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

["Verhaag Geert (GEN)" <g.verhaag@maastrichtuniversity.nl>]

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
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