* mode = b / (c+1.0); */
-
- /* for (i = 0; i < vlen - newlen; ++i) */
- /* newvar[i] = mode; */
-@@ -3002,11 +3002,11 @@ InvGammaEMFixedC(CdsArray *cdsA, const d
- double *variance = NULL;
- double precision = FLT_EPSILON; // cdsA->algo->precision;
- const int vlen = cdsA->vlen, cnum = cdsA->cnum;
-- double nd, oldb, oldc, b = 0.0, chi2 = 0.0, logL;
-+ double /* nd, */oldb, oldc, b = 0.0, chi2 = 0.0, logL;
- int count;
-
- newvar = malloc(vlen * sizeof(double));
-- nd = 3.0 * cnum;
-+ /* nd = 3.0 * cnum; */
- oldb = oldc = DBL_MAX;
-
- if (cdsA->algo->varweight > 0)
---- a/MultiPose.c
-+++ b/MultiPose.c
-@@ -1795,7 +1795,7 @@ MultiPose(CdsArray *baseA)
- /* FILE *fp; */
- int i, round, innerround;
- int slxn; /* index of random coord to select as first */
-- double frobnorm, sumdev, percent, lastpercent, logL, lastlogL, lastscale;
-+ double frobnorm, sumdev, /* percent, lastpercent, */ logL, lastlogL, lastscale;
- double deviation_sum = 0.0;
- const int cnum = baseA->cnum;
- const int vlen = baseA->vlen;
-@@ -1944,7 +1944,7 @@ MultiPose(CdsArray *baseA)
- matrices and corresponding weight matrices, looping till
- convergence when using a dimensional/axial covariance matrix */
- round = 0;
-- percent = lastpercent = 0.0;
-+ /* percent = lastpercent = 0.0; */
- logL = lastlogL = lastscale = -DBL_MAX;
- while(1)
- {
-@@ -2066,10 +2066,10 @@ MultiPose(CdsArray *baseA)
- CheckConvergenceOuter(scratchA, round, algo->precision) == 1)
- goto outsidetheloops;
-
-- if (stats->precision > 0.0)
-+/* if (stats->precision > 0.0)
- percent = 100.0 * log(fabs(stats->precision))/log(algo->precision);
- else
-- percent = 0.0;
-+ percent = 0.0; */
-
- // if (percent > lastpercent)
- // {
---- a/MultiPoseMix.c
-+++ b/MultiPoseMix.c
-@@ -1388,7 +1388,7 @@ MultiPoseMix(CdsArray *baseA, const doub
- Statistics *stats = NULL;
- Cds **cds = NULL;
- Cds *avecds = NULL;
-- Cds *tcds = NULL;
-+ /* Cds *tcds = NULL; */
- CdsArray *scratchA = NULL;
-
- gsl_rng *r2 = NULL;
-@@ -1411,7 +1411,7 @@ MultiPoseMix(CdsArray *baseA, const doub
- stats = scratchA->stats;
- cds = scratchA->cds;
- avecds = scratchA->avecds;
-- tcds = scratchA->tcds;
-+ /* tcds = scratchA->tcds; */
-
- memcpy(scratchA->w, probs, vlen * sizeof(double));
- memcpy(baseA->w, probs, vlen * sizeof(double));
---- a/PCAstats.c
-+++ b/PCAstats.c
-@@ -58,7 +58,7 @@ CalcPCA(CdsArray *cdsA)
- {
- int i, j;
- int vlen = (int) cdsA->vlen;
-- int upper, lower, pcanum;
-+ int /*upper, lower, */ pcanum;
- double **CovMat = cdsA->CovMat;
- double sum, runsum;
- PDBCds *pdbave;
-@@ -101,8 +101,8 @@ CalcPCA(CdsArray *cdsA)
- for (i = 0; i < vlen; ++i)
- sum += CovMat[i][i];
-
-- lower = vlen - pcanum + 1; /* careful -- inclusive indices */
-- upper = vlen - 0;
-+ /* lower = vlen - pcanum + 1; / * careful -- inclusive indices */
-+ /* upper = vlen - 0; */
- //cdsA->pcamat = MatAlloc(pcanum, vlen);
