[BioLib-dev] installation

[Joel Martin]

Hello,

e > 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)
> 
> What I see is that you need to tell the dynamic loader where to find
> the shared libraries in a non-standard location to find
> 
>   /scratch/j_martin/biotrash/lib/libbiolib_staden_io_lib-0.0.4.so 
> 
> These libraries are 'system wide' libraries simply containing the
> StadenIO binaries. These also link against Ruby etc. Perl does not
> know about their non-standard location (Perl on OSX being the
> exception). Try setting LD_LIBRARY_PATH.

boo, no LD_LIBRARY_PATH :) I don't know how to check this on linux but
solaris with ldd -s will tell you where it's looking and where it got
the idea to look there from.  <arch>/auto/Tk/Tk.so builds in a libpath
for /usr/openwin/lib.  

Where might I add an option like

-Wl,-rpath,/scratch/j_martin/biotrash/lib
or
-Wl,-rpath,/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE

cpan added modules pick the second one up from 
ccdlflags='-Wl,-E -Wl,-rpath,/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE'

and if I need a library in an especially odd spot I edit a Makefile, not being
familiar with cmake it's unclear where to add that.  It doesn't pick it up from
LDFLAGS in my environment.

> > ** note, out of over 100 .so files in my perl install, these are the
> > only one linked against
> >    libperl.so
> 
> SWIG generated code makes Perl XS calls - I think they are in
> libperl.

I have many XS modules, they don't link against the libperl.so, well it's not in
the ldd output and I did check them all with
foreach i ( `find . -name "*.so"` )
foreach? ldd $i >> /tmp/libperl.list
foreach? end

but my install is a bit mangled, probably best to ignore this for now, I'll try
and track down why cpan installed modules don't link against it.

Here is my perl -V fwiw

Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
  Platform:
    osname=linux, osvers=2.6.17.8-2jgi-amd64-k8-smp, archname=x86_64-linux-thread-multi
    uname='linux node64t-99 2.6.17.8-2jgi-amd64-k8-smp #1 smp tue aug 8 15:08:01 pdt 2006 x86_64 gnulinux '
    config_args='-Dmksymlinks -Dusethreads -Duselargefiles -Duse64bitint -Dprefix=/jgi/tools -Dbin=/jgi/tools/perl5/5.8.8/bin -Dsitebin=/jgi/tools/perl5/5.8.8/bin -Dperlpath=/jgi/tools/bin/perl -Dstartperl=#!/jgi/tools/bin/perl -Doptimize=-O2 -Dpager=/usr/bin/less -Duseshrplib -des -Dlibpth=/lib /usr/lib'
    hint=recommended, useposix=true, d_sigaction=define
    usethreads=define use5005threads=undef useithreads=define usemultiplicity=define
    useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
    use64bitint=define use64bitall=define uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -I/opt/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
    optimize='-O2',
    cppflags='-D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -I/opt/local/include'
    ccversion='', gccversion='4.0.3 20060212 (prerelease) (Debian 4.0.2-9)', gccosandvers=''
    intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
    ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
    alignbytes=8, prototype=define
  Linker and Libraries:
    ld='cc', ldflags =''
    libpth=/lib /usr/lib
    libs=-lnsl -lgdbm -ldl -lm -lcrypt -lutil -lpthread -lc
    perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
    libc=/lib/libc-2.3.6.so, so=so, useshrplib=true, libperl=libperl.so
    gnulibc_version='2.3.6'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E -Wl,-rpath,/jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi/CORE'
    cccdlflags='-fpic', lddlflags='-shared'
 
 
Characteristics of this binary (from libperl): 
  Compile-time options: MULTIPLICITY PERL_IMPLICIT_CONTEXT
                        PERL_MALLOC_WRAP THREADS_HAVE_PIDS USE_64_BIT_ALL
                        USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
                        USE_PERLIO USE_REENTRANT_API
  Built under linux
  Compiled at Sep 22 2006 11:05:25
  @INC:
    /jgi/tools/lib/perl5/5.8.8/x86_64-linux-thread-multi
    /jgi/tools/lib/perl5/5.8.8
    /jgi/tools/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
    /jgi/tools/lib/perl5/site_perl/5.8.8
    /jgi/tools/lib/perl5/site_perl
    .