Hi Shannon, Which flavor of Linux are you compiling from? When I compiled the latest version of TPP from Redhat EL5, the perl library 'libperl.a' was missing. So, I have to recompiled perl and set the parameters so that the static library is built. That's how I fixed the problem.
Good luck. Kossi -----Original Message----- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of shannon Sent: Thursday, March 05, 2009 3:05 PM To: spctools-discuss Subject: [spctools-discuss] Re: TPP4.2 compile problem 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 > > 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 --------------------------------------------------------------------- SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. 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