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

[Nomi Meixner <nomi.meixner@student.uni-tuebingen.de>]

Dear Manuel, dear all,

> 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

Thank you very much for this valuable hint! I removed and re-created the bin directory and executed the above mentioned command. This indeed solves the problem of not finding the boost library.
  
> Don't hesitate to send another email if this does not help you.

However, I have to come back to your offer to ask further questions. The next problem is that the installation fails a few steps afterwards.
{TARGET_DIR}/seqan-trunk/core/demos/align/global_alignment_banded.cpp:3:24: Fehler: seqan/base.h: Datei oder Verzeichnis nicht gefunden

This time, I agree that the file it is looking for is not present at the location it is searching for it:
{TARGET_DIR}> find . -iname base.h
./seqan-trunk/extras/apps/insegt/base.h

{TARGET_DIR}> find . -iname seqan
./seqan-trunk/extras/include/seqan
./seqan-trunk/core/include/seqan
./seqan-trunk/misc/py_lib/seqan
./seqan-trunk/util/ports/science/seqan
./seqan-trunk/util/py_lib/seqan

Where am I supposed to get this file from? And am I right assuming it should go to ./seqan-trunk/core/include/seqan?

I hope you can help me again... Let me know, if you need further details like complete output of the process etc.
Thank you very much in advance!

Best,
Nomi

> ________________________________________
> 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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