[med-svn] [salmon] 01/02: fix Boost build issue

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

satta pushed a commit to branch master
in repository salmon.

commit 650b75f1b65221b9ccded751730fd1f7d85f89fe
Author: Sascha Steinbiss <satta at debian.org>
Date:   Wed Sep 7 13:03:15 2016 +0000

    fix Boost build issue
---
 debian/control                                     |  1 +
 ...007-Remove-unnecessarily-linked-libraries.patch |  8 +++----
 debian/patches/dependency-fix                      | 25 +++++++++++++++-------
 3 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/debian/control b/debian/control
index b178a96..efc3742 100644
--- a/debian/control
+++ b/debian/control
@@ -10,6 +10,7 @@ Build-Depends: debhelper (>= 9),
                libboost-system-dev,
                libboost-thread-dev,
                libboost-program-options-dev,
+               libboost-timer-dev,
                libjellyfish-2.0-dev (>> 2.2.3-2),
                libbwa-dev,
                pkg-config,
diff --git a/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
index 0f1e7a5..b07b979 100644
--- a/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
+++ b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
@@ -9,7 +9,7 @@ Subject: Remove unnecessarily linked libraries
 
 --- a/src/CMakeLists.txt
 +++ b/src/CMakeLists.txt
-@@ -134,16 +134,12 @@ target_link_libraries(salmon
+@@ -134,16 +134,12 @@
      libjellyfish-2.0.so
      /usr/lib/libbwa.a
      m
@@ -29,12 +29,12 @@ Subject: Remove unnecessarily linked libraries
      salmon_core
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -240,7 +240,7 @@ endif()
+@@ -240,7 +240,7 @@
  # Set the latest version and look for what we need
  ##
  set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59" "1.60" "1.61")
--find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
-+find_package(Boost 1.53.0 COMPONENTS filesystem system thread timer program_options)
+-find_package(Boost 1.61.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
++find_package(Boost 1.61.0 COMPONENTS filesystem system thread timer program_options)
  message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
  message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
  message("Boost_FOUND = ${Boost_FOUND}")
diff --git a/debian/patches/dependency-fix b/debian/patches/dependency-fix
index 20a4735..374ee9b 100644
--- a/debian/patches/dependency-fix
+++ b/debian/patches/dependency-fix
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
 Description: Use Debian version of dependencies, don't download them
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -23,7 +23,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PAT
+@@ -23,7 +23,7 @@
  set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
  set (BOOST_CXX_FLAGS "-Wno-deprecated-register -std=c++11")
  ## Prefer static to dynamic libraries
@@ -11,7 +11,7 @@ Description: Use Debian version of dependencies, don't download them
  
  ## Set the standard required compile flags
  # Nov 18th --- removed -DHAVE_CONFIG_H
-@@ -176,7 +176,7 @@ endif ( DEFINED CUSTOM_BOOST_PATH )
+@@ -176,7 +176,7 @@
  ##
  # We want static, multithreaded boost libraries
  ##
@@ -20,7 +20,16 @@ Description: Use Debian version of dependencies, don't download them
  set (Boost_USE_MULTITHREADED ON)
  #set (Boost_USE_STATIC_RUNTIME OFF)
  
-@@ -347,56 +347,56 @@ ExternalProject_Add(libdivsufsort
+@@ -237,7 +237,7 @@
+ # Set the latest version and look for what we need
+ ##
+ set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59" "1.60" "1.61")
+-find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
++find_package(Boost 1.61.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
+@@ -347,56 +347,56 @@
  )
  set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
  
@@ -127,7 +136,7 @@ Description: Use Debian version of dependencies, don't download them
  
  find_package(TBB)
  
-@@ -405,94 +405,94 @@ find_package(TBB)
+@@ -405,94 +405,94 @@
  # Fetch and build Intel's Threading Building Blocks library.
  #
  ##
@@ -288,7 +297,7 @@ Description: Use Debian version of dependencies, don't download them
  
  # Because of the way that Apple has changed SIP 
  # in el capitan, some headers may be in a new location
-@@ -502,39 +502,39 @@ if (APPLE)
+@@ -502,39 +502,39 @@
  endif()
  
  
@@ -361,7 +370,7 @@ Description: Use Debian version of dependencies, don't download them
  
  set (FAST_MALLOC_LIB "")
  set (HAVE_FAST_MALLOC FALSE)
-@@ -558,23 +558,23 @@ if (NOT HAVE_FAST_MALLOC)
+@@ -558,23 +558,23 @@
      endif()
  endif()
  
@@ -418,7 +427,7 @@ Description: Use Debian version of dependencies, don't download them
  ${ZLIB_INCLUDE_DIR}
  ${TBB_INCLUDE_DIRS}
  ${Boost_INCLUDE_DIRS}
-@@ -107,7 +103,7 @@ else()
+@@ -107,7 +103,7 @@
  endif()
  
  # Build the Salmon library
@@ -427,7 +436,7 @@ Description: Use Debian version of dependencies, don't download them
  
  # Build the salmon executable
  add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
-@@ -131,12 +127,12 @@ target_link_libraries(salmon
+@@ -131,12 +127,12 @@
      gff
      ${PTHREAD_LIB}
      ${Boost_LIBRARIES}

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/salmon.git