[med-svn] [nanopolish] 02/02: DEP3

[Andreas Tille]

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tille pushed a commit to branch master
in repository nanopolish.

commit 08b25faf228f182168bc72be6d26f0c796155efd
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 16 07:34:33 2017 +0200

    DEP3
---
 debian/changelog                                 |  1 +
 debian/patches/dontinstalleigen.patch            | 10 ++++++----
 debian/patches/fprintf_sizet.patch               | 16 ++++++++--------
 debian/patches/gcc7.patch                        | 11 +++++++----
 debian/patches/write_return_values_ignored.patch | 10 ++++++----
 5 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 9ff8b0e..d95a447 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,7 @@ nanopolish (0.8.1-2) UNRELEASED; urgency=medium
   * Team upload.
   * Hack around broken clean target which tries to build dependencies from
     external sources
+  * DEP3
 
  -- Andreas Tille <tille at debian.org>  Sat, 16 Sep 2017 07:25:45 +0200
 
diff --git a/debian/patches/dontinstalleigen.patch b/debian/patches/dontinstalleigen.patch
index 3241833..2a8a702 100644
--- a/debian/patches/dontinstalleigen.patch
+++ b/debian/patches/dontinstalleigen.patch
@@ -1,7 +1,9 @@
-Index: nanopolish/Makefile
-===================================================================
---- nanopolish.orig/Makefile
-+++ nanopolish/Makefile
+Author: Steffen Moeller
+Last-Update: 2017-09-16 02:14:07 +0200
+Description: Use Debian packaged libeigen
+
+--- a/Makefile
++++ b/Makefile
 @@ -16,7 +16,7 @@ CXX ?= g++
  CC ?= gcc
  
diff --git a/debian/patches/fprintf_sizet.patch b/debian/patches/fprintf_sizet.patch
index 869707e..ad0bf61 100644
--- a/debian/patches/fprintf_sizet.patch
+++ b/debian/patches/fprintf_sizet.patch
@@ -1,7 +1,9 @@
-Index: nanopolish/src/common/nanopolish_variant.cpp
-===================================================================
---- nanopolish.orig/src/common/nanopolish_variant.cpp
-+++ nanopolish/src/common/nanopolish_variant.cpp
+Author: Steffen Moeller
+Last-Update: 2017-09-16 02:14:07 +0200
+Description: Fix format-error issues blamed by gcc-7
+
+--- a/src/common/nanopolish_variant.cpp
++++ b/src/common/nanopolish_variant.cpp
 @@ -175,7 +175,7 @@ void score_variant_group(VariantGroup& v
      max_r -= 1;
  
@@ -11,10 +13,8 @@ Index: nanopolish/src/common/nanopolish_variant.cpp
      }
  
      // Construct haplotypes (including the base haplotype with no variants)
-Index: nanopolish/src/nanopolish_haplotype.cpp
-===================================================================
---- nanopolish.orig/src/nanopolish_haplotype.cpp
-+++ nanopolish/src/nanopolish_haplotype.cpp
+--- a/src/nanopolish_haplotype.cpp
++++ b/src/nanopolish_haplotype.cpp
 @@ -169,7 +169,7 @@ size_t Haplotype::_find_derived_index_by
  
  void Haplotype::print_debug_info() const
diff --git a/debian/patches/gcc7.patch b/debian/patches/gcc7.patch
index 104ca19..c972825 100644
--- a/debian/patches/gcc7.patch
+++ b/debian/patches/gcc7.patch
@@ -1,7 +1,10 @@
-Index: nanopolish/src/common/logger.hpp
-===================================================================
---- nanopolish.orig/src/common/logger.hpp
-+++ nanopolish/src/common/logger.hpp
+Author: Steffen Moeller
+Last-Update: 2017-09-16 02:14:07 +0200
+Bug-Debian: https://bugs.debian.org/853568
+Description: Add missing header file to build with gcc-7
+
+--- a/src/common/logger.hpp
++++ b/src/common/logger.hpp
 @@ -72,6 +72,7 @@
  #include <iostream>
  #include <mutex>
diff --git a/debian/patches/write_return_values_ignored.patch b/debian/patches/write_return_values_ignored.patch
index be1b66f..d8f1153 100644
--- a/debian/patches/write_return_values_ignored.patch
+++ b/debian/patches/write_return_values_ignored.patch
@@ -1,7 +1,9 @@
-Index: nanopolish/src/alignment/nanopolish_eventalign.cpp
-===================================================================
---- nanopolish.orig/src/alignment/nanopolish_eventalign.cpp
-+++ nanopolish/src/alignment/nanopolish_eventalign.cpp
+Author: Steffen Moeller
+Last-Updated: 2017-09-16 02:14:07 +0200
+Description: Do not ignore return values of samtool functions
+
+--- a/src/alignment/nanopolish_eventalign.cpp
++++ b/src/alignment/nanopolish_eventalign.cpp
 @@ -221,7 +221,7 @@ void emit_tsv_header(FILE* fp)
  
  void emit_sam_header(samFile* fp, const bam_hdr_t* hdr)

-- 
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