[med-svn] [Git][med-team/clustalo][master] 2 commits: No optimisation for valgrind - FIXME: This needs to be restricted to mipsel only

[Andreas Tille]

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 <tille at debian.org>
+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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200501/59ec7be7/attachment-0001.html>