- cdsA->pcamat = MatAlloc(vlen, vlen);
- cdsA->pcavals = malloc(vlen * sizeof(double));
-@@ -237,7 +237,7 @@ Calc3NPCA(CdsArray *cdsA)
- int i, j;
- int vlen = (int) 3 * cdsA->vlen;
- double **mat = NULL;
-- int upper, lower, pcanum;
-+ int /* upper, lower, */ pcanum;
- double **evecs = NULL, *evals = NULL;
- double sum, runsum;
- PDBCds *pdbave = NULL;
-@@ -273,8 +273,8 @@ Calc3NPCA(CdsArray *cdsA)
- for (i = 0; i < vlen; ++i)
- sum += mat[i][i];
-
-- lower = vlen - pcanum + 1; /* careful -- inclusive indices */
-- upper = vlen - 0;
-+ /* lower = vlen - pcanum + 1; / * careful -- inclusive indices */
-+ /* upper = vlen - 0; */
- evecs = MatAlloc(vlen, vlen);
- evals = malloc(vlen * sizeof(double));
-
---- a/pdbStats.c
-+++ b/pdbStats.c
-@@ -1596,7 +1596,7 @@ CalcHierarchLogL(CdsArray *cdsA)
- if (algo->varweight != 0)
- {
- double *newvar = malloc(vlen * sizeof(double));
-- double b, c, xn1;
-+ double b, c/*, xn1*/;
-
- b = stats->hierarch_p1;
- c = stats->hierarch_p2;
-@@ -1604,7 +1604,7 @@ CalcHierarchLogL(CdsArray *cdsA)
- memcpy(newvar, cdsA->var, vlen * sizeof(double));
- qsort(newvar, vlen, sizeof(double), dblcmp_rev);
- /* qsort-dblcmp_rev sorts big to small */
-- xn1 = newvar[vlen-4];
-+ /* xn1 = newvar[vlen-4]; */
-
- logL = invgamma_logL(newvar, vlen-3, b, c);
- //- b * ExpInvXn(xn1, b, c) - (1+c)*ExpLogXn(xn1, b, c)
-@@ -1778,13 +1778,13 @@ CalcLogL(CdsArray *cdsA)
- if (algo->hierarch != 0)
- {
- double *newvar = malloc(vlen * sizeof(double));
-- double xn1;
-+ /* double xn1; */
-
- memcpy(newvar, var, vlen * sizeof(double));
- qsort(newvar, vlen, sizeof(double), dblcmp_rev);
- /* qsort-dblcmp_rev sorts big to small */
-
-- xn1 = newvar[vlen - 4];
-+ /*xn1 = newvar[vlen - 4];*/
-
- lndetrow = 0.0;
- for (i = 0; i < vlen-3; ++i)
---- a/QuarticHornFrag.c
-+++ b/QuarticHornFrag.c
-@@ -318,11 +318,11 @@ CalcQuarticCoeffsPu2(const FragCds *frag
- lambdamax = QCProot(coeff, 0.5 * innerprod, precision);
-
- /* Now calculate the optimal rotation from one row of the cofactor matrix */
-- double a11, a12, a13, a14, a21, a22, a23, a24;
-+ double /* a11, a12, */ a13, a14, a21, a22, a23, a24;
- double a31, a32, a33, a34, a41, a42, a43, a44;
-
-- a11 = SxxpSyy + Szz - lambdamax;
-- a12 = SyzmSzy;
-+ /* a11 = SxxpSyy + Szz - lambdamax; */
-+ /* a12 = SyzmSzy; */
- a13 = -SxzmSzx;
- a14 = SxymSyx;
- a21 = SyzmSzy;
-@@ -652,7 +652,7 @@ FragDistPu(CdsArray *cdsA, int fraglen,
- double *coeff = NULL;
- double var;
- FILE *distfile = NULL, *distfile2 = NULL;
-- double biggest;
-+ /* double biggest; */
- double *array = NULL;
-
- double **Rmat = MatAlloc(3, 3);
-@@ -686,7 +686,7 @@ FragDistPu(CdsArray *cdsA, int fraglen,
-
- start_time = clock();
-
-- biggest = 0.0;
-+ /* biggest = 0.0; */
- count = 0;
- for (coord1 = 0; coord1 < cdsA->cnum; ++coord1)
- {
Modified: trunk/packages/theseus/trunk/debian/patches/30_fix_gcc_options.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/30_fix_gcc_options.patch 2014-05-20 13:15:51 UTC (rev 16968)
+++ trunk/packages/theseus/trunk/debian/patches/30_fix_gcc_options.patch 2014-05-20 13:34:07 UTC (rev 16969)
@@ -1,34 +1,53 @@
Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 20 May 2014 15:08:38 +0200
Descriptions: Set options for Linux
Default options seem to be addressing MacOS by default - just enable clean
on Linux
--- a/make.inc
+++ b/make.inc
-@@ -49,7 +49,7 @@ RANLIB = ranlib
+@@ -6,12 +6,12 @@
+ RANLIB = ranlib
+
+ # for universal OSX binary
+-ARCH = libtool
+-ARCHFLAGS = -static -o
++# ARCH = libtool
++# ARCHFLAGS = -static -o
+
+ # for normal arch-native tuned OSX binary
+-# ARCH = ar
+-# ARCHFLAGS = -rvs
++ARCH = ar
++ARCHFLAGS = -rvs
+
+ #MACOSX_DEPLOYMENT_TARGET=10.4
+ #export MACOSX_DEPLOYMENT_TARGET
+@@ -38,7 +38,7 @@ ARCHFLAGS = -static -o
# Mac OSX Universal
#
LOCALLIBDIR = /usr/local/lib
-LIBS = -lgsl -lgslcblas -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
+LIBS = -lgsl -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
- #SYSLIBS = -framework CoreServices
SYSLIBS = -lpthread -lgsl -lgslcblas -lm -lc
LIBDIR = -L./lib
-@@ -59,7 +59,7 @@ INSTALLDIR = /usr/local/bin
- OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
+ INSTALLDIR = /usr/local/bin
+@@ -46,7 +46,7 @@ INSTALLDIR = /usr/local/bin
+ OPT = -O3 -ffast-math #-fstrict-aliasing -funroll-loops -fomit-frame-pointer
#WARN = -Werror -Wno-error=unused-result -Wall -pedantic -std=c99
WARN = -Werror -Wall -pedantic -std=c99 # for APPLE MACOSX
-CFLAGS += $(WARN) -force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch x86_64 -arch i386 #-DNDEBUG
+#CFLAGS += $(WARN) -force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch x86_64 -arch i386 #-DNDEBUG
- #CFLAGS += $(WARN)
# CPPFLAGS are ignored by the rest of the build system but necessary for hardening flags
CFLAGS += $(CPPFLAGS)
-@@ -79,10 +79,10 @@ CC = /usr/bin/gcc
+ # Filter out -O2 which overwrites the default -O3 because OPT is used before CFLAGS
+@@ -65,11 +65,11 @@ CC = gcc
# LIBDIR = -L./lib/ -L/usr/lib/
# INCDIR = -I/usr/local/include/
# INSTALLDIR = /usr/local/bin
-# OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
+OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
+ # # OPT = -m64 -O3 -march=native -funroll-loops -ffast-math -mfpmath=sse
# #OPT = -O0 -ggdb
-# WARN = -Wall -pedantic -std=c99 -Wno-unused-result
-# CFLAGS = $(WARN) -pthread
Modified: trunk/packages/theseus/trunk/debian/patches/series
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/series 2014-05-20 13:15:51 UTC (rev 16968)
+++ trunk/packages/theseus/trunk/debian/patches/series 2014-05-20 13:34:07 UTC (rev 16969)
@@ -1,2 +1 @@
-20_hardening.patch
30_fix_gcc_options.patch
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