[BioLib-dev] installation

Joel Martin j_martin at lbl.gov
Sun Apr 26 01:52:25 UTC 2009 

Hello,

On Sun, Apr 26, 2009 at 03:03:49AM +0200, Pjotr Prins wrote:
> On Fri, Apr 24, 2009 at 10:58:54PM -0700, Joel Martin wrote:
> > I had to futz about with cmake quite a bit and as I don't know
> > anything about cmake I've probably done something horrible.  Here is
> > what 'make install' ended up doing, I did want it to go into
> > /scratch so that part all looks good but the perl locations seem odd
> > as they aren't using 'auto'
> 
> The current FindPerl cmake files haven't been fully tested on all
> platforms, so your help is very welcome. I'll try and help with the
> installation paths. One at at time.
> 
> > -- Install configuration: "Release"
> > -- Installing: /scratch/j_martin/biotrash/lib/libbiolib_core-0.0.4.so
> > -- Set runtime path of "/scratch/j_martin/biotrash/lib/libbiolib_core-0.0.4.so" to "#{CMAKE_INSTALL_PREFIX}/lib"
> 
> Strange. CMAKE_INSTALL_PREFIX should be filled in - normally /usr.
> What cmake version are you running and what version of OS/X?
> 
> I have committed a small patch forcing the PREFIX to /usr. Can you
> send me the output of './configure --with-staden'?

I wouldn't be installing into /usr though, for now I'm putting it into
/scratch and if deploying it I'd put it into an nfs mounted directory
that's shared across lots of machines and not in /usr

 the rpath for the libbiolib_*.so where I installed all seem correct like,

ldd /scratch/j_martin/biotrash/lib/libbiolib_staden_io_lib-0.0.4.so 
        libz.so.1 => /usr/lib/libz.so.1 (0x00002b1f89a60000)
        libc.so.6 => /lib/libc.so.6 (0x00002b1f89b76000)
        /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

the ones that are in the perl tree are missing rpaths,

ldd /jgi/tools/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/staden_io_lib.so
        libbiolib_staden_io_lib-0.0.4.so => not found
        libperl.so => not found
        libz.so.1 => /usr/lib/libz.so.1 (0x00002ac2b898e000)
        libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00002ac2b8aa5000)
        libm.so.6 => /lib/libm.so.6 (0x00002ac2b8ca3000)
        libc.so.6 => /lib/libc.so.6 (0x00002ac2b8e25000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002ac2b9063000)
        /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

** note, out of over 100 .so files in my perl install, these are the only one linked against
   libperl.so

 the output for ./configure --with-staden is at the very bottom, it's after I added 
those previous 2 changes.

> > when I try
> > perl -Mbiolib::staden_io_lib  it complains as Dynaloader can't find it ( not using auto )
> 
> Probably related to above. The shared library is not in the RPATH
> now. Let's fix that first.

Should have pasted the whole message... but yes it's probably the unfound lib.

perl -Mbiolib::staden_io_lib
Can't load '/jgi/tools/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/staden_io_lib.so' for module staden_io_lib: libbiolib_staden_io_lib-0.0.4.so: cannot open shared object file: No such file or directory at /jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230.
 at /jgi/tools/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/biolib/staden_io_lib.pm line 11
Compilation failed in require.
BEGIN failed--compilation aborted.

------- output of ./configure --with-staden (i've commented out somr RQTL lines in the make files 
------- and added some prints )

