The Makefile does not install two files required by third-party applications using this library. For example, bioperl-ext requires those two headers. Read bioperl-ext/README: o Notes for Bio::SeqIO::staden::read This extension needs the rest of the main bioperl distribution to function properly. It is only useful as a helper module for the SeqIO system to read sequence trace files handled by the Staden package's io_lib "read" library. You should have this library installed prior to installing Bio::SeqIO::staden::read, it's currently available at: https://sourceforge.net/project/showfiles.php?group_id=100316 Currently, the Bio::SeqIO::staden::read extension only works with io_lib v. 1.8.11 or 1.8.12; v. 1.9 and higher have several prototype changes in the "read" library which have broken compatibility in those versions for now. It is possible these changes may be addressed in the future. Many users have noted that the io_lib install process often forgets to install the "os.h" file along with the rest of the include files; you may have to do this manually. If so, you may also have to install the "config.h" file for "os.h" to find all the information it needs. Finally, you may also need to edit "os.h" to #include <config.h> instead of #include "config.h" if you continue to get undefined symbol errors during compilation. On some OSes you may in fact have to do the OPPOSITE, meaning change <config.h> to "config.h". The bioperl-ext make process will prompt you for the LIB and INCLUDE locations (usually /usr/local/lib and usr/local/include/io_lib, respectively) of the io_lib "libread" library and Read.h header files, after trying to automatically find them. You may also specify these via the environment variables "IOLIB_LIB" and "IOLIB_INC", or via identically named options to perl Makefile.PL: perl Makefile.PL IOLIB_LIB=/opt/lib IOLIB_INC=/opt/include/io_lib Ignore any warnings about these options being unknown to MakeMaker. A failed compilation is most likely due to an incomplete io_lib installation; make sure that all the required io_lib ".h" files are in place (see above regarding "os.h" and "config.h").
Created attachment 95436 [details] io_lib-1.8.12b-r1.ebuild Fixed ebuild
Martin: "os.h" is installed in io_lib 1.9.0 in Portage. I could not find any "config.h" in the package, and you reported being able to compile bioperl-ext against this version, so I suppose the issue is now fixed. Thanks for your work, and feel free to reopen if I missed something.
The config.h gets created during the make process. The ebuild really worked an installed both files. ;-)
Fixed in Portage (for both 1.8 and 1.9). Sorry for the delay.
