Re: [Seqan-dev] Build seqan on RedHat 6!

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Could you try to setup CMake 2.8.x? I think the CMake team did a lot of changes in CMake 3.0.

Birte, which exact version works for you?

Cheers,
Manuel
________________________________________
From: Verhaag Geert (GEN) [g.verhaag@maastrichtuniversity.nl]
Sent: Monday, September 08, 2014 3:49 PM
To: SeqAn Development
Subject: Re: [Seqan-dev] Build seqan on RedHat 6!

Hi Birte,

Thanks for your hint! Tried the local install of cmake 3.0.1.

Running:

~/ cmake ../../seqan-trunk -G "Eclipse CDT4 - Unix Makefiles" -DCMAKE_BUILD_TYPE=Debug

Yields the following output:

-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Found Eclipse version 4.3 (Kepler)
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Initializing SeqAn Build System...
--   Determined repository date is 2014-08-27 11:21:24 +0200 (Wed, 27 Aug 2014)
--   Determined repository revision is 4770
-- Configuring core
-- Configuring core/apps
-- Configuring core/apps/splazers
-- Looking for include file execinfo.h
-- Looking for include file execinfo.h - found
--   Determined version is 1.4.2
-- Found PythonInterp: /usr/bin/python (found version "2.6.6")
-- Configuring core/apps/snp_store
-- Zlib could not be found!
Boost  found.
--
--   Boost or zlib not found: Not building snp_store.
-- Configuring core/apps/samcat
-- Zlib could not be found!
-- Configuring core/apps/sam2matrix
-- Zlib could not be found!
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Configuring core/apps/dfi
-- Configuring core/apps/rabema
-- Zlib could not be found!
--   ZLIB not found: RABEMA will not be built.
-- Configuring core/apps/seqan_tcoffee
-- Configuring core/apps/micro_razers
-- Configuring core/apps/stellar
-- Configuring core/apps/razers
-- Configuring core/apps/seqcons
-- Configuring core/apps/razers2
-- Zlib could not be found!
-- Configuring core/apps/tree_recon
-- Configuring core/apps/mason
-- Configuring core/apps/pair_align
-- Configuring core/apps/sak
-- Configuring core/apps/fiona
-- Zlib could not be found!
Boost  found.
-- Configuring core/demos
-- BZip2 libraries could not be found!
-- Configuring core/tests
-- Configuring core/tests/random
-- Configuring core/tests/basic
-- Configuring core/tests/consensus
-- Configuring core/tests/index
-- Configuring core/tests/stream
-- BZip2 libraries could not be found!
-- Configuring core/tests/arg_parse
-- Configuring core/tests/find_swift
-- Configuring core/tests/graph_algorithms
-- Configuring core/tests/bam_io
-- Configuring core/tests/parallel
-- Configuring core/tests/graph_msa
-- Configuring core/tests/misc
-- Configuring core/tests/map
-- Configuring core/tests/seq_io
-- BZip2 libraries could not be found!
-- Configuring core/tests/graph_types
-- Configuring core/tests/sequence_journaled
-- Configuring core/tests/file
-- Configuring core/tests/find
-- Configuring core/tests/sequence
-- Configuring core/tests/align
-- Configuring core/tests/graph_align
-- Configuring core/tests/modifier
-- Configuring core/tests/pipe
-- Configuring core/tests/seeds
-- Configuring core/tests/score
-- Configuring core/tests/store
-- Configuring core/tests/gff_io
-- Configuring extras
-- Configuring extras/apps
-- Configuring extras/apps/seqan_flexbar
-- BZip2 libraries could not be found!
-- Configuring extras/apps/insegt
-- Configuring extras/apps/variant_comp
-- Configuring sandbox/jagla/apps/ngs_roi
-- Configuring extras/apps/razers3
-- Performing Test CXX11_FOUND
-- Performing Test CXX11_FOUND - Failed
--   RazerS 3 cannot be built with MinGW or with MS Visual C++ 8 and earlier.
-- Configuring extras/apps/fx_tools
-- Configuring extras/apps/sgip
--   SGIP cannot be built with MinGW or with MS Visual C++ 8 and earlier.
-- Configuring extras/apps/param_chooser
-- Configuring extras/apps/searchjoin
-- Configuring extras/apps/alf
-- Configuring extras/apps/gustaf
-- Configuring extras/apps/breakpoint_calculator
--   LEMON library not found: Not building breakpoint_calculator.
-- Configuring extras/apps/mason2
-- Configuring extras/apps/rep_sep
-- Configuring extras/apps/bs_tools
Boost  found.
-- Configuring extras/demos
-- BZip2 libraries could not be found!
-- Configuring extras/tests
-- Configuring extras/tests/index
-- Configuring extras/tests/vcf_io
-- Configuring extras/tests/align_extend
-- Configuring extras/tests/statistics
-- Configuring extras/tests/bed_io
-- Configuring extras/tests/align_profile
-- Configuring extras/tests/multiple_translation_units
-- Configuring extras/tests/translation
-- Configuring extras/tests/parse_lm
-- Configuring extras/tests/roi_io
-- Configuring extras/tests/find_motif
-- Configuring extras/tests/alignment_free
-- Configuring extras/tests/align_split
-- Configuring docs
-- Configuring sandbox
-- Configuring util/py_lib
--   nosetests for seqan.dox
-- Found Java: /usr/bin/java (found version "1.7.0.65")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/g.verhaag/SeqAnDevelopment/seqan-trunk-build/debug-eclipse

ZLib and BZip2 libraries are a problem, but the following packages are installed:
zlib.x86_64                          1.2.3-29.el6
zlib-devel.x86_64             1.2.3-29.el6
bzip2.x86_64                 1.0.5-7.el6_0
bzip2-libs.x86_64           1.0.5-7.el6_0
What am I doing wrong here? Any idea!?
Regards,
Gerard


From: Kehr, Birte [mailto:Birte.Kehr@fu-berlin.de]
Sent: Monday, September 08, 2014 15:08
To: SeqAn Development
Subject: Re: [Seqan-dev] Build seqan on RedHat 6!

Hi Gerard,

I am working with SeqAn on RedHat 6.5 without having any problems. However, in order to use the SeqAn build system you'll have to use a (local) installation of cmake 2.8 or higher, or you can write your own Makefiles that include the library:
http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem

- Birte
________________________________
Von: Verhaag Geert (GEN) [g.verhaag@maastrichtuniversity.nl]
Gesendet: Montag, 8. September 2014 13:11
An: seqan-dev@lists.fu-berlin.de<mailto:seqan-dev@lists.fu-berlin.de>
Betreff: [Seqan-dev] Build seqan on RedHat 6!
Dear SeqAn developers,

I’m considering the usage of SeqAn but are bound to a RedHat 6 system with for example cmake 2.6.4!

Is that possible?

Gerard