BioLib defaulting to Perl build
--with-staden: -DBUILD_PERL:BOOLEAN=TRUE
--with-staden: -DSTADEN_LIB:BOOLEAN=TRUE
removed `cmake_install.cmake'
removed `./src/clibs/staden_io_lib-1.11.6/io_lib/cmake_install.cmake'
removed `./src/clibs/cmake_install.cmake'
removed `./src/mappings/swig/perl/staden_io_lib/cmake_install.cmake'
removed `./src/mappings/swig/perl/cmake_install.cmake'
removed `./src/cmake_install.cmake'
removed `CTestTestfile.cmake'
removed `./src/clibs/CTestTestfile.cmake'
removed `./src/clibs/staden_io_lib-1.11.6/io_lib/CTestTestfile.cmake'
removed `./src/mappings/swig/perl/CTestTestfile.cmake'
removed `./src/mappings/swig/perl/staden_io_lib/CTestTestfile.cmake'
removed `./src/CTestTestfile.cmake'
removed `CMakeCache.txt'
removed `Makefile'
removed `./src/clibs/staden_io_lib-1.11.6/io_lib/Makefile'
removed `./src/clibs/Makefile'
removed `./src/mappings/swig/perl/staden_io_lib/Makefile'
removed `./src/mappings/swig/perl/Makefile'
removed `./src/Makefile'
removed `./src/clibs/staden_io_lib-1.11.6/io_lib/CMakeFiles/progress.make'
removed `./src/clibs/staden_io_lib-1.11.6/io_lib/CMakeFiles/biolib_staden_io_lib-0.0.4.dir/build.make'
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removed directory: `./CMakeFiles/CompilerIdCXX'
removed `./CMakeFiles/CMakeCCompiler.cmake'
removed directory: `./CMakeFiles'
find: ./CMakeFiles: No such file or directory
rm: cannot remove `biolib-*.tar.gz': No such file or directory
rm: cannot remove `biolib-*.tgz': No such file or directory
rm: cannot remove `biolib-*.tar.bz2': No such file or directory
rm: cannot remove `biolib-*.zip': No such file or directory
cmake -DBUILD_PERL:BOOLEAN=TRUE -DSTADEN_LIB:BOOLEAN=TRUE .
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- 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
CMake modules: /scratch/j_martin/biolib/cmake_modules/
Building biolib:
  Perl interface
  Biolib libraries
-- Install Affyio FALSE
-- Install Staden TRUE
-- Install RQTL FALSE
-- Install Example FALSE
PREFIX: /usr
CMAKE_INSTALL_PREFIX=/usr
BIOLIB_ROOT=/scratch/j_martin/biolib
BIOLIB_CLIBS_PATH=/scratch/j_martin/biolib/src/clibs
BIOLIB_VERSION=0.0.4
-- Found xRLibs: 0.0.4
PREFIX: /usr
CMAKE_INSTALL_PREFIX=/usr
BIOLIB_ROOT=/scratch/j_martin/biolib
BIOLIB_CLIBS_PATH=/scratch/j_martin/biolib/src/clibs
BIOLIB_VERSION=0.0.4
/jgi/tools/lib:/jgi/tools/oracle_client/DEFAULT/lib:/usr/local/lib
NIX_INCLUDE_PATH=/home/j_martin/.nix-profile/include
NIX_LIB_PATH=/home/j_martin/.nix-profile/lib
ZLIB_INCLUDE_DIR=/usr/include
ZLIB_LIBRARY=/usr/lib/libz.so
ZLIB_NAME=libz.so
-- Found ZLIB: /usr/lib/libz.so
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of int
-- Check size of int - done
-- Check size of long
-- Check size of long - done
-- Check size of void*
-- Check size of void* - done
-- Check size of char
-- Check size of char - done
-- Check size of short
-- Check size of short - done
-- Check size of float
-- Check size of float - done
-- Check size of double
-- Check size of double - done
-- Looking for limits.h
-- Looking for limits.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for include files CMAKE_HAVE_SYS_PRCTL_H
-- Looking for include files CMAKE_HAVE_SYS_PRCTL_H - found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for XOpenDisplay in /usr/lib/libX11.so;/usr/lib/libXext.so
-- Looking for XOpenDisplay in /usr/lib/libX11.so;/usr/lib/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib/libX11.so
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
Creating Perl module staden_io_lib (1.11.6)
PREFIX: /usr
CMAKE_INSTALL_PREFIX=/usr
BIOLIB_ROOT=/scratch/j_martin/biolib
BIOLIB_CLIBS_PATH=/scratch/j_martin/biolib/src/clibs
BIOLIB_VERSION=0.0.4
Found Perl on PATH
-- PERL_EXECUTABLE=/jgi/tools/bin/perl
-- PLIBPERL=libperl.so
-- PSITEARCH=/jgi/tools/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
-- PARCHLIB=/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi
-- PERL_INCLUDE_PATH=/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE 
-- PERL_LIB_PATH=/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi
PERLLIB_LIBRARY=/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE/libperl.so
-- PERL_INCLUDE_PATH=/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE
-- PERL_LIB_PATH=/jgi/tools/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
-- PERL_SLIB_PATH=/jgi/tools/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
-- PERL_LIBRARY=/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE/libperl.so
-- Found PERL: /jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE
MODULE_SOURCE_PATH=/scratch/j_martin/biolib/src/clibs/staden_io_lib-1.11.6
Looking for libbiolib_staden_io_lib-0.0.4.so
MODULE_LIBRARY=biolib_staden_io_lib-0.0.4
/jgi/tools/lib:/jgi/tools/oracle_client/DEFAULT/lib:/usr/local/lib
NIX_INCLUDE_PATH=/home/j_martin/.nix-profile/include
NIX_LIB_PATH=/home/j_martin/.nix-profile/lib
ZLIB_INCLUDE_DIR=/usr/include
ZLIB_LIBRARY=/usr/lib/libz.so
ZLIB_NAME=libz.so
-- USE_LANGUAGE=perl
-- USE_LANGUAGE_LIBRARY=/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE/libperl.so
-- USE_SWIG_FLAGS=
-- SWIG M_MODULE=staden_io_lib
-- CMAKE_INCLUDE_PATH=/usr/include
-- CMAKE_LIBRARY_PATH=
-- Found all SWIG prerequisites for perl: perl
CMake: .-
SWIG: /jgi/tools/bin/swig 1.3.39
System: x86_64 Linux 2.6.22.18-1jgi-amd64-k8-smp
  Build type: Release for x86_64
Sat Apr 25 18:44:38 PDT 2009
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/j_martin/biolib

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