You can ignore the sym link issue. I discovered later that was due to not having the lib boost directory in my ld.so.conf, so that was an error on my part.
As for the perl scripts, the problem was that those files were not in the build path, and they were only in the posted locations. To get the install to work, I ended up copying the files to the build directory, so I could obtain a full list of the missing files. Just to be sure, I went ahead and did a make clean, and remade everything. But for some reason, this time all of the perl files were there. I'm not sure what happened with the previous compile, since it claimed the make was complete. So ignore the missing files. Greg On Fri, Feb 20, 2009 at 3:24 PM, Natalie Tasman <[email protected]>wrote: > > Hi Greg, > > The "make install" gets these files from the build directory on > purpose, because some paths in the perl scripts are potentially > rewritten at build time for your installation system (mingw, linux, os > x) as well as based on settings in Makefile.config.incl (see last > message.) So if you do a diff between the build dir. versions and the > tpp/perl or tpp/CGI versions, you might see some differences specific > to your system. Does this make sense for what you're seeing? > > -Natalie > > > On Fri, Feb 20, 2009 at 12:12 PM, Greg Bowersock <[email protected]> > wrote: > > I found a few more issues, since I didn't do the make install this > morning. > > The Makefile is looking for all of the following files in the build/linux > > folder instead of where they are actually located: > > testing/StatUtilities.pm > > testing/calctppstat.pl > > perl/SSRCalc3.pl > > perl/ProtProphModels.pl > > CGI/show_tmp_pngfile.pl > > Greg > > On Fri, Feb 20, 2009 at 9:24 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.pmline > >> 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 -~----------~----~----~----~------~----~------~--~---
