cython and numpy

[aymenbh]

I am using Funtoo. Trying to install sage but having this error message :

# emerge -av sage

These are the packages that would be merged, in order:

Calculating dependencies... done!

emerge: there are no ebuilds to satisfy "~dev-python/numpy-1.5.1".
(dependency required by "sci-mathematics/sage-4.8" [ebuild])
(dependency required by "sage" [argument])

If I mask numpy-1.5.1, I get the same error message but with cython-0.15.1. Masking the last one doesn't change the error message... Should I actually mask the packages ot is there any other solution ?

Right now, the versions installed on my system are numpy-1.6.1-r2 and cython-0.16_rc2.

[kiwifb]

Sorry for the delay week end has been busy. It is technically possible to build sage with numpy-1.6.1 but some behaviour will be unexpected. See http://trac.sagemath.org/sage_trac/ticket/11334 So right now sage is locked to numpy-1.5.1. cython is potentially more dangerous. I have no idea whether or not sage-4.8 can be built with cython-0.16_rc2. I would need to ask Robert Bradshaw directly, but he usually doesn't promise and certainly not with an unreleased version. So my recommendation is for you to mask cython-0.16*. Overall I think you have the whole masking thing backwards.

[aymenbh]

Masking cython-0.16* gives the same error message with numpy-1.5.1. So, probably I should wait for a new version to be released :(

[kiwifb]

What about masking >=dev-python/numpy-1.6 ?

[aymenbh]

keep having this :

#emerge -av sage

These are the packages that would be merged, in order:

Calculating dependencies... done!                                                        

emerge: there are no ebuilds to satisfy "~dev-python/cython-0.15.1".                     
(dependency required by "sci-mathematics/sage-4.8" [ebuild])                             
(dependency required by "sage" [argument])

I am using Funtoo and it seems that some old packages on which sage depends have been cleaned from portage...

[kiwifb]

OK, I don't have a funtoo install to check but that's really a possible no-go. I don't have a cython-0.16_r2 in gentoo to check whether or not this would work. Same with sage-5.0_beta*.

If you want to experiment you will have to manually modify the ebuild yourself. Are you OK with doing that?

[strogdon]

FWIW, I've tried cython-0.16rc0 with sage-5.0_beta13 to see if there was any impact on the numpy issue, http://trac.sagemath.org/sage_trac/ticket/11334 and there are some nasty build issues.

[kiwifb]

I cannot say I am surprised at all. I am afraid you will have to import a cython-0.15.1 ebuild in a local overlay if you want to build any current sage (4.8 or 5.0).

[aymenbh]

Yes, I would like to experiment... But I don't have any idea of how to change an ebuild... and I am actually new to Gentoo/Funtoo systems. Please guide me :)

[kiwifb]

Sorry for the long reaction time. Real life is getting in the way :(

Let's try some basic stuff first. Try "emerge -v --nodeps sage" it won't check for correct dependency and use what is present. If the build fails I may add a cython ebuild for you in the overlay.

[aymenbh]

This is what I get as error message :

#emerge -av --nodeps sage

These are the packages that would be merged, in order:

[ebuild  N     ] sci-mathematics/sage-4.8::sage-on-gentoo  USE="latex -testsuite" 0 kB

Total: 1 package (1 new), Size of downloads: 0 kB

Would you like to merge these packages? [Yes/No] Yes
>>> Verifying ebuild manifests
>>> Emerging (1 of 1) sci-mathematics/sage-4.8 from sage-on-gentoo
>>> Failed to emerge sci-mathematics/sage-4.8, Log file:
>>>  '/var/tmp/portage/sci-mathematics/sage-4.8/temp/build.log'
>>> Jobs: 0 of 1 complete, 1 failed                 Load avg: 1.39, 1.16, 0.90
 * Package:    sci-mathematics/sage-4.8
 * Repository: sage-on-gentoo
 * Maintainer: sci@gentoo.org
 * USE:        amd64 elibc_glibc kernel_linux latex multilib userland_GNU
 * FEATURES:   preserve-libs sandbox
 * Please rebuild dev-lang/python:2.7 with the following USE flags enabled: readline sage sqlite
 * ERROR: sci-mathematics/sage-4.8 failed (setup phase):
 *   Please rebuild dev-lang/python:2.7 with the following USE flags enabled: readline sage sqlite
 * 
 * Call stack:
 *         ebuild.sh, line   85:  Called pkg_setup
 *   sage-4.8.ebuild, line  130:  Called python_pkg_setup
 *     python.eclass, line 1000:  Called python_pkg_setup_check_USE_flags
 *     python.eclass, line  981:  Called die
 * The specific snippet of code:
 *                                      die "Please rebuild ${python_atom} with the following USE flags enabled: ${PYTHON_USE_WITH}"
 * 
 * If you need support, post the output of 'emerge --info =sci-mathematics/sage-4.8',
 * the complete build log and the output of 'emerge -pqv =sci-mathematics/sage-4.8'.
 * This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-gentoo/'
 * The complete build log is located at '/var/tmp/portage/sci-mathematics/sage-4.8/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/sage-4.8/temp/die.env'.
 * S: '/var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8'

