[Seqan-dev] CMake and ZLIB

[Peter Robinson <Peter.Robinson@jax.org>]

Hi everybody,

I am having some difficulty getting a CMake build to work. I have split the build over a few files since I am also integrating google-test code.

The relevant part of the CMakeList.txt file is here:

## Download seqan from GitHub
configure_file(CMakeLists.seqan.in seqan-download/CMakeLists.txt)
execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
  RESULT_VARIABLE result
  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/seqan-download )
if(result)
  message(FATAL_ERROR "CMake step for seqan failed: ${result}")
endif()
set (CMAKE_MODULE_PATH ${CMAKE_BINARY_DIR}/seqan/util/cmake)
set (SEQAN_INCLUDE_PATH ${CMAKE_BINARY_DIR}/seqan/include)

execute_process(COMMAND ${CMAKE_COMMAND} --build .
  RESULT_VARIABLE result
  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/seqan-download )
if(result)
  message(FATAL_ERROR "Build step for seqan failed: ${result}")
endif()

(...)

# Search for zlib as a dependency for SeqAn.
find_package (ZLIB)

# set required flags, definitions and includes for seqan
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
include_directories(${SEQAN_INCLUDE_DIRS})
add_definitions (${SEQAN_DEFINITIONS})
(...)

This is calling CMakeLists.seqan.in

cmake_minimum_required(VERSION 3.0.0)
project(seqan-download NONE)
include(ExternalProject)
ExternalProject_Add(seqan
  GIT_REPOSITORY    https://github.com/seqan/seqan
  GIT_TAG           develop
  SOURCE_DIR        "${CMAKE_BINARY_DIR}/seqan"
  CONFIGURE_COMMAND ""
  BUILD_COMMAND     ""
  INSTALL_COMMAND   ""
  TEST_COMMAND      ""
)

After going

mkdir build

cmake ..

make

there is a link error for zlib with error messages like this

 In function `zlib_stream::basic_unzip_streambuf<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_unzip_streambuf()':

I am on an Ubuntu system and zlib is installed

sudo apt-get install zlib1g-dev
(....)
zlib1g-dev is already the newest version (1:1.2.11.dfsg-0ubuntu2).

Any ideas or suggestions how to solve this?

thanks & Gruesse nach Berlin
-Peter

Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | peter.robinson@jax.org | https://robinsongroup.github.io/
Peter Robinson

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