shogun: update to 2.0.0

[sammysheep@…]

SHOGUN Version 1.1.0 (lib 11.0, data 0.3, param 0) was officially released on 1 Dec 2011.

I am requesting upgrading the current version (0.9.3) to (1.1.0) as this is a significant improvement over the previous version.

Best wishes,

• Sam

[nerdling (Jeremy Lavergne)]

Also:

• license needs set
• should depend on Python 2.7
• if the patch needs updated, consider renaming it to fit the patch-*.diff pattern

[ryandesign (Ryan Carsten Schmidt)]

This was requested again in #34990.

[cdeil (Christoph Deil)]

SHOGUN 2.0 just came out: ​http://www.shogun-toolbox.org/ Could you please upgrade and also make variants for more recent python versions (2.7 and 3.x if python3 is supported). Thanks!

[cdeil (Christoph Deil)]

I've also made a ticket in the SHOGUN issue tracker: ​https://github.com/shogun-toolbox/shogun/issues/770

[wiking@…]

I've tested it locally on a 10.8 osx and works fine, but please test it and let me know if something is wrong on your machine.

[cdeil (Christoph Deil)]

Thank you!

The new portfile also works for me on OS X 10.8.

Given that the existing port has been broken for a while on older OS X versions also (see #28873 and #34990) I think it would be OK to commit the new version even if not tested extensively yet.

I also tried installing some of the variants:

$ port variants shogun
shogun has the variants:
   elwms: Build elwms interface. requires python plus  one other interface
   hmm_parallel: Enable parallel structures in hmm training
   no_glpk: Disable glpk support
   no_python27: Do not build Python 2.7 API
   octave: Build the Octave API
   python32: Build Python 3.3 API
     * requires no_python27
   r: Build the R API
   svm_light: Enable parallel structures in hmm training

I think no_* variants are discouraged. You should instead have a python27 and glpk variant and enable it by default. Also note that the python32 variant description mentions python 3.3.

The elwms variant doesn't work:

$ sudo port install shogun +elwms +octave +r
Error: Unable to open port: Must set python and both r and octave variants to build elwms interface

The error message doesn't make sense to me, because with this selection python27 and r and octave variants are set. Adding +python32 doesn't help either.

I couldn't install the r variant:

$ sudo port install shogun +r
--->  Computing dependencies for shogun
Error: Unable to execute port: Can't install R because conflicting ports are installed: R-framework

It should be possible to optionally accept r-framework as a dependency instead of r.

[cdeil (Christoph Deil)]

The octave variant doesn't work for me:

$ port installed octave
The following ports are currently installed:
  octave @3.2.4_10+atlas+gcc45 (active)

$ sudo port -d install shogun +octave
...
--->  Configuring shogun
DEBUG: Using compiler 'Mac OS X clang'
DEBUG: Executing proc-pre-org.macports.configure-configure-0
DEBUG: Executing reinplace: /usr/bin/sed s|@@PREFIX@@|/opt/local|g < /opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src/configure >@ file12
DEBUG: euid/egid changed to: 0/0
DEBUG: chowned /opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src/configure to macports
DEBUG: euid/egid changed to: 502/501
DEBUG: euid/egid changed to: 0/0
DEBUG: setting attributes on /opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src/configure
DEBUG: euid/egid changed to: 502/501
DEBUG: Executing reinplace: /usr/bin/sed {s|= ${_libdir}/${_pydir}|= ${_pydir}|g} < /opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src/configure >@ file12
DEBUG: euid/egid changed to: 0/0
DEBUG: chowned /opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src/configure to macports
DEBUG: euid/egid changed to: 502/501
DEBUG: euid/egid changed to: 0/0
DEBUG: setting attributes on /opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src/configure
DEBUG: euid/egid changed to: 502/501
DEBUG: Executing org.macports.configure (shogun)
DEBUG: Environment: CPATH='/opt/local/include' CFLAGS='-pipe -O2 -arch x86_64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -O2 -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.8' CXX='/usr/bin/clang++' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -O2 -m64' LDFLAGS='-L/opt/local/lib -arch x86_64' OBJC='/usr/bin/clang' FCFLAGS='-pipe -O2 -m64' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -O2 -arch x86_64' FFLAGS='-pipe -O2 -m64' CC_PRINT_OPTIONS='YES' CC='/usr/bin/clang'
DEBUG: Assembled command: 'cd "/opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src" && ./configure --prefix=/opt/local --disable-svm-light --libs=/usr/lib:/opt/local/lib --install-path=/opt/local --includes=/opt/local/include --destdir=/opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/destroot --includes=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 --python=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 --pydir=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages --disable-doxygen --interfaces=cmdline_static,python_modular,octave,octave_modular'
DEBUG: Executing command line:  cd "/opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src" && ./configure --prefix=/opt/local --disable-svm-light --libs=/usr/lib:/opt/local/lib --install-path=/opt/local --includes=/opt/local/include --destdir=/opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/destroot --includes=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 --python=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 --pydir=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages --disable-doxygen --interfaces=cmdline_static,python_modular,octave,octave_modular 
Running configure for SHOGUN version 2.0.0

Error: Unknown interface: octave

Command failed:  cd "/opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/shogun-2.0.0/src" && ./configure --prefix=/opt/local --disable-svm-light --libs=/usr/lib:/opt/local/lib --install-path=/opt/local --includes=/opt/local/include --destdir=/opt/local/var/macports/build/_Users_deil_software_ports_math_shogun/shogun/work/destroot --includes=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 --python=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 --pydir=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages --disable-doxygen --interfaces=cmdline_static,python_modular,octave,octave_modular 
Exit code: 1
Error: org.macports.configure for port shogun returned: configure failure: command execution failed
DEBUG: Error code: NONE
DEBUG: Backtrace: configure failure: command execution failed
    while executing
"$procedure $targetname"
Warning: targets not executed for shogun: org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install
Please see the log file for port shogun for details:
    /opt/local/var/macports/logs/_Users_deil_software_ports_math_shogun/shogun/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port shogun failed

[wiking@…]

hey cool!

thanks for the report, i'll try to fix these issues ASAP

[wiking@…]

Portfile for shogun 2.0 release

[wiking@…]

so here's a quickfix that should solve the problem of octave interface.

the problem with your R interface installation was that you have R-Framework installed while swig-r depends on R, thus it won't install... that you'll have to resolve by yourself on your machine.

elwms variant is still not working... will update ASAP once i have a fix. let me know if anything else pops up

[wiking@…]

Cc Me!

[wiking@…]

is this going to be applied to the upstream?

[ryandesign (Ryan Carsten Schmidt)]

The port was updated to 2.1.0 in #38596 but I don't know if the Portfiles attached here were considered. If anything from these Portfiles remains to be done in the current version of the port, please file a new ticket and attach a diff.