[med-svn] r12398 - in trunk/packages/theseus/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Fri Oct 12 22:26:28 UTC 2012
Author: tille
Date: 2012-10-12 22:26:27 +0000 (Fri, 12 Oct 2012)
New Revision: 12398
Removed:
trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch
trunk/packages/theseus/trunk/debian/patches/20_exclude_apple_options.patch
trunk/packages/theseus/trunk/debian/patches/21_use_dpkg_buildflags.patch
trunk/packages/theseus/trunk/debian/patches/22_hardening_compile.patch
Modified:
trunk/packages/theseus/trunk/debian/changelog
trunk/packages/theseus/trunk/debian/control
trunk/packages/theseus/trunk/debian/patches/20_hardening.patch
trunk/packages/theseus/trunk/debian/patches/series
Log:
New upstream version (most patches applied)
Modified: trunk/packages/theseus/trunk/debian/changelog
===================================================================
--- trunk/packages/theseus/trunk/debian/changelog 2012-10-12 13:30:42 UTC (rev 12397)
+++ trunk/packages/theseus/trunk/debian/changelog 2012-10-12 22:26:27 UTC (rev 12398)
@@ -1,11 +1,14 @@
-theseus (1.6.2-3) UNRELEASED; urgency=low
+theseus (2.0.1-1) UNRELEASED; urgency=low
- * debian/control: Fix typo: s/clustlaw/clustalw/
- Closes: #682994
+ * New upstream version (most patches applied)
+ * debian/control:
+ - Fix typo: s/clustlaw/clustalw/
+ Closes: #682994
+ - Standards-Version: 3.9.4 (no changes needed)
* removed debian/citation.bib because the very same information
is now in debian/upstream
- -- Andreas Tille <tille at debian.org> Fri, 27 Jul 2012 20:55:45 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 11 Oct 2012 18:15:43 +0200
theseus (1.6.2-2) unstable; urgency=low
Modified: trunk/packages/theseus/trunk/debian/control
===================================================================
--- trunk/packages/theseus/trunk/debian/control 2012-10-12 13:30:42 UTC (rev 12397)
+++ trunk/packages/theseus/trunk/debian/control 2012-10-12 22:26:27 UTC (rev 12398)
@@ -6,7 +6,7 @@
Andreas Tille <tille at debian.org>
DM-Upload-Allowed: yes
Build-Depends: debhelper (>= 9), libgsl0-dev
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
Homepage: http://www.theseus3d.org
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/theseus/trunk/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/theseus/trunk
Deleted: trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch 2012-10-12 13:30:42 UTC (rev 12397)
+++ trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch 2012-10-12 22:26:27 UTC (rev 12398)
@@ -1,35 +0,0 @@
-Purpose: Enable Building on kbsd architecture
-Author: Cyril Brulebois <kibi at debian.org>, Andreas Tille <tille at debian.org>
-Fixes: #542879
-
---- theseus_src.orig/distfit.h
-+++ theseus_src/distfit.h
-@@ -749,7 +749,7 @@
- #ifndef LOGNORMAL_SEEN
- #define LOGNORMAL_SEEN
-
--#ifdef __linux__
-+#if defined(__linux__) || defined(__GLIBC__)
- extern double erf(double x);
- #endif
-
-@@ -1516,7 +1516,7 @@
- #ifndef VONMISES_DIST_SEEN
- #define VONMISES_DIST_SEEN
-
--#ifdef __linux__
-+#if defined(__linux__) || defined(__GLIBC__)
- extern double jn(int n, double x);
- #endif
-
---- theseus_src.orig/theseus.h
-+++ theseus_src/theseus.h
-@@ -49,7 +49,7 @@
- #include <string.h>
- #include <stdio.h>
- #include <unistd.h>
--#ifdef __linux__
-+#if defined(__linux__) || defined(__GLIBC__)
- #include <getopt.h>
- #endif
- #include <ctype.h>
Deleted: trunk/packages/theseus/trunk/debian/patches/20_exclude_apple_options.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/20_exclude_apple_options.patch 2012-10-12 13:30:42 UTC (rev 12397)
+++ trunk/packages/theseus/trunk/debian/patches/20_exclude_apple_options.patch 2012-10-12 22:26:27 UTC (rev 12398)
@@ -1,20 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Sat, 24 Mar 2012 07:48:57 +0100
-Description: Exclude Apple specific linker option, enable pthread
- Attention: I have no idea whether the variable APPLE is
- set when building on Apple machines - please adapt!!!
