[med-svn] [bcl2fastq2] 01/02: Add patches to compile with current boost and correct library patch d/p/fix_TRUE..: undefine the macros if they are defined because they are later used to define the tristate d/p/fix_prop..: always give template parameter d/p/fix_lib..: correct the libexslt cmake library variable

[Gert Wollny]

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gewo pushed a commit to branch master
in repository bcl2fastq2.

commit 64853f532eb35e7764be581a5da0f78e21204a76
Author: Gert Wollny <gewo at debian.org>
Date:   Sat Jun 24 17:54:09 2017 +0000

    Add patches to compile with current boost and correct library patch
     d/p/fix_TRUE..: undefine the macros if they are defined because they
     are later used to define the tristate
     d/p/fix_prop..: always give template parameter
     d/p/fix_lib..: correct the libexslt cmake library variable
---
 debian/patches/fix_TRUE_FALSE_enum.patch | 21 +++++++++++++++++++++
 debian/patches/fix_lib_versions.patch    | 10 ++++++++--
 debian/patches/fix_property_writer.patch | 28 ++++++++++++++++++++++++++++
 debian/patches/series                    |  2 ++
 4 files changed, 59 insertions(+), 2 deletions(-)

diff --git a/debian/patches/fix_TRUE_FALSE_enum.patch b/debian/patches/fix_TRUE_FALSE_enum.patch
new file mode 100644
index 0000000..90a5f10
--- /dev/null
+++ b/debian/patches/fix_TRUE_FALSE_enum.patch
@@ -0,0 +1,21 @@
+Author: Gert Wollny <gewo at debian.org>
+Last-Update: Tue, 24 Jun 2017 20:18:44 +0200
+Description: undefine TRUE and FALSE, because they may be define in some
+ header. 
+--- a/src/cxx/include/config/SampleSheetCsv.hh
++++ b/src/cxx/include/config/SampleSheetCsv.hh
+@@ -29,6 +29,14 @@
+ 
+ #include <boost/shared_ptr.hpp>
+ 
++#ifdef TRUE
++#undef TRUE
++#endif
++
++#ifdef FALSE
++#undef FALSE
++#endif
++
+ namespace bcl2fastq {
+ 
+ 
diff --git a/debian/patches/fix_lib_versions.patch b/debian/patches/fix_lib_versions.patch
index 343321e..b7028af 100644
--- a/debian/patches/fix_lib_versions.patch
+++ b/debian/patches/fix_lib_versions.patch
@@ -1,11 +1,12 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 20 Jun 2017 14:40:44 +0200
+Last-Update: Tue, 24 Jun 2017 20:21:44 +0200
 Description: Redist untaring attempt even after correct version was found
  just force cmake to ignore the redistributed code copies.
+ Also correct name of libexslt library variable to LIBXSLT_EXSLT_LIBRARIES.
 
 --- a/src/cmake/cxxConfigure.cmake
 +++ b/src/cmake/cxxConfigure.cmake
-@@ -103,15 +103,6 @@ if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXS
+@@ -103,19 +103,10 @@
    find_package_version(LibXslt ${BCL2FASTQ_LIBXSLT_VERSION})
  endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
  
@@ -21,3 +22,8 @@ Description: Redist untaring attempt even after correct version was found
  include_directories(BEFORE SYSTEM ${LIBXML2_INCLUDE_DIR})
  include_directories(BEFORE SYSTEM ${LIBXSLT_INCLUDE_DIR})
  include_directories(BEFORE SYSTEM ${LIBEXSLT_INCLUDE_DIR})
+-set(BCL2FASTQ_DEP_LIB ${BCL2FASTQ_DEP_LIB} "${LIBEXSLT_LIBRARIES}" "${LIBXSLT_LIBRARIES}" "${LIBXML2_LIBRARIES}")
++set(BCL2FASTQ_DEP_LIB ${BCL2FASTQ_DEP_LIB} "${LIBXSLT_EXSLT_LIBRARIES}" "${LIBXSLT_LIBRARIES}" "${LIBXML2_LIBRARIES}")
+ 
+ #set (CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} $ENV{CXXFLAGS} -fopenmp -msse2 -Werror -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith" CACHE STRING "g++ flags" FORCE)
+ set (CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} $ENV{CXXFLAGS} -std=c++11 -fopenmp -msse2 -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith" CACHE STRING "g++ flags" FORCE)
diff --git a/debian/patches/fix_property_writer.patch b/debian/patches/fix_property_writer.patch
new file mode 100644
index 0000000..80f2a1f
--- /dev/null
+++ b/debian/patches/fix_property_writer.patch
@@ -0,0 +1,28 @@
+Author: Gert Wollny <gewo at debian.org>
+Last-Update: Tue, 24 Jun 2017 20:18:44 +0200
+Description: Always give the template parameter
+ Also on Linux the template parameter can not be automatically deducted,
+ hence give it unconditionally
+
+--- a/src/cxx/lib/io/Xml.cpp
++++ b/src/cxx/lib/io/Xml.cpp
+@@ -168,19 +168,11 @@
+     if (!tree.empty())
+     {
+         unindex(*tree.begin(), treeWithIndexAttributes);
+-#ifndef WIN32
+-        boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings(' ', 2));
+-#else
+         boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings<std::string>(' ', 2));
+-#endif
+     }
+     else
+     {
+-#ifndef WIN32
+-        boost::property_tree::write_xml(os, tree, boost::property_tree::xml_writer_make_settings(' ', 2));
+-#else
+         boost::property_tree::write_xml(os, tree, boost::property_tree::xml_writer_make_settings<std::string>(' ', 2));
+-#endif
+     }
+     return os;
+ }
diff --git a/debian/patches/series b/debian/patches/series
index 66b09b1..c1879a2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
 fix_lib_versions.patch
+fix_property_writer.patch
+fix_TRUE_FALSE_enum.patch

-- 
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