[med-svn] [spades] 04/04: fix building

[Sascha Steinbiss]

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satta pushed a commit to branch next311
in repository spades.

commit 8d1888bda1d5b8b6fedccebe49c7d9b001dbbfbb
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Sep 10 06:32:52 2017 +0200

    fix building
---
 debian/patches/0114_use_debian_provided_libs.patch | 32 ++++++++++++++++++++--
 1 file changed, 29 insertions(+), 3 deletions(-)

diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index 33a3f70..524b744 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -64,11 +64,11 @@ Author: Sascha Steinbiss <satta at debian.org>
  #include <vector>
  
  #include "utils/logger/logger.hpp"
-+#include "utils/memory_limit.hpp"
++#include "utils/perf/memory_limit.hpp"
  
  #include "config.hpp"
  
-@@ -104,11 +105,12 @@
+@@ -104,15 +105,16 @@
    size_t max_rss;
  
  #ifdef SPADES_USE_JEMALLOC
@@ -80,10 +80,15 @@ Author: Sascha Steinbiss <satta at debian.org>
    je_mallctl("stats.cactive", &cmem, &clen, NULL, 0);
 -  je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);
 +  //je_mallctl("stats.cactive_max", &cmem_max, &clen, NULL, 0);
-+  cmem_max = get_max_rss();
++  *cmem_max = utils::get_max_rss();
    mem = (*cmem) / 1024;
    max_rss = (*cmem_max) / 1024;
  #else
+-  max_rss = get_max_rss();
++  max_rss = utils::get_max_rss();
+ #endif
+ 
+   for (auto it = writers_.begin(); it != writers_.end(); ++it)
 --- a/ext/src/CMakeLists.txt
 +++ b/ext/src/CMakeLists.txt
 @@ -1,13 +1,9 @@
@@ -100,3 +105,24 @@ Author: Sascha Steinbiss <satta at debian.org>
  add_subdirectory(getopt_pp)
  add_subdirectory(llvm)
 -add_subdirectory(htrie)
+--- a/src/common/modules/coverage_model/kmer_coverage_model.cpp
++++ b/src/common/modules/coverage_model/kmer_coverage_model.cpp
+@@ -18,7 +18,7 @@
+ #include <boost/math/distributions/geometric.hpp>
+ #include <boost/math/distributions/pareto.hpp>
+ 
+-#include <nlopt/nlopt.hpp>
++#include <nlopt.hpp>
+ 
+ #include <vector>
+ 
+--- a/src/common/utils/perf/memory_limit.hpp
++++ b/src/common/utils/perf/memory_limit.hpp
+@@ -28,6 +28,7 @@
+ #endif
+ 
+ #include <common/utils/logger/logger.hpp>
++#include <common/utils/verify.hpp>
+ 
+ namespace utils {
+ 

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