On Nov 9, 2009, at 6:21 PM, Keren Lasker wrote:

> hi, > > Compiling an external exe, I am getting an error in the linkage > stage, basically saying that helper can not see misc: > /usr/bin/ld: warning: libimp_misc.so, needed by /viola1/home/kerenl/ > bioinformatics/projects/imp/build/lib/libi\ > mp_helper.so, not found (try using -rpath or -rpath-link) > /viola1/home/kerenl/bioinformatics/projects/imp/build/lib/ > libimp_helper.so: undefined reference to `IMP::misc:\ > :get_module_version_info()' > /viola1/home/kerenl/bioinformatics/projects/imp/build/lib/ > libimp_helper.so: undefined reference to `IMP::misc:\ > :LowestRefinedPairScore::LowestRefinedPairScore(IMP::Refiner*, > IMP::PairScore*)' > collect2: ld returned 1 exit status > scons: *** [bin/clustering_coefficient] Error 1 How are you linking against imp_helper? How did you tell your executable to find imp misc/helper? Do you set the rpath in your executable or use imppy.sh? Is misc in the same dir as helper?

If you just passed the full path to imp helper to the link call for the exe then the compiler has no way to find other libraries. You should link as is done by binaries created within (say benchmarks/bin) and either - run everything using imppy.sh - or install imp in some place and add that place to your LD_LIBRARY_PATH and link search path

> I tried changing the dependency order in the SCons files, but did > not succeed - can someone help ? Link order only matters for static linking. ]

On Nov 9, 2009, at 9:54 PM, Keren Lasker wrote:

> Daniel - thanks. It turned out that I did not include imp_misc in my > linked libs. probably easier installing imp ... I didn't think you should have to include imp_misc directly if the symbols are only referenced through imp_helper and you are doing dynamic linking on linux. It should pull it in automatically as long as the directory is in your linking rpath or your LD_LIBRARY_PATH. That is g++ main.cc -limp_helper -Lpath/to/libs -Wl,-rpath,path/to/libs will work, but if you leave off the rpath it will not.

> On Nov 9, 2009, at 6:49 PM, Daniel Russel wrote: > >> >> On Nov 9, 2009, at 6:21 PM, Keren Lasker wrote: >> >>> hi, >>> >>> Compiling an external exe, I am getting an error in the linkage >>> stage, basically saying that helper can not see misc: >>> /usr/bin/ld: warning: libimp_misc.so, needed by /viola1/home/ >>> kerenl/bioinformatics/projects/imp/build/lib/libi\ >>> mp_helper.so, not found (try using -rpath or -rpath-link) >>> /viola1/home/kerenl/bioinformatics/projects/imp/build/lib/ >>> libimp_helper.so: undefined reference to `IMP::misc:\ >>> :get_module_version_info()' >>> /viola1/home/kerenl/bioinformatics/projects/imp/build/lib/ >>> libimp_helper.so: undefined reference to `IMP::misc:\ >>> :LowestRefinedPairScore::LowestRefinedPairScore(IMP::Refiner*, >>> IMP::PairScore*)' >>> collect2: ld returned 1 exit status >>> scons: *** [bin/clustering_coefficient] Error 1 >> How are you linking against imp_helper? How did you tell your >> executable to find imp misc/helper? Do you set the rpath in your >> executable or use imppy.sh? Is misc in the same dir as helper? >> >> If you just passed the full path to imp helper to the link call for >> the exe then the compiler has no way to find other libraries. You >> should link as is done by binaries created within (say benchmarks/ >> bin) and either >> - run everything using imppy.sh >> - or install imp in some place and add that place to your >> LD_LIBRARY_PATH and link search path >> >> >>> I tried changing the dependency order in the SCons files, but did >>> not succeed - can someone help ? >> Link order only matters for static linking. >> ] >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev