The error is actually related to Boost. What you need to do is add the lib
directory with the boost shared object files into the ld.so.conf (or place a
configuration file in /etc/ld.so.conf.d/), and then reload the ldconfig and
it should work fine. I had the same issue, since I recently did a fresh
install of Boost and forgot to do that step also.
Greg
On Thu, Mar 5, 2009 at 5:05 PM, shannon <u0125...@gmail.com> wrote:
>
> Hi Natalie,
>
> I now change it to:
> PERL_LIB_CORE=/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/
> #PERL_LIB=/opt/ActivePerl-5.8/lib
> PERL_BIN=/usr/bin/perl
> However, the error still the same.
>
> Thank you very much for your help!
> Shannon
>
> On Mar 5, 2:57 pm, Natalie Tasman <ntas...@systemsbiology.org> wrote:
> > All perl-related settings must match, and you must also set PERL_BIN
> > as well to the same setup. You don't need PERL_LIB.
> >
> > So if you're using something besides your system perl, such as a
> > verison of perl in /opt, everything should be set to opt (perl bin,
> > perl lib core).
> >
> > Also, ActivePerl is only required for the windows distribution, not
> > linux, if that helps simplify things.
> >
> > -Natalie
> >
> - Show quoted text -
> > On Thu, Mar 5, 2009 at 2:44 PM, shannon <u0125...@gmail.com> wrote:
> >
> > > Hi Natalie,
> >
> > > I've set it in the Makefile.config.incl already. Sorry I didn't post
> > > it at beginning.
> > > I have this 2 lines:
> > > PERL_LIB_CORE=/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/
> > > PERL_LIB=/opt/ActivePerl-5.8/lib
> >
> > > Thank you very much,
> > > Shannon
> >
> > > On Mar 5, 2:41 pm, Natalie Tasman <ntas...@systemsbiology.org> wrote:
> > >> Hi Shannon,
> >
> > >> You'll want to search for perl's CORE directory and set that with
> > >> PERL_LIB_CORE= /usr/lib/perl5/5.8.8/x86_64-linux-ld/CORE/
> >
> > >> (setting to whatever directory it's installed to on your system.)
> >
> > >> Please let us know how it goes,
> >
> > >> Natalie
> >
> > >> On Thu, Mar 5, 2009 at 2:33 PM, shannon <u0125...@gmail.com> wrote:
> >
> > >> > Thank you, Brian and Natalie!
> >
> > >> > Now it made some progress. However I still got some errors:
> >
> > >> > perl -pe
> "s/\/cygdrive\/c\/Inetpub\/tpp-bin\//\/usr\/local\/tpp\/cgi\-
> > >> >
> bin\//g;s/\x24\{base_dir\}users\//\/usr\/local\/tpp\/cgi-bin\/users\//
> > >> > g;s/\/tools\/bin\/TPP\/tpp\//\/usr\/local\/tpp\//g;s/cygpath \-wp //
> > >> > g;s/\"\/cygdrive\/c\/Inetpub\/wwwroot\/\"/\\x24ENV\{\'WEBSERVER_ROOT
> > >> >
> \'\}\.'\/'/g;s/\/tpp\-bin/\/tpp\/cgi\-bin/g;s/'\/usr\/bin\//'/g;s/'\/
> > >> > bin\//'/g " < ../../perl/ProphetModels.pl > ../../build/linux/
> > >> > ProphetModels.pl
> > >> > perl -c ../../build/linux/ProphetModels.pl
> > >> > Can't load '/usr/local/src/trans_proteomic_pipeline/build/linux/
> > >> > tpplib_perl.so' for module tpplib_perl: libboost_filesystem-gcc41-
> > >> > mt-1_35.so.1.35.0: cannot open shared object file: No such file or
> > >> > directory at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/
> > >> > DynaLoader.pm line 230.
> > >> > at /usr/local/src/trans_proteomic_pipeline/build/linux/
> tpplib_perl.pm
> > >> > line 8
> > >> > Compilation failed in require at ../../build/linux/ProphetModels.pl
> > >> > line 44.
> > >> > BEGIN failed--compilation aborted at ../../build/linux/
> > >> > ProphetModels.pl line 44.
> > >> > make[2]: *** [../../build/linux/ProphetModels.pl] Error 2
> > >> > make[2]: *** Deleting file `../../build/linux/ProphetModels.pl'
> > >> > make[2]: Leaving directory `/usr/local/src/trans_proteomic_pipeline/
> > >> > src/perl_paths'
> > >> > make[1]: *** [perl_paths] Error 2
> > >> > make[1]: Leaving directory `/usr/local/src/trans_proteomic_pipeline/
> > >> > src'
> > >> > make: *** [default] Error 2
> >
> > >> > Thank you so much!
> > >> > Shannon
> >
> > >> > On Mar 5, 1:50 pm, Natalie Tasman <ntas...@systemsbiology.org>
> wrote:
> > >> >> Hi Shannon,
> >
> > >> >> Also, since your boost libs are built with the compiler and
> threading
> > >> >> info in their names, you'll need to set
> >
> > >> >> BOOST_LIBSPEC=-gcc41-mt
> >
> > >> >> or
> >
> > >> >> BOOST_LIBSPEC=-gcc41-mt-1_35
> >
> > >> >> (depending on how specific you want to be.)
> >
> > >> >> -Natalie
> >
> > >> >> On Thu, Mar 5, 2009 at 12:51 PM, Brian Pratt <
> brian.pr...@insilicos.com> wrote:
> >
> > >> >> > Perhaps try this?
> >
> > >> >> > BOOST_LIBDIR=/usr/lib/lib/
> >
> > >> >> > -----Original Message-----
> > >> >> > From: spctools-discuss@googlegroups.com
> > >> >> > [mailto:spctools-disc...@googlegroups.com] On Behalf Of shannon
> > >> >> > Sent: Thursday, March 05, 2009 12:43 PM
> > >> >> > To: spctools-discuss
> > >> >> > Cc: tsa...@u.washington.edu
> > >> >> > Subject: [spctools-discuss] TPP4.2 compile problem
> >
> > >> >> > Hi,
> >
> > >> >> > I've downloaded the latest TPP and upgrade my boost to 1.35.
> > >> >> > Here is my Makefile.config.incl :
> >
> > >> >> > ## for Boost
> > >> >> > BOOST_INCL=-I/usr/lib/boost_1_35_0/
> > >> >> > BOOST_LIBDIR=/usr/lib/boost_1_35_0/libs
> > >> >> > BOOST_LIBSPEC=-gcc41-mt
> > >> >> > LINK=shared
> > >> >> > LIBEXT=so
> >
> > >> >> > However, I still got the error:
> > >> >> > g++: /usr/lib/libboost_system.so: No such file or directory
> >
> > >> >> > but I can't find any libboost_system.so file under the library.
> > >> >> > The only similar files I have is:
> > >> >> > /usr/lib/boost_1_35_0/bin.v2/libs/system/build/gcc-4.1.2/release/
> > >> >> > threading-multi/libboost_system-gcc41-mt-1_35.so.1.35.0
> > >> >> > /usr/lib/lib/libboost_system-gcc41-mt.so
> > >> >> > /usr/lib/lib/libboost_system-gcc41-mt-1_35.so
> > >> >> > /usr/lib/lib/libboost_system-gcc41-mt-1_35.so.1.35.0
> >
> > >> >> > My OS is linux Red Hat Enterprise Linux 4
> > >> >> > Any help will be highly appreciated.
> >
> > >> >> > Thanks very much!
> > >> >> > Shannon
> >
>
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