Andreas Tille pushed to branch master at Debian Med / clustalo
Commits: 9ac92b60 by Andreas Tille at 2020-05-01T07:28:54+02:00 No optimisation for valgrind - FIXME: This needs to be restricted to mipsel only - - - - - 4362a443 by Andreas Tille at 2020-05-01T07:50:15+02:00 Fix syntax error that are exposed only in debug mode - - - - - 3 changed files: - + debian/patches/fix_syntax.patch - debian/patches/series - debian/rules Changes: ===================================== debian/patches/fix_syntax.patch ===================================== @@ -0,0 +1,44 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 17 Apr 2020 17:06:22 +0200 +Description: Fix syntax error that are exposed only in debug mode + +--- a/src/clustal/mbed.c ++++ b/src/clustal/mbed.c +@@ -88,9 +88,9 @@ static const int RESTARTS_PER_SPLIT = 10 + #define USE_KMEANS_LLOYDS 0 + + +-//#ifndef HAVE_LOG2 ++/*#ifndef HAVE_LOG2*/ + #ifndef CLUSTAL_OMEGA_HAVE_LOG2 +-//#define log2(x) (log(x) / 0.69314718055994530942) ++/*#define log2(x) (log(x) / 0.69314718055994530942)*/ + #define log2(x) ( x<=0 ? (float)(-100000) : 1.442695041*log(x) ) + #endif + #define NUMBER_OF_SEEDS(n) pow(log2(((double)n)), 2) +--- a/src/hhalign/util-C.h ++++ b/src/hhalign/util-C.h +@@ -53,10 +53,10 @@ inline double fmean(double x, double y, + + // log base 2 + //#ifndef CLUSTAL_OMEGA_HAVE_LOG2 +-//#ifndef HAVE_LOG2 ++/*#ifndef HAVE_LOG2*/ + inline float Log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} + inline float Log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));} +-//#endif ++/*#endif*/ + + + ///////////////////////////////////////////////////////////////////////////////////// +--- a/src/hhalign/hhalignment-C.h ++++ b/src/hhalign/hhalignment-C.h +@@ -655,7 +655,7 @@ Alignment::Compress(const char infile[]) + if it is too big (L/2) then telomere logic has no effect, + don't think it should be changed (much) */ + #define TELOMER_FRACTION 0.10 +- //#define HMM_MIN_LENGTH 0.923 ++ /*//#define HMM_MIN_LENGTH 0.923*/ + #define HMM_MIN_LENGTH 0.950 + #define FORTRAN_OFFSET 1 + double dDefaultMgaps; ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ clustalo-log-format-calls.patch array_out_of_bounds.patch memory_leak.patch +fix_syntax.patch ===================================== debian/rules ===================================== @@ -6,9 +6,17 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all +# FIXME: this needs to be restricted to mipsel only +export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS | sed 's/-O[1-9]//') -O0 +export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS | sed 's/-O[1-9]//') -O0 + %: dh $@ +# FIXME: this needs to be restricted to mipsel only +override_dh_auto_configure: + dh_auto_configure -- --enable-debug + override_dh_auto_build-indep: # nothing to do here View it on GitLab: https://salsa.debian.org/med-team/clustalo/-/compare/9c43fd1341dfbe127be2a2d506d5d26a8de63f0e...4362a44382ecca118e6658ec6593b55efe640c52 -- View it on GitLab: https://salsa.debian.org/med-team/clustalo/-/compare/9c43fd1341dfbe127be2a2d506d5d26a8de63f0e...4362a44382ecca118e6658ec6593b55efe640c52 You're receiving this email because of your account on salsa.debian.org.
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