Re: [Open-ms-general] building on ubuntu 14.04 with libbz2 installed

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Hi Stephan,

You are right. For a reason I don't remember I built against the contrib libbz2 in Ubuntu 12.04. I never thought of using the system-provided libbz2 in 14.04 even though it was staring me in the face. Leaving the contrib out solves the problem.  Thanks loads!

cheers,
— 
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden

On 26 May 2014, at 15:10, Aiche, Stephan <Ste...@fu...> wrote:

> He Jorrit,
> 
> I'm not sure if I understand your problem correctly. You assume the bzip lib shipped when installing percolator isn't compatible with the one used by OpenMS? Isn't percolator using the system libbz2-dev. If so, it should be fine as we can compile OpenMS also against this version of bzip. I just made a small test on a fresh Ubuntu 14.04 and was able to compile OpenMS using the system libbz2. Here is a rough sketch of what I did. I also attached a small patch that fixes the issues with finding the system xerces-c on ubuntu systems. 
> 
> I hope this helps, if not please specify exactly what problems you encounter when compiling OpenMS using the system libbz2? 
> 
> Cheers
> Stephan
> 
> # sys-info 
> $ lsb_release -a
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description: Ubuntu 14.04 LTS
> Release: 14.04
> Codename: trusty
> 
> # install dev tools
> $ sudo apt-get install cmake git autoconf libtool g++
> 
> # install contrib libs
> $ sudo apt-get install libxerces-c-dev libglpk-dev libboost1.54-all-dev libsvm-dev libgsl0-dev libbz2-dev qt4-dev-tools libqt4-dev libqt4-core libqt4-gui
> 
> # clone and build missing libs from contrib
> $ git clone git://github.com/OpenMS/contrib/
> $ mkdir contrib-build
> $ cd contrib-build
> $ cmake ../contrib -DBUILD_TYPE=SEQAN
> $ cd ..
> 
> # clone OpenMS  
> $ git clone https://github.com/OpenMS/OpenMS 
> $ cd OpenMS
> $ git checkout Release1.11.1 
> $ git apply xerces-c.patch
> $ cd ..
> 
> # OpenMS build dir
> $ mkdir OpenMS-build
> $ cd OpenMS-build
> 
> # configure OpenMS using contrib and system libs
> $ cmake -DCMAKE_FIND_ROOT_PATH="<PATH to contrib build>/contrib-build/;/usr/" -DBOOST_USE_STATIC=Off ../OpenMS
> $ make
> 
> On 26 May 2014, at 09:41, Jorrit Boekel <jor...@sc...> wrote:
> 
>> Dear all,
>> 
>> I tried out building TOPP on Ubuntu trusty (I know a package exists). Basically using only SEQAN and BZIP from contrib, the other dependencies installed as packages (which worked on Ubuntu 12). I have to mention here that I also run percolator on the same system, which comes with a (package installed) libbz2-dev dependency. This gives issues on Ubuntu 12 as well, therefore I build BZIP from contrib and symlink it to solve those. However, it does not seem to work in Ubuntu 14 (see make error below).
>> 
>> I do not have enough C++ building knowledge to know what to do about it. Between 12 and 14 some libraries seem to have changed place (hence the libxerces symlinks in my build script), which may have something to do with it. Libbz2 seems to be here:
>> admin@testbox:~$ locate libbz2
>> /lib/x86_64-linux-gnu/libbz2.so.1
>> /lib/x86_64-linux-gnu/libbz2.so.1.0
>> /lib/x86_64-linux-gnu/libbz2.so.1.0.4
>> 
>> Is it a bad idea to apt-get remove libbz2-dev before building and then reinstalling it afterwards as a workaround? It seems like a rather dirty solution. Of course, I would prefer to build everything completely isolated, but I don’t think we’re really there yet.
>> 
>> My build script (on docker, just ignore the RUN directives):
>> RUN apt-get -y install cmake g++ autoconf qt4-dev-tools patch libtool make
>> RUN apt-get -y install libxerces-c-dev libgsl0-dev libboost-regex-dev libboost-iostreams-dev libboost-date-time-dev libboost-math-dev libsvm-dev libglpk-dev libzip-dev zlib1g-dev
>> RUN apt-get -y install git-core
>> 
>> RUN git clone https://github.com/OpenMS/OpenMS openms
>> RUN git clone https://github.com/OpenMS/contrib contrib
>> RUN cd openms && git checkout 6a515dd1e23882ec60578a289920bf46ca4f525d
>> RUN apt-get -y install libbz2-dev
>> RUN cd contrib && cmake -DBUILD_TYPE=BZIP2 .
>> RUN cd contrib && cmake -DBUILD_TYPE=SEQAN .
>> RUN ln -s contrib/lib/libbz2.a /usr/local/lib/libbz2.a
>> RUN ln -s /usr/lib/x86_64-linux-gnu/libxerces-c.a /usr/local/lib/libxerces-c.a
>> RUN ln -s /usr/lib/x86_64-linux-gnu/libxerces-c.so /usr/local/lib/libxerces-c.so
>> RUN cd openms && cmake -DCMAKE_FIND_ROOT_PATH="/usr;/usr/local" -DBOOST_USE_STATIC=OFF -DSEQAN_INCLUDE_DIR=../contrib/include -DBZIP2_INCLUDE_DIR=../contrib/include -DBZIP2_LIBRARIES=libbz2.a .
>> RUN cd openms && make
>> 
>> 
>> The last bit of stderr from make: 
>> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/libbz2.a(bzlib.o): relocation R_X86_64_32S against `BZ2_crc32Table' can not be used when making a shared object; recompile with -fPIC
>> /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/libbz2.a: error adding symbols: Bad value
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [lib/libOpenMS.so] Error 1
>> make[1]: *** [CMakeFiles/OpenMS.dir/all] Error 2
>> make: *** [all] Error 2
>> 
>> cheers,
>> — 
>> Jorrit Boekel
>> Proteomics systems developer
>> BILS / Lehtiö lab
>> Scilifelab Stockholm, Sweden
>> 
>> 
>> 
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> <xerces-c.patch>------------------------------------------------------------------------------
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