Hi Greg, I'm not sure I understand what you did with the symlinks, but you can control perl paths with
PERL_LIB_CORE= /somedir/lib/perl5/5.8.8/x86_64-linux-ld/CORE/ PERL_BIN=/somdir/bin/perl in Makefile.config.incl. Note, the perl bin and perl core versions must match. I regularly successfully build and install on linux using a stock Makefile.incl and only adjusting Makefile.config.incl. I use boot non-system boost and perl (that is, they are not in the usual /usr tree.) Does this allow you to get around the need for the symlink? -Natalie On Fri, Feb 20, 2009 at 7:24 AM, Greg Bowersock <[email protected]> wrote: > Thanks, that fixed the fPIC issue, but then it hit another issue: > Can't load > '/home/TPP/tpp/trans_proteomic_pipeline/build/linux/tpplib_perl.so' for > module tpplib_perl: libboost_filesystem-gcc41-mt-1_37.so.1.37.0: 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 /home/TPP/tpp/trans_proteomic_pipeline/build/linux/tpplib_perl.pm line 8 > Compilation failed in require at ProphetModels.pl line 44. > BEGIN failed--compilation aborted at ProphetModels.pl line 44. > > The file did exist, and I was able to fix it by putting a soft-link into the > /usr/lib and /usr/lib64 (I just put it in both without trying one at a > time), since for some reason it wasn't looking in /usr/local/lib as all of > the files instructed. So it is compiled now, but I wanted to report the > issue. > > Greg > > > On Fri, Feb 20, 2009 at 2:08 AM, Natalie Tasman <[email protected]> > wrote: >> >> Hi Greg, >> >> First off, we use boost 1.35 here, so that's one variable that's >> different. But I think it's probably your Makefile.config.incl file; >> the libdir line, at least, should be a little different. Here are the >> relevant lines from my Makefile.config.incl: >> >> BOOST_INCL= -I/somedir/include/boost-1_35 >> BOOST_LIBSPEC=-gcc41-mt >> BOOST_LIBDIR=/somedir/lib >> LINK=shared >> LIBEXT=so >> >> Add the last two lines to get around the annoying "-fPIC" issue. >> >> Let me know how this goes, >> >> Natalie >> >> >> >> On Feb 19, 2009, at 7:41 PM, [email protected] wrote: >> >> > >> > Ok, 2 issues so far. One I can get around, the other is keeping me >> > from being able to finish the compile. First (the one I can get >> > around), I had to hard code where my libboost files were located in >> > the Makefile.incl file, as the settings in the Makefile.config.incl >> > of: >> > BOOST_INCL= -I/usr/local/lib >> > BOOST_LIBDIR= -I/usr/local/lib >> > BOOST_LIBSPEC=-gcc41-mt >> > >> > did absolutely nothing. Even hardcoding those values in the >> > Makefile.incl file did nothing, so I had to modify the BOOST_XXX_LIB >> > values to make it see my files in /usr/local/lib. >> > >> > The second issue may be boost related, but I haven't had an issue in >> > the past. >> > I am getting the following error: >> > /usr/bin/ld: /usr/local/lib/libboost_filesystem-gcc41-mt.a >> > (operations.o): relocation R_X86_64_32 against `a local symbol' can >> > not be used when making a shared object; recompile with -fPIC >> > /usr/local/lib/libboost_filesystem-gcc41-mt.a: could not read symbols: >> > Bad value >> > collect2: ld returned 1 exit status >> > >> > I added the -fPIC, but I am still getting the error. This is the line >> > triggering the error: >> > g++ -I. -I/home/TPP/tpp/trans_proteomic_pipeline/src/ -I../extern/ >> > gzstream -I../extern/libarchive-2.2.7/libarchive -I/home/TPP/tpp/ >> > trans_proteomic_pipeline/src/../extern/expat-2.0.0/lib -I/usr/local/ >> > lib -iprefix /home/TPP/tpp/trans_proteomic_pipeline/src/../extern/ >> > pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/home/ >> > TPP/ >> > tpp/trans_proteomic_pipeline/src/../extern/pwiz -iwithprefix pwiz - >> > iwithprefix pwiz/utility/misc -iwithprefix pwiz/utility/math -I/usr/ >> > local/lib -iwithprefix pwiz_boost_additions -I/home/TPP/tpp/ >> > trans_proteomic_pipeline/src/Parsers/ramp -D_FILE_OFFSET_BITS=64 - >> > D_LARGEFILE_SOURCE -O2 -shared -o /home/TPP/tpp/ >> > trans_proteomic_pipeline/src/../build/linux/tpplib_perl.so /home/TPP/ >> > tpp/trans_proteomic_pipeline/src/../build/linux/tpplib_perl_wrap.o / >> > home/TPP/tpp/trans_proteomic_pipeline/src/../build/linux/libtpp.a / >> > home/TPP/tpp/trans_proteomic_pipeline/src/../build/linux/libpwiz.a / >> > usr/local/lib/libboost_filesystem-gcc41-mt.a /usr/local/lib/ >> > libboost_system-gcc41-mt.a /usr/local/lib/libboost_iostreams-gcc41- >> > mt.a /usr/local/lib/libboost_thread-gcc41-mt.a /usr/local/lib/ >> > libboost_regex-gcc41-mt.a /usr/local/lib/libboost_program_options- >> > gcc41-mt.a /usr/local/lib/libboost_serialization-gcc41-mt.a /home/TPP/ >> > tpp/trans_proteomic_pipeline/src/../build/linux/libgzstream.a -lm - >> > lz -lbz2 -lpthread -fPIC >> > >> > Any ideas? I am using boost 1.37, and everything was working fine with >> > 4.1.1. >> > >> > Greg >> > > >> >> >> > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
