[Seqan-dev] I'm interested in making SeqAn faster but am stopped by these CMake errors

[Neil Justice <njjustice@gmail.com>]

Hello SeqAn developers,

My name is Neil Justice and I'm interested in helping advance genetics
research by contributing my programming skills to the task of making
SeqAn faster. I work on performance tuning the C++ of a high-frequency
algorithmic trading program at a hedge fund in Houston. Lately I've
been interested in finding an interesting and good-for-humanity open
source project to work on at home, and SeqAn appears to be that
project.

I am on Windows and am trying to generate a Visual Studio 2008 .sln
for SeqAn using CMake. I've pulled the code using svn per tutorial
http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake
errors I encounter in response to CMake command "cmake
C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached
as a screenshot):

PS C:\Seqan\build> cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"
-- Check for working C compiler using: Visual Studio 9 2008
-- Check for working C compiler using: Visual Studio 9 2008 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler using: Visual Studio 9 2008
-- Check for working CXX compiler using: Visual Studio 9 2008 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
SEQAN_CONTRIB_BASE is undefined!
-- CMAKE_FIND_ROOT_PATH is "".
-- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3")
-- Zlib could not be found!
-- BZip2 libraries could not be found!
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY
-- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed
-- Performing Test TR1_SHARED_PTR_USE_MEMORY
-- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success
-- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP
-- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed
-- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP
-- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success
-- Could NOT find Boost
-- Looking for include file execinfo.h
-- Looking for include file execinfo.h - not found.
-- INFO: Rabema not build because zlib was not found.
CMake Error at core/apps/rabema/CMakeLists.txt:43 (install):
  install TARGETS given target "rabema_build_gold_standard" which does not
  exist in this directory.

-- Boost not found, not building snp_store.
-- Configuring incomplete, errors occurred!
PS C:\Seqan\build>
PS C:\Seqan\build>

How would you fix these errors? I don't have Zlib or BZip2 (do I need
to download these libraries?). I have Boost (which was not found - do
I need to specify its path somewhere?). I have Python (which was
found).

Thanks and I look forward to finding some SeqAn performance issues.

Neil

Attachment: SeqAnCmakeErrors.PNG
Description: PNG image