Python 2.7 is already installed with sqlite and readline support but it seems that sage is not one of its USE flags:

 #emerge -av dev-lang/python:2.7

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] dev-lang/python-2.7.4_pre20120422  USE="berkdb gdbm ipv6 ncurses readline sqlite ssl (threads) (wide-unicode) xml -build -doc -examples -tk -wininst" 0 kB             

Total: 1 package (1 reinstall), Size of downloads: 0 kB

Would you like to merge these packages? [Yes/No] Yes
>>> Verifying ebuild manifests
>>> Emerging (1 of 1) dev-lang/python-2.7.4_pre20120422
>>> Installing (1 of 1) dev-lang/python-2.7.4_pre20120422
>>> Recording dev-lang/python:2.7 in "world" favorites file...
>>> Jobs: 1 of 1 complete                           Load avg: 2.60, 2.06, 1.41

 * Messages for package dev-lang/python-2.7.4_pre20120422:

 * "bsddb" module is out-of-date and no longer maintained inside dev-lang/python.
 * "bsddb" and "dbhash" modules have been additionally removed in Python 3.
 * You should use external, still maintained "bsddb3" module provided by dev-python/bsddb3,
 * which supports both Python 2 and Python 3.
>>> Auto-cleaning packages...

>>> No outdated packages were found on your system.

 * GNU info directory index is up-to-date.

[kiwifb]

python-2.7.4_pre? With that python doesn't need the sage useflag. This is needed for python-2.7.2 and under, the only reason it is still in the overlay is that prefix is not quite ready for 2.7.3.

OK with the text editor of your choice you edit the sage ebuild (in gentoo it would be in /var/lib/layman/sage-on-gentoo/sci-mathematics/sage/sage-4.8.ebuild I see no reason for it to be different in funtoo). On the line PYTHON_USE_WITH="readline sage sqlite" remove sage. Then do ebuild /var/lib/layman/sage-on-gentoo/sci-mathematics/sage/sage-4.8.ebuild manifest You probably need to be root to do all this. Then emerge sage again with the command I gave you previously.

[cschwan]

Since dev-lang/python-2.7.3 is in the tree I suggest that we get rid of our python versions completely. If no one disagrees, I will test and make the changes next weekend.

[aymenbh]

I edited the sage ebuild as you said and built the manifest, but when emerging sage, I got this... :

These are the packages that would be merged, in order:

[ebuild  N     ] sci-mathematics/sage-4.8::sage-on-gentoo  USE="latex -testsuite" 0 kB