-
---- theseus_src.orig/make.inc
-+++ theseus_src/make.inc
-@@ -14,7 +14,11 @@
- # Mac OSX Universal?
- LOCALLIBDIR = /usr/local/lib
- LIBS = -lgsl -lgslcblas -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
-+ifdef APPLE
- SYSLIBS = -framework CoreServices #-lmudflap
-+else
-+SYSLIBS = -lpthread
-+endif
- LIBDIR = -L./lib
- #LAPACKLIB = -framework vecLib
- INSTALLDIR = /usr/local/bin
Modified: trunk/packages/theseus/trunk/debian/patches/20_hardening.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/20_hardening.patch 2012-10-12 13:30:42 UTC (rev 12397)
+++ trunk/packages/theseus/trunk/debian/patches/20_hardening.patch 2012-10-12 22:26:27 UTC (rev 12398)
@@ -4,49 +4,9 @@
When compiling with hardening flags variables that are set but not used
[-Werror=unused-but-set-variable] all warnings being treated as errors
---- theseus_src.orig/libdistfit/chisqrgen_dist.c
-+++ theseus_src/libdistfit/chisqrgen_dist.c
-@@ -161,7 +161,7 @@
- double
- chisqrgen_fit(const double *data, const int num, double *nu, double *lambda, double *prob)
- {
-- double ave, var, logterm, fx, dfx, guess_nu, guess_lambda;
-+ double ave, var, logterm, fx, dfx, guess_nu;
- int i;
- double iter = 100;
- double tol = 1e-8;
-@@ -187,7 +187,7 @@
- var /= (double) num;
-
- guess_nu = *nu = 2.0 * ave * ave / var;
-- guess_lambda = *lambda = 0.5 * var / ave;
-+ *lambda = 0.5 * var / ave;
-
- logterm = 0.0;
- for (i = 0; i < num; ++i)
---- theseus_src.orig/libdistfit/gamma_dist.c
-+++ theseus_src/libdistfit/gamma_dist.c
-@@ -418,7 +418,7 @@
- double
- gamma_fit(const double *data, const int num, double *b, double *c, double *logL)
- {
-- 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;
-
-@@ -465,8 +465,8 @@
- 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
-@@ -550,7 +550,7 @@
+--- 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)
{
@@ -55,7 +15,7 @@
int i, maxiter = 500;
double tol = FLT_EPSILON;
-@@ -607,8 +607,8 @@
+@@ -604,8 +604,8 @@ gamma_fit_no_stats(const double *data, c
if (*c > FLT_MAX)
*c = FLT_MAX;
@@ -66,70 +26,10 @@
/* Maximum likelihood fit. */
/* Use Newton-Raphson to find ML estimate of c
Based on _Statistical Distributions_ 3rd ed. Evans, Hastings, and Peacock, p 41.
-@@ -701,7 +701,7 @@
- void
- gamma_bayes_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;
-
-@@ -758,8 +758,8 @@
- if (*c > FLT_MAX)
- *c = FLT_MAX;
-
-- guess_b = *b;
-- guess_c = *c;
-+ /* guess_b = *b; */
-+ /* guess_c = *c; */
- /* Bayesian maximum posterior probability fit.
- Use Newton-Raphson to find ML estimate of c.
