[med-svn] [seqan2] 01/02: switch to upstream's patch

[Michael Crusoe]

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misterc-guest pushed a commit to tag debian/2.2.0+dfsg-4
in repository seqan2.

commit 6f65bc6484847da4e356082c8ea83d8c7103f813
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Tue Oct 11 04:11:10 2016 -0700

    switch to upstream's patch
---
 debian/patches/pthread-linking | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/debian/patches/pthread-linking b/debian/patches/pthread-linking
index 9d07ca6..394132c 100644
--- a/debian/patches/pthread-linking
+++ b/debian/patches/pthread-linking
@@ -1,11 +1,34 @@
+From: rrahn <rene.rahn at fu-berlin.de>
+Date: Mon, 10 Oct 2016 16:55:04 +0200
+Subject: Fix static linking against pthread on some linux kernels.
+--- seqan2.orig/manual/source/Infrastructure/Use/CustomBuildSystem.rst
++++ seqan2/manual/source/Infrastructure/Use/CustomBuildSystem.rst
+@@ -45,6 +45,10 @@
+ 
+ Add ``-lrt -lpthread`` to the compiler call.
+ 
++Note static linking against pthread might cause issues on some linux distributions.
++In this case you need to explicitly link against the whole archive like: ``-Wl,--whole-archive -lpthread -Wl,--no-whole-archive``.
++You can read more about this issue `here <https://gcc.gnu.org/bugzilla/show_bug.cgi?id=52590>`_.
++
+ BSD
+ ^^^
+ 
 --- seqan2.orig/util/cmake/FindSeqAn.cmake
 +++ seqan2/util/cmake/FindSeqAn.cmake
-@@ -287,7 +287,7 @@
+@@ -287,8 +287,13 @@
  
  # librt, libpthread -- implicit, on Linux only
  
 -if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
-+if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux") || (${CMAKE_SYSTEM_NAME} STREQUAL "kFreeBSD") || (${CMAKE_SYSTEM_NAME} STREQUAL "GNU") 
-   set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} rt pthread)
+-  set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} rt pthread)
++if ((${CMAKE_SYSTEM_NAME} STREQUAL "Linux") OR (${CMAKE_SYSTEM_NAME} STREQUAL "kFreeBSD") OR (${CMAKE_SYSTEM_NAME} STREQUAL "GNU"))
++  set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} rt)
++  if ((CMAKE_CXX_FLAGS MATCHES "-static") OR (SEQAN_CXX_FLAGS MATCHES "-static") OR (CMAKE_EXE_LINKER_FLAGS MATCHES "-static"))
++    set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--whole-archive -lpthread -Wl,--no-whole-archive")
++  else ()
++    set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} pthread)
++  endif ()
  elseif ((${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") OR (${CMAKE_SYSTEM_NAME} STREQUAL "OpenBSD"))
    set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} pthread)
+   set (SEQAN_DEFINITIONS ${SEQAN_DEFINITIONS} "-D_GLIBCXX_USE_C99=1")

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