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Re: [Seqan-dev] SeqAn installation with manually compiled boost library

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Dear Nomi,

this looks as if SeqAn picks up Boost from the system root (i.e. installed through the Red Hat package manager).

You have to set the variable "BOOST_ROOT" to the "${TARGET_DIR}/include/boost" for the build system to pick up your manual Boost installation.

If you are lucky, then you can do "ccmake ." in the "bin" directory and simply set the variable.

If you are less lucky or if you want to have a clean start then you can remove "bin", recreate it and then execute

cmake ../seqan-trunk -DBOOST_ROOT=../include

Note that you can omit the -DCMAKE_BUILD_TYPE=Release parameter in recent checkouts (for some months now) since this is the default build type.

Don't hesitate to send another email if this does not help you.

Cheers,
Manuel
________________________________________
From: Nomi Meixner [nomi.meixner@student.uni-tuebingen.de]
Sent: Monday, June 24, 2013 6:39 PM
To: SeqAn Mailing list
Subject: [Seqan-dev] SeqAn installation with manually compiled boost library

Hello everyone,

I have trouble installing SeqAn on a RHEL system, where I installed the zlib and boost libraries manually.

My folder structure looks the following:
{TARGET_DIR}/bin -> preferred build directory
{TARGET_DIR}/doc
{TARGET_DIR}/include/boost/ -> contains all the boost subfolders .hpp files etc.
{TARGET_DIR}/lib -> contains libboost* and libz*
{TARGET_DIR}/seqan-trunk -> as checked out from SVN
{TARGET_DIR}/share

Following the tutorial (trac.seqan.de/wiki/Tutorial/GettingStarted/LinuxMakefiles), from the {TARGET_DIR}/bin folder I call cmake ../seqan-trunk -DCMAKE_BUILD_TYPE=Release, which succeeds.
Then >make
Make fails at approximately 5% having trouble to find the boost math libraries while installing snp_store.

The (potentially crucial part of the) environment looks like this:
{TARGET_DIR}/bin$ env | grep CMAKE
CMAKE_MAN_DIR=/opt/.../.../cmake/2.8.6/man
CMAKE_DOC_DIR=/opt/.../.../cmake/2.8.6/doc
CMAKE_LIBRARY_PATH={TARGET_DIR}/lib
CMAKE_BIN_DIR=/opt/.../.../cmake/2.8.6/bin
CMAKE_HOME=/opt/.../.../cmake/2.8.6
DCMAKE_INCLUDE_PATH={TARGET_DIR}/include
CMAKE_VERSION=2.8.6
CMAKE_INCLUDE_PATH={TARGET_DIR}/include

{TARGET_DIR}/bin$  env | grep LIBR
CMAKE_LIBRARY_PATH={TARGET_DIR}/lib
LD_LIBRARY_PATH={TARGET_DIR}/lib

{TARGET_DIR}/bin$  env | grep INCLUDE
DCMAKE_INCLUDE_PATH={TARGET_DIR}/include
CMAKE_INCLUDE_PATH={TARGET_DIR}/include
INCLUDE={TARGET_DIR}/include

The error looks the following and produces many more lines of errors:

[  5%] Building CXX object core/apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o
In Datei, eingefügt von {TARGET_DIR}/seqan-trunk/core/apps/snp_store/snp_store.cpp:53:
{TARGET_DIR}/seqan-trunk/core/apps/snp_store/snp_store.h:36:40: Fehler: boost/math/distributions.hpp: Datei oder Verzeichnis nicht gefunden

However the file{TARGET_DIR}> ls include/boost/math/distributions.hpp
include/boost/math/distributions.hpp
DOES exist. It is just not found.

What am I doing wrong?
Any help would be greatly appreciated.
Thank you very much,

Nomi

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