-
-@@ -837,7 +837,7 @@
- void
- gamma_bayes_ref_fit_no_stats(const double *data, const int num, double *b, double *c)
- {
-- double sumx, /* var, */logterm, logdata, fx, dfx, fxdfx, guess_b, guess_c;
-+ double sumx, /* var, */logterm, logdata, fx, dfx, fxdfx/*, guess_b, guess_c*/;
- int i, maxiter = 500;
- double tol = FLT_EPSILON;
-
-@@ -892,8 +892,8 @@
- if (*c > FLT_MAX)
- *c = FLT_MAX;
-
-- guess_b = *b;
-- guess_c = *c;
-+ /* guess_b = *b; */
-+ /* guess_c = *c; */
- /* Bayesian maximum posterior probability fit.
- Use Newton-Raphson to find ML estimate of c.
-
---- theseus_src.orig/libdistfit/invgamma_dist.c
-+++ theseus_src/libdistfit/invgamma_dist.c
-@@ -764,7 +764,7 @@
+--- a/libdistfit/lognormal_dist.c
++++ b/libdistfit/lognormal_dist.c
+@@ -128,7 +128,7 @@ lognormal_logL(const double zeta, const
double
- invgamma_EMsmall_fit(const double *data, const int numt, int missing, double *b, double *c, double *logL)
- {
-- double sum_ln, sum_inv, ave_ln, ave_inv, harm_ave, x;
-+ double sum_ln, sum_inv, ave_ln, /* ave_inv, */ harm_ave, x;
- double *newdata = malloc(numt * sizeof(double));
- double chi2 = 0.0, xn1, expinvxn, explogxn;
- double fx = 0.0, dfx = 1.0, fxdfx = 0.0;
-@@ -798,7 +798,7 @@
- numm = numt - missing;
-
- ave_ln = sum_ln / numm;
-- ave_inv = sum_inv / numm;
-+ /* ave_inv = sum_inv / numm; */
- harm_ave = numm / sum_inv;
-
- /* MMEs are:
---- theseus_src.orig/libdistfit/lognormal_dist.c
-+++ theseus_src/libdistfit/lognormal_dist.c
-@@ -128,7 +128,7 @@
- double
lognormal_fit(const double *data, const int num, double *zeta, double *sigma, double *prob)
{
- double ave, avesqr, var, /* m, */ x, theta;
@@ -137,7 +37,7 @@
int i;
ave = avesqr = 0.0;
-@@ -165,7 +165,7 @@
+@@ -165,7 +165,7 @@ lognormal_fit(const double *data, const
*zeta = ave;
*sigma = sqrt(var);
@@ -146,9 +46,9 @@
/* printf(" LogNormal theta: %f %e\n", theta, theta*theta + theta - avesqr); */
/* printf("\n LogNormal logL: %f", lognormal_logL(*zeta, *sigma)); */
---- theseus_src.orig/libdssplite/dssplite.c
-+++ theseus_src/libdssplite/dssplite.c
-@@ -167,7 +167,7 @@
+--- 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;
@@ -157,7 +57,7 @@
char *summary;
/* Setup DSSP structure */
-@@ -184,7 +184,7 @@
+@@ -184,7 +184,7 @@ char
/* do the DSSP algorithm, Doug-style */
GetCONHCA(dssp);
@@ -166,9 +66,9 @@
FlagBends(dssp);
FlagTurns(dssp);
---- theseus_src.orig/Embed.c
-+++ theseus_src/Embed.c
-@@ -856,7 +856,7 @@
+--- 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;
@@ -177,7 +77,7 @@
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 @@
+@@ -932,7 +932,7 @@ int FastCalcRMSDAndRotation(double *rot,
}
}
@@ -186,9 +86,9 @@
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;
---- theseus_src.orig/HierarchVars.c
-+++ theseus_src/HierarchVars.c
-@@ -650,7 +650,7 @@
+--- 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;
@@ -197,7 +97,7 @@
int i, count, newlen;
newvar = malloc(vlen * sizeof(double));
