pjotrp/biolib

BioLib brings together a set of opensource libraries written in C/C++ and makes them available for all Bio* languages

biolib's Issues

python bindings fail to build due to versioned affyio/staden

Tried to build python bindings today, but cmake was looking for a src/clibs/{affyio-1.8, staden_io_lib-1.11.6} directories which does not exist. Removing SET (M_VERSION X) from src/mappings/swig/python/{affyio, staden_io_lib}/CMakeLists.txt fixes issues. From git history, it looks like this was done for perl and ruby, but not python.

build isue

I've been trying to compile the project from a fresh "git clone":

cd biolib/
./install.sh
Checking for git submodules
Submodule 'contrib/EMBOSS' (git://github.com/pjotrp/EMBOSS.git) registered for path 'contrib/EMBOSS'
Submodule 'contrib/boost' (git://gitorious.org/boost/svn.git) registered for path 'contrib/boost'
Submodule 'contrib/libsequence-1.6.6' (git://github.com/pjotrp/libsequence.git) registered for path 'contrib/libsequence-1.6.6'
Submodule 'contrib/staden_io_lib' (http://github.com/pjotrp/biolib_staden_io_lib.git) registered for path 'contrib/staden_io_lib'
Submodule 'src/clibs/rqtl' (git://github.com/pjotrp/rqtl-mqm.git) registered for path 'src/clibs/rqtl'
Submodule 'tools/cmake-support' (git://github.com/pjotrp/cmake-support.git) registered for path 'tools/cmake-support'
Submodule 'tools/rubydoctest' (git://github.com/pjotrp/rubydoctest.git) registered for path 'tools/rubydoctest'
Cloning into 'contrib/EMBOSS'...
remote: Counting objects: 115874, done.
remote: Compressing objects: 100% (21931/21931), done.
remote: Total 115874 (delta 92562), reused 115874 (delta 92562), pack-reused 0
Receiving objects: 100% (115874/115874), 88.06 MiB | 1.55 MiB/s, done.
Resolving deltas: 100% (92562/92562), done.
Submodule path 'contrib/EMBOSS': checked out 'a59a6d42642a824b529785e4908ba51979949f50'
Cloning into 'contrib/boost'...
fatal: unable to connect to gitorious.org:
gitorious.org[0: 64.13.172.37]: errno=Conexi?n rehusada

Clone of 'git://gitorious.org/boost/svn.git' into submodule path 'contrib/boost' failed
Cloning into 'contrib/boost'...
fatal: unable to connect to gitorious.org:
gitorious.org[0: 64.13.172.37]: errno=Conexi?n rehusada

Clone of 'git://gitorious.org/boost/svn.git' into submodule path 'contrib/boost' failed
Cloning into 'contrib/boost'...
fatal: unable to connect to gitorious.org:
gitorious.org[0: 64.13.172.37]: errno=Conexi?n rehusada

Clone of 'git://gitorious.org/boost/svn.git' into submodule path 'contrib/boost' failed
Cloning into 'contrib/boost'...
fatal: unable to connect to gitorious.org:
gitorious.org[0: 64.13.172.37]: errno=Conexi?n rehusada

Clone of 'git://gitorious.org/boost/svn.git' into submodule path 'contrib/boost' failed
BioLib building all libraries
--with-perl: -DBUILD_PERL:BOOLEAN=TRUE
:
rm: no se puede borrar «biolib-*.tar.gz»: No existe el fichero o el directorio
rm: no se puede borrar «biolib-*.tgz»: No existe el fichero o el directorio
rm: no se puede borrar «biolib-*.tar.bz2»: No existe el fichero o el directorio
rm: no se puede borrar «biolib-*.zip»: No existe el fichero o el directorio
cmake -DBUILD_PERL:BOOLEAN=TRUE .
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
CMake modules: /home/fons/tmp/biolib/tools/cmake-support/modules/
CMake Warning at CMakeLists.txt:62 (FIND_PACKAGE):
  By not providing "FindGitSubmodule.cmake" in CMAKE_MODULE_PATH this project
  has asked CMake to find a package configuration file provided by
  "GitSubmodule", but CMake did not find one.

  Could not find a package configuration file provided by "GitSubmodule" with
  any of the following names:

    GitSubmoduleConfig.cmake
    gitsubmodule-config.cmake

  Add the installation prefix of "GitSubmodule" to CMAKE_PREFIX_PATH or set
  "GitSubmodule_DIR" to a directory containing one of the above files.  If
  "GitSubmodule" provides a separate development package or SDK, be sure it
  has been installed.


Building biolib:
  Perl interface
  Biolib libraries
-- Install Biolib_R TRUE
-- Install Affyio TRUE
-- Install Staden TRUE
-- Install EMBOSS TRUE
-- Install RQTL FALSE
-- Install Libsequence FALSE
-- Install Example TRUE
CMake Warning at CMakeLists.txt:194 (FIND_PACKAGE):
  By not providing "FindMap.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "Map", but
  CMake did not find one.

  Could not find a package configuration file provided by "Map" with any of
  the following names:

    MapConfig.cmake
    map-config.cmake

  Add the installation prefix of "Map" to CMAKE_PREFIX_PATH or set "Map_DIR"
  to a directory containing one of the above files.  If "Map" provides a
  separate development package or SDK, be sure it has been installed.


CMake Error at src/clibs/biolib_core/src/CMakeLists.txt:13 (FIND_PACKAGE):
  By not providing "FindMap.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "Map", but
  CMake did not find one.

  Could not find a package configuration file provided by "Map" with any of
  the following names:

    MapConfig.cmake
    map-config.cmake

  Add the installation prefix of "Map" to CMAKE_PREFIX_PATH or set "Map_DIR"
  to a directory containing one of the above files.  If "Map" provides a
  separate development package or SDK, be sure it has been installed.


-- Configuring incomplete, errors occurred!
make: *** No se especificó ningún objetivo y no se encontró ningún makefile.  Alto.
make: *** No hay ninguna regla para construir el objetivo `test'.  Alto.
-- No errors? Run 'make install' to complete the installation

I don't know if the problem is that some git repos couldn't be downloaded or if "FIND_PACKAGE" instructions of some CMakeLists.txt es are wrong...
In any case I'm not able to build it.... any suggestions?