Total: 1 package (1 new), Size of downloads: 0 kB

Would you like to merge these packages? [Yes/No] Yes
>>> Verifying ebuild manifests
>>> Emerging (1 of 1) sci-mathematics/sage-4.8 from sage-on-gentoo
>>> Failed to emerge sci-mathematics/sage-4.8, Log file:
>>>  '/var/tmp/portage/sci-mathematics/sage-4.8/temp/build.log'
>>> Jobs: 0 of 1 complete, 1 failed                 Load avg: 1.36, 0.90, 0.57
 * Package:    sci-mathematics/sage-4.8
 * Repository: sage-on-gentoo
 * Maintainer: sci@gentoo.org
 * USE:        amd64 elibc_glibc kernel_linux latex multilib userland_GNU
 * FEATURES:   preserve-libs sandbox
>>> Unpacking source...
>>> Unpacking sage-4.8.tar.bz2 to /var/tmp/portage/sci-mathematics/sage-4.8/work
>>> Source unpacked in /var/tmp/portage/sci-mathematics/sage-4.8/work
>>> Preparing source in /var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8 ...
 * QA Notice: The 'hasq' function is deprecated (replaced by 'has')
 * Applying 9958_float_printing.patch.bz2 ...
 [ ok ]
 * Applying 9958_exceptions.patch.bz2 ...
 [ ok ]
 * Applying 9958_combinat.patch.bz2 ...
 [ ok ]
 * Applying 9958_misc.patch.bz2 ...
 [ ok ]
 * Applying 11986_integer_hash-sage.patch ...
 [ ok ]
 * Applying sage-4.7.2-site-packages.patch ...
 [ ok ]
 * Applying sage-4.8-dist.py.patch ...
 [ ok ]
 * Applying sage-4.8-sagestarted.patch ...
 [ ok ]
 * Applying sage-4.6.2-gfan-0.5.patch ...
 [ ok ]
 * Applying trac_12171a.patch ...
 [ ok ]
 * Applying trac_12171b.patch ...
 [ ok ]
 * Applying trac_9238_script_extension.patch ...
 [ ok ]
 * Applying trac_10764-fix_deprecation_warning.patch ...
 [ ok ]
 * Applying trac_10764-fix-gen_interpreters_doctest.patch ...
 [ ok ]
 * Applying sage-4.4.2-flint.patch ...
 [ ok ]
 * Applying sage-4.5.1-fix-qepcad-path.patch ...
 [ ok ]
 * Applying sage-4.7.1-fix-SAGE_LOCAL.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8 ...
python2.7 setup.py build
Traceback (most recent call last):
  File "setup.py", line 18, in 
    from module_list import ext_modules
  File "/var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8/module_list.py", line 66, in 
    for line in open(SAGE_INC + "m4ri/m4ri_config.h"):
IOError: [Errno 2] No such file or directory: '/usr//include/m4ri/m4ri_config.h'
 * ERROR: sci-mathematics/sage-4.8 failed (compile phase):
 *   Building failed
 * 
 * Call stack:
 *     ebuild.sh, line   85:  Called src_compile
 *   environment, line 5893:  Called distutils_src_compile
 *   environment, line 1466:  Called die
 * The specific snippet of code:
 *               _distutils_execute "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build "$@" || die "Building failed";
 * 
 * If you need support, post the output of 'emerge --info =sci-mathematics/sage-4.8',
 * the complete build log and the output of 'emerge -pqv =sci-mathematics/sage-4.8'.
 * This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-gentoo/'
 * The complete build log is located at '/var/tmp/portage/sci-mathematics/sage-4.8/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/sage-4.8/temp/environment'.
 * S: '/var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8'

[kiwifb]

Is sci-libs/m4ri installed and if so which version?

[aymenbh]

Actually, no version of m4ri is installed... The only one is on sage-on-gentoo overlay, which is not yet installed.

[kiwifb]

Ok you need to install m4ri-20111004 and m4rie-20111004. There may be more. I am experimenting removing the need for the sage useflag in python in sage-5.0_beta13. Doing it on prefix where python-2.7.3* is still masked so it may be interesting.

[aymenbh]

Well, I installed m4ri and m4rie. I had also to install polybori. And now I don't understand this error:

#emerge -av --nodeps sage

These are the packages that would be merged, in order:

[ebuild  N     ] sci-mathematics/sage-4.8::sage-on-gentoo  USE="latex -testsuite" 0 kB