-@@ -754,7 +754,7 @@
+@@ -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 */
@@ -206,7 +106,7 @@
/* for (i = 0; i < vlen - newlen; ++i) */
/* newvar[i] = mode; */
-@@ -820,7 +820,7 @@
+@@ -820,7 +820,7 @@ InvGammaFitEvalsNoN(CdsArray *cdsA, int
double **evecs = NULL;
double precision = cdsA->algo->precision;
const int vlen = cdsA->vlen, cnum = cdsA->cnum;
@@ -215,7 +115,7 @@
int i, count, newlen;
newvar = malloc(vlen * sizeof(double));
-@@ -924,7 +924,7 @@
+@@ -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 */
@@ -224,7 +124,7 @@
/* for (i = 0; i < vlen - newlen; ++i) */
/* newvar[i] = mode; */
-@@ -1178,7 +1178,7 @@
+@@ -1178,7 +1178,7 @@ InvGammaBayesFitEvals(CdsArray *cdsA, in
double **evecs = NULL;
double precision = cdsA->algo->precision;
const int vlen = cdsA->vlen, cnum = cdsA->cnum;
@@ -233,7 +133,7 @@
int i, count, newlen;
newvar = malloc(vlen * sizeof(double));
-@@ -1282,7 +1282,7 @@
+@@ -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 */
@@ -242,7 +142,7 @@
/* for (i = 0; i < vlen - newlen; ++i) */
/* newvar[i] = mode; */
-@@ -3002,11 +3002,11 @@
+@@ -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;
@@ -256,9 +156,9 @@
oldb = oldc = DBL_MAX;
if (cdsA->algo->varweight > 0)
---- theseus_src.orig/MultiPose.c
-+++ theseus_src/MultiPose.c
-@@ -1797,7 +1797,7 @@
+--- a/MultiPose.c
++++ b/MultiPose.c
+@@ -1797,7 +1797,7 @@ MultiPose(CdsArray *baseA)
/* FILE *fp; */
int i, round, innerround;
int slxn; /* index of random coord to select as first */
@@ -267,7 +167,7 @@
double deviation_sum = 0.0;
const int cnum = baseA->cnum;
const int vlen = baseA->vlen;
-@@ -1946,7 +1946,7 @@
+@@ -1946,7 +1946,7 @@ MultiPose(CdsArray *baseA)
matrices and corresponding weight matrices, looping till
convergence when using a dimensional/axial covariance matrix */
round = 0;
@@ -276,7 +176,7 @@
logL = lastlogL = lastscale = -DBL_MAX;
while(1)
{
-@@ -2068,10 +2068,10 @@
+@@ -2068,10 +2068,10 @@ MultiPose(CdsArray *baseA)
CheckConvergenceOuter(scratchA, round, algo->precision) == 1)
goto outsidetheloops;
@@ -289,9 +189,9 @@
// if (percent > lastpercent)
// {
---- theseus_src.orig/MultiPoseMix.c
-+++ theseus_src/MultiPoseMix.c
-@@ -1388,7 +1388,7 @@
+--- a/MultiPoseMix.c
++++ b/MultiPoseMix.c
+@@ -1388,7 +1388,7 @@ MultiPoseMix(CdsArray *baseA, const doub
Statistics *stats = NULL;
Cds **cds = NULL;
Cds *avecds = NULL;
@@ -300,7 +200,7 @@
CdsArray *scratchA = NULL;
gsl_rng *r2 = NULL;
-@@ -1411,7 +1411,7 @@
+@@ -1411,7 +1411,7 @@ MultiPoseMix(CdsArray *baseA, const doub
stats = scratchA->stats;
cds = scratchA->cds;
avecds = scratchA->avecds;
@@ -309,9 +209,9 @@
memcpy(scratchA->w, probs, vlen * sizeof(double));
memcpy(baseA->w, probs, vlen * sizeof(double));
---- theseus_src.orig/PCAstats.c
-+++ theseus_src/PCAstats.c
-@@ -58,7 +58,7 @@
+--- a/PCAstats.c
++++ b/PCAstats.c
+@@ -58,7 +58,7 @@ CalcPCA(CdsArray *cdsA)
{
int i, j;
int vlen = (int) cdsA->vlen;
@@ -320,7 +220,7 @@
