[med-svn] r10075 - trunk/packages/theseus/trunk/debian/patches
Andreas Tille
tille at alioth.debian.org
Sat Mar 24 16:21:59 UTC 2012
Author: tille
Date: 2012-03-24 16:21:58 +0000 (Sat, 24 Mar 2012)
New Revision: 10075
Modified:
trunk/packages/theseus/trunk/debian/patches/20_hardening.patch
Log:
Some more patches removing assigned but not used variables; does not yet build!
Modified: trunk/packages/theseus/trunk/debian/patches/20_hardening.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/20_hardening.patch 2012-03-24 07:32:55 UTC (rev 10074)
+++ trunk/packages/theseus/trunk/debian/patches/20_hardening.patch 2012-03-24 16:21:58 UTC (rev 10075)
@@ -140,3 +140,166 @@
/* 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 @@
+ 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 @@
+
+ /* do the DSSP algorithm, Doug-style */
+ GetCONHCA(dssp);
+- Hbonds = FlagHBonds(dssp);
++ /*Hbonds =*/ FlagHBonds(dssp);
+
+ FlagBends(dssp);
+ FlagTurns(dssp);
+--- theseus_src.orig/Embed.c
++++ theseus_src/Embed.c
+@@ -856,7 +856,7 @@
+ 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 @@
+ }
+ }
+
+- 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;
+--- theseus_src.orig/HierarchVars.c
++++ theseus_src/HierarchVars.c
+@@ -650,7 +650,7 @@
+ 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 @@
+ 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 @@
+ 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 @@
+ 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 @@
+ 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 @@
+ 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 @@
+ 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)
+--- theseus_src.orig/MultiPose.c
++++ theseus_src/MultiPose.c
+@@ -1797,7 +1797,7 @@
+ /* 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;
+@@ -1946,7 +1946,7 @@
+ 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)
+ {
+@@ -2068,10 +2068,10 @@
+ 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)
+ // {
+--- theseus_src.orig/MultiPoseMix.c
++++ theseus_src/MultiPoseMix.c
+@@ -1388,7 +1388,7 @@
+ 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 @@
+ 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));
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