[med-svn] [dindel] 01/01: fix FTBFS with newer Boost versions

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository dindel.

commit 5ec3b5aface7fea0e2c8fce009d9c426f29c570a
Author: Sascha Steinbiss <satta at debian.org>
Date:   Fri Aug 19 14:30:23 2016 +0000

    fix FTBFS with newer Boost versions
---
 debian/changelog                              |  9 +++
 debian/control                                |  4 +-
 debian/patches/fix-ftbfs-with-new-boost.patch | 90 +++++++++++++++++++++++++++
 debian/patches/series                         |  1 +
 4 files changed, 102 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 3e51f11..a72e214 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+dindel (1.01+dfsg-4) unstable; urgency=medium
+
+  * Team upload.
+  * Make code compatible with latest Boost version (1.61 and up).
+    Thanks to Graham Inggs for the patch.
+    Closes: #833958
+
+ -- Sascha Steinbiss <satta at debian.org>  Wed, 10 Aug 2016 21:34:19 +0000
+
 dindel (1.01+dfsg-3) unstable; urgency=medium
 
   * Team upload.
diff --git a/debian/control b/debian/control
index d5e5480..12a689c 100644
--- a/debian/control
+++ b/debian/control
@@ -8,8 +8,8 @@ Priority: optional
 Build-Depends: debhelper (>= 9),
                seqan-dev,
                libbam-dev,
-               libboost-program-options1.58-dev,
-               libboost-math1.58-dev,
+               libboost-program-options-dev,
+               libboost-math-dev,
                zlib1g-dev
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/dindel.git
diff --git a/debian/patches/fix-ftbfs-with-new-boost.patch b/debian/patches/fix-ftbfs-with-new-boost.patch
new file mode 100644
index 0000000..5594740
--- /dev/null
+++ b/debian/patches/fix-ftbfs-with-new-boost.patch
@@ -0,0 +1,90 @@
+Description: Use Boost's foreach.hpp instead of embedded copy
+ This fixes a FTBFS with recent versions of Boost
+Bug-Debian: https://bugs.debian.org/833958
+Author: Graham Inggs <ginggs at debian.org>
+Last-Update: 2016-08-19
+--- a/DInDel.cpp
++++ b/DInDel.cpp
+@@ -24,7 +24,7 @@
+ #include <boost/math/special_functions/digamma.hpp>
+ #include <seqan/align.h>
+ #include <seqan/graph_align.h>
+-#include "foreach.hpp"
++#include <boost/foreach.hpp>
+ #include "bam.h"
+ #include "DInDel.hpp"
+ #include "Haplotype.hpp"
+--- a/Faster.cpp
++++ b/Faster.cpp
+@@ -35,7 +35,7 @@
+ #include "Haplotype.hpp"
+ #include "Faster.hpp"
+ #include "Utils.hpp"
+-#include "foreach.hpp"
++#include <boost/foreach.hpp>
+ using namespace std;
+ const int DEBUGS=0;
+ 
+--- a/GetCandidates.cpp
++++ b/GetCandidates.cpp
+@@ -22,7 +22,7 @@
+ #include <fstream>
+ #include <string>
+ #include "MyBam.hpp"
+-#include "foreach.hpp"
++#include <boost/foreach.hpp>
+ #include "ObservationModelSeqAn.hpp"
+ #include "GetCandidates.hpp"
+ #include "Variant.hpp"
+@@ -32,7 +32,6 @@
+ #include "Fasta.hpp"
+ #include "StringHash.hpp"
+ #include <set>
+-#include "foreach.hpp"
+ using namespace std;
+ 
+ int GetCandidatesFromCIGAR::getIndelFromCIGARFetchFunc(const bam1_t *b, void *data)
+--- a/Haplotype.hpp
++++ b/Haplotype.hpp
+@@ -23,7 +23,7 @@
+ #include <vector>
+ #include "Variant.hpp"
+ #include "MLAlignment.hpp"
+-#include "foreach.hpp"
++#include <boost/foreach.hpp>
+ #include <ext/hash_map>
+ #include <set>
+ //#include "Fast.hpp"
+--- a/HaplotypeDistribution.hpp
++++ b/HaplotypeDistribution.hpp
+@@ -27,7 +27,7 @@
+ #include "bam.h"
+ #include "Haplotype.hpp"
+ #include "HapBlock.hpp"
+-#include "foreach.hpp"
++#include <boost/foreach.hpp>
+ #include "VariantFile.hpp"
+ using namespace std;
+ 
+--- a/OutputData.hpp
++++ b/OutputData.hpp
+@@ -25,7 +25,7 @@
+ #include "StringHash.hpp"
+ #include <string>
+ #include <iostream>
+-#include "foreach.hpp"
++#include <boost/foreach.hpp>
+ using namespace std;
+ using namespace boost;
+ 
+--- a/StringHash.hpp
++++ b/StringHash.hpp
+@@ -25,7 +25,7 @@
+ #include <ext/hash_map>
+ #include <string>
+ #include <iostream>
+-#include "foreach.hpp"
++#include <boost/foreach.hpp>
+ using namespace std;
+ using namespace boost;
+ using __gnu_cxx::hash;
diff --git a/debian/patches/series b/debian/patches/series
index 8fb20f6..f6ef95f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 modernize-Makefile.patch
 compiler_errors.patch
 fix-ftbfs-with-gcc6.patch
+fix-ftbfs-with-new-boost.patch

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