OOPS, I forgot to even look at something. Have you looked at the command: R CMD SHLIB
?? The documentation says: <quote> $R CMD SHLIB --help Usage: R CMD SHLIB [options] files | linker options Build a shared object for dynamic loading from the specified source or object files (which are automagically made from their sources) or linker options. If not given via '--output', the name for the shared object is determined from the first source or object file. Options: -h, --help print short help message and exit -v, --version print version info and exit -o, --output=LIB use LIB as (full) name for the built library -c, --clean remove files created during compilation --preclean remove files created during a previous run -n, --dry-run dry run, showing commands that would be used Windows only: -d, --debug build a debug DLL Report bugs at b...@r-project.org . </quote> On Sat, Jul 26, 2014 at 9:37 AM, John McKown <john.archie.mck...@gmail.com> wrote: > On Fri, Jul 25, 2014 at 9:07 AM, Pierre Lindenbaum > <pierre.lindenb...@univ-nantes.fr> wrote: >> ( cross-posted on SO: http://stackoverflow.com/questions/24955829/ ) >> >> I'm building a C extension for R, this library also uses the HDF5 library. >> >> I compiled a dynamic library (gcc flags: -fPIC -shared -Wl,-soname,libmy.so > > I am not any kind of expert, so that this as just a vague possibility > from someone who just wants to try to help. But I am "concerned" about > the options in the above. In particular, you have > "-Wl,-soname,libmy.so" Which looks slightly wrong to me, based on the > man for "ld". I think that, perhaps, this should be: > ""-Wl,-soname=libmy.so". Notice the = instead of the , > >> -o ../lib/libmy.so in a 'lib' directory: >> > <snip> >> the library seems to be loaded but R is still missing the symbols from the >> hdf5 library: > > Have you looked at the /usr/bin/h5cc-<system type> helper script? It > has some more stuff in it with gcc parameters, such as: > -Wl,z,relro,-rpath -lz -ldl -lm -lhdf5, -lhdf5_hl > apparently the -lhdf5_hl is only needed if > > In fact, from my reading, you might want to use "h5cc" instead of > "gcc" to compile your shared library. > >> >> Error in dyn.load("libmy.so") : >> unable to load shared object ' /path/to/my/src/libmy.so': >> /path/to/my/src/libmy.so: undefined symbol: H5T_C_S1_g >> Execution halted >> >> I also tried load("my.so") instead of "libmy.so". >> >> How can I load my dynamic library ? >> >> Thanks >> Pierre > > Again, I'm no expert. I'm not even a Linux professional. I work on an > old-style "mainframe" (z/OS from IBM - aka "big iron"). So please > excuse me if I am leading you down a blind alley. > > -- > There is nothing more pleasant than traveling and meeting new people! > Genghis Khan > > Maranatha! <>< > John McKown -- There is nothing more pleasant than traveling and meeting new people! Genghis Khan Maranatha! <>< John McKown ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