double **CovMat = cdsA->CovMat;
double sum, runsum;
PDBCds *pdbave;
-@@ -101,8 +101,8 @@
+@@ -101,8 +101,8 @@ CalcPCA(CdsArray *cdsA)
for (i = 0; i < vlen; ++i)
sum += CovMat[i][i];
@@ -331,7 +231,7 @@
//cdsA->pcamat = MatAlloc(pcanum, vlen);
cdsA->pcamat = MatAlloc(vlen, vlen);
cdsA->pcavals = malloc(vlen * sizeof(double));
-@@ -237,7 +237,7 @@
+@@ -237,7 +237,7 @@ Calc3NPCA(CdsArray *cdsA)
int i, j;
int vlen = (int) 3 * cdsA->vlen;
double **mat = NULL;
@@ -340,7 +240,7 @@
double **evecs = NULL, *evals = NULL;
double sum, runsum;
PDBCds *pdbave = NULL;
-@@ -273,8 +273,8 @@
+@@ -273,8 +273,8 @@ Calc3NPCA(CdsArray *cdsA)
for (i = 0; i < vlen; ++i)
sum += mat[i][i];
@@ -351,9 +251,9 @@
evecs = MatAlloc(vlen, vlen);
evals = malloc(vlen * sizeof(double));
---- theseus_src.orig/pdbStats.c
-+++ theseus_src/pdbStats.c
-@@ -1662,7 +1662,7 @@
+--- a/pdbStats.c
++++ b/pdbStats.c
+@@ -1595,7 +1595,7 @@ CalcHierarchLogL(CdsArray *cdsA)
if (algo->varweight != 0)
{
double *newvar = malloc(vlen * sizeof(double));
@@ -362,16 +262,16 @@
b = stats->hierarch_p1;
c = stats->hierarch_p2;
-@@ -1670,7 +1670,7 @@
- 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]*/;
+@@ -1603,7 +1603,7 @@ 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)
-@@ -1844,13 +1844,13 @@
+@@ -1777,13 +1777,13 @@ CalcLogL(CdsArray *cdsA)
if (algo->hierarch != 0)
{
double *newvar = malloc(vlen * sizeof(double));
@@ -387,9 +287,9 @@
lndetrow = 0.0;
for (i = 0; i < vlen-3; ++i)
---- theseus_src.orig/QuarticHornFrag.c
-+++ theseus_src/QuarticHornFrag.c
-@@ -318,11 +318,11 @@
+--- 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 */
@@ -404,7 +304,7 @@
a13 = -SxzmSzx;
a14 = SxymSyx;
a21 = SyzmSzy;
-@@ -652,7 +652,7 @@
+@@ -652,7 +652,7 @@ FragDistPu(CdsArray *cdsA, int fraglen,
double *coeff = NULL;
double var;
FILE *distfile = NULL, *distfile2 = NULL;
@@ -413,7 +313,7 @@
double *array = NULL;
double **Rmat = MatAlloc(3, 3);
-@@ -686,7 +686,7 @@
+@@ -686,7 +686,7 @@ FragDistPu(CdsArray *cdsA, int fraglen,
start_time = clock();
Deleted: trunk/packages/theseus/trunk/debian/patches/21_use_dpkg_buildflags.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/21_use_dpkg_buildflags.patch 2012-10-12 13:30:42 UTC (rev 12397)
+++ trunk/packages/theseus/trunk/debian/patches/21_use_dpkg_buildflags.patch 2012-10-12 22:26:27 UTC (rev 12398)
@@ -1,38 +0,0 @@
-Description: Use build flags from environment (dpkg-buildflags).
- Necessary for hardening flags.
- .
- Also use CPPFLAGS and LDFLAGS where appropriate.
-Author: Simon Ruderich <simon at ruderich.org>
-Last-Update: 2012-04-09
-
---- theseus-1.6.2.orig/make.inc
-+++ theseus-1.6.2/make.inc
-@@ -25,7 +25,10 @@
- #OPT = -O0 -ggdb
- OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
- WARN = -Werror -Wall -pedantic -std=c99 #-Wstrict-aliasing=2
--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
-+# CPPFLAGS are ignored by the rest of the build system but necessary for
-+# hardening flags.
