Author: tille Date: 2012-03-24 20:26:21 +0000 (Sat, 24 Mar 2012) New Revision: 10078
Modified: trunk/packages/theseus/trunk/debian/patches/20_hardening.patch Log: Does compile with hardening flags but linker problem remains Modified: trunk/packages/theseus/trunk/debian/patches/20_hardening.patch =================================================================== --- trunk/packages/theseus/trunk/debian/patches/20_hardening.patch 2012-03-24 17:33:48 UTC (rev 10077) +++ trunk/packages/theseus/trunk/debian/patches/20_hardening.patch 2012-03-24 20:26:21 UTC (rev 10078) @@ -1,3 +1,9 @@ +Author: Andreas Tille <[email protected]> +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 + --- theseus_src.orig/libdistfit/chisqrgen_dist.c +++ theseus_src/libdistfit/chisqrgen_dist.c @@ -161,7 +161,7 @@ @@ -303,3 +309,116 @@ 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 @@ + { + 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 @@ + 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 @@ + 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 @@ + 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)); + +--- theseus_src.orig/pdbStats.c ++++ theseus_src/pdbStats.c +@@ -1662,7 +1662,7 @@ + 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; +@@ -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]*/; + + logL = invgamma_logL(newvar, vlen-3, b, c); + //- b * ExpInvXn(xn1, b, c) - (1+c)*ExpLogXn(xn1, b, c) +@@ -1844,13 +1844,13 @@ + 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) +--- theseus_src.orig/QuarticHornFrag.c ++++ theseus_src/QuarticHornFrag.c +@@ -318,11 +318,11 @@ + 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 @@ + 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 @@ + + start_time = clock(); + +- biggest = 0.0; ++ /* biggest = 0.0; */ + count = 0; + for (coord1 = 0; coord1 < cdsA->cnum; ++coord1) + { _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