-+CFLAGS += $(CPPFLAGS)
- CC = /usr/bin/gcc
-
- #
---- theseus-1.6.2.orig/Makefile
-+++ theseus-1.6.2/Makefile
-@@ -36,12 +36,12 @@
-
- distfitexe:
- $(CC) $(OPT) $(CFLAGS) -c distfit.c
-- $(CC) $(OPT) $(CFLAGS) $(LIBDIR) $(LAPACKLIBDIR) $(BLASLIBDIR) distfit.o $(LIBS) $(LAPACKLIB) $(BLASLIB) $(SYSLIBS) -o distfit
-+ $(CC) $(OPT) $(CFLAGS) $(LDFLAGS) $(LIBDIR) $(LAPACKLIBDIR) $(BLASLIBDIR) distfit.o $(LIBS) $(LAPACKLIB) $(BLASLIB) $(SYSLIBS) -o distfit
-
-
- # THESEUS-specific files
- theseus: theseus.o $(OBJECTS)
-- $(CC) $(OPT) $(CFLAGS) $(LIBDIR) $(LAPACKLIBDIR) $(BLASLIBDIR) theseus.o $(OBJECTS) $(LIBS) $(LAPACKLIB) $(BLASLIB) $(SYSLIBS) -o theseus
-+ $(CC) $(OPT) $(CFLAGS) $(LDFLAGS) $(LIBDIR) $(LAPACKLIBDIR) $(BLASLIBDIR) theseus.o $(OBJECTS) $(LIBS) $(LAPACKLIB) $(BLASLIB) $(SYSLIBS) -o theseus
-
- CovMat.o: CovMat.c
- $(CC) $(OPT) $(CFLAGS) $(INCDIR) -c CovMat.c
Deleted: trunk/packages/theseus/trunk/debian/patches/22_hardening_compile.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/22_hardening_compile.patch 2012-10-12 13:30:42 UTC (rev 12397)
+++ trunk/packages/theseus/trunk/debian/patches/22_hardening_compile.patch 2012-10-12 22:26:27 UTC (rev 12398)
@@ -1,24 +0,0 @@
-Description: Fix compile with dpkg-buildflags.
- Use -Wno-error=unused-result to ignore unimportant warnings and filter out
- -O2.
-Author: Simon Ruderich <simon at ruderich.org>
-Last-Update: 2012-04-09
-
---- theseus-1.6.2.orig/make.inc
-+++ theseus-1.6.2/make.inc
-@@ -24,11 +24,14 @@
- INSTALLDIR = /usr/local/bin
- #OPT = -O0 -ggdb
- OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
--WARN = -Werror -Wall -pedantic -std=c99 #-Wstrict-aliasing=2
-+WARN = -Werror -Wno-error=unused-result -Wall -pedantic -std=c99 #-Wstrict-aliasing=2
- CFLAGS += $(WARN) #-force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch x86_64 -arch i386 #-DNDEBUG
- # CPPFLAGS are ignored by the rest of the build system but necessary for
- # hardening flags.
- CFLAGS += $(CPPFLAGS)
-+# Filter out -O2 which overwrites the default -O3 because OPT is used before
-+# CFLAGS.
-+CFLAGS := $(filter-out -O2,$(CFLAGS))
- CC = /usr/bin/gcc
-
- #
Modified: trunk/packages/theseus/trunk/debian/patches/series
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/series 2012-10-12 13:30:42 UTC (rev 12397)
+++ trunk/packages/theseus/trunk/debian/patches/series 2012-10-12 22:26:27 UTC (rev 12398)
@@ -1,5 +1 @@
-10_kbsd.patch
20_hardening.patch
-20_exclude_apple_options.patch
-21_use_dpkg_buildflags.patch
-22_hardening_compile.patch
More information about the debian-med-commit
mailing list