Total: 1 package (1 new), Size of downloads: 0 kB

Would you like to merge these packages? [Yes/No] Yes
>>> Verifying ebuild manifests
>>> Emerging (1 of 1) sci-mathematics/sage-4.8 from sage-on-gentoo
>>> Failed to emerge sci-mathematics/sage-4.8, Log file:
>>>  '/var/tmp/portage/sci-mathematics/sage-4.8/temp/build.log'
>>> Jobs: 0 of 1 complete, 1 failed                 Load avg: 3.44, 3.09, 1.87
 * Package:    sci-mathematics/sage-4.8
 * Repository: sage-on-gentoo
 * Maintainer: sci@gentoo.org
 * USE:        amd64 elibc_glibc kernel_linux latex multilib userland_GNU
 * FEATURES:   preserve-libs sandbox
>>> Unpacking source...
>>> Unpacking sage-4.8.tar.bz2 to /var/tmp/portage/sci-mathematics/sage-4.8/work
>>> Source unpacked in /var/tmp/portage/sci-mathematics/sage-4.8/work
>>> Preparing source in /var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8 ...
 * QA Notice: The 'hasq' function is deprecated (replaced by 'has')
 * Applying 9958_float_printing.patch.bz2 ...
 [ ok ]
 * Applying 9958_exceptions.patch.bz2 ...
 [ ok ]
 * Applying 9958_combinat.patch.bz2 ...
 [ ok ]
 * Applying 9958_misc.patch.bz2 ...
 [ ok ]
 * Applying 11986_integer_hash-sage.patch ...
 [ ok ]
 * Applying sage-4.7.2-site-packages.patch ...
 [ ok ]
 * Applying sage-4.8-dist.py.patch ...
 [ ok ]
 * Applying sage-4.8-sagestarted.patch ...
 [ ok ]
 * Applying sage-4.6.2-gfan-0.5.patch ...
 [ ok ]
 * Applying trac_12171a.patch ...
 [ ok ]
 * Applying trac_12171b.patch ...
 [ ok ]
 * Applying trac_9238_script_extension.patch ...
 [ ok ]
 * Applying trac_10764-fix_deprecation_warning.patch ...
 [ ok ]
 * Applying trac_10764-fix-gen_interpreters_doctest.patch ...
 [ ok ]
 * Applying sage-4.4.2-flint.patch ...
 [ ok ]
 * Applying sage-4.5.1-fix-qepcad-path.patch ...
 [ ok ]
 * Applying sage-4.7.1-fix-SAGE_LOCAL.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8 ...
python2.7 setup.py build
sh: sage: command not found
Traceback (most recent call last):
  File "setup.py", line 18, in 
    from module_list import ext_modules
  File "/var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8/module_list.py", line 1806, in 
    if is_package_installed('cbc'):
  File "/var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8/sage/misc/package.py", line 170, in is_package_installed
    return any(p.startswith(package) for p in install_package()) 
  File "/var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8/sage/misc/package.py", line 127, in install_package
    i = X.index('Currently installed packages:')
ValueError: 'Currently installed packages:' is not in list
 * ERROR: sci-mathematics/sage-4.8 failed (compile phase):
 *   Building failed
 * 
 * Call stack:
 *     ebuild.sh, line   85:  Called src_compile
 *   environment, line 5893:  Called distutils_src_compile
 *   environment, line 1466:  Called die
 * The specific snippet of code:
 *               _distutils_execute "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build "$@" || die "Building failed";
 * 
 * If you need support, post the output of 'emerge --info =sci-mathematics/sage-4.8',
 * the complete build log and the output of 'emerge -pqv =sci-mathematics/sage-4.8'.
 * This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-gentoo/'
 * The complete build log is located at '/var/tmp/portage/sci-mathematics/sage-4.8/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/sage-4.8/temp/environment'.
 * S: '/var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8'

[kiwifb]

Try to emerge sage-baselayout and sage-clib first.

[aymenbh]

I think it is better that you give me all the main packages that I need to install before the last step of installing sage-4.8. I have the feeling that I will keep having these errors for a long time... :D

This time, I have:

 >>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8 ...
python2.7 setup.py build
Traceback (most recent call last):
  File "setup.py", line 19, in 
    import sage.ext.gen_interpreters
  File "/var/tmp/portage/sci-mathematics/sage-4.8/work/sage-4.8/sage/ext/gen_interpreters.py", line 101, in 
    from jinja2 import Environment
ImportError: No module named jinja2
 * ERROR: sci-mathematics/sage-4.8 failed (compile phase):
 *   Building failed

[kiwifb]

I was hoping that the last two I gave would take of a lot of stuff. Let's see. Emerge the following if not already installed: ppl, maxima flint fplll linbox-1.1.6 symmetrica glpk lcalc ratpoint libsingular singular ipython-0.10.2 matplotlib sympy gap gfan palp-1.1 let's see how far you go with that.

[aymenbh]

Well, I installed all the packages you mentionned except singular which failed to build... And for ipython, I have a new version installed: ipython-0.12-r1, is that a problem ?

Anyways, the last error in my previous comment was solved by installing jinja2 (easy_install jinja2) and afterwards, I kept having many dependencies issues, which I solved by installing these packages in order: libcliquer, ecm, eclib, iml, mpfi, twisted.

But at the end, sage still fail to build because of many error compiling Cython file messages, which I do not understand...

Well, if you find a solution for building sage for a prefix, it would be nice !

[kiwifb]

ipython-0.12 is a problem. We may have to give you a cython-0.15.1 in the overlay.

[strogdon]

I'm wondering, at http://www.funtoo.org/wiki/Portage_Tree there is a link, http://github.com/funtoo/portage to the funtoo portage tree that has dev-python/cython-0.15.1-r1 and maybe this will suffice.

[aymenbh]

In my /etc/make.conf, the variable SYNC is: SYNC="git://github.com/funtoo/ports-2012.git". And in that tree, There is only the 0.16 version as you see here: https://github.com/funtoo/ports-2012/tree/funtoo.org/dev-python/cython

[aymenbh]

Hi... Me again... I have installed a new Funtoo system on my laptop and tried again the installation of sage but still have an issue with cython. Was it included or not yet in the overlay ?

 #emerge -av sage
These are the packages that would be merged, in order:

Calculating dependencies... done!

emerge: there are no ebuilds to satisfy "~dev-python/cython-0.15.1".
(dependency required by "sci-mathematics/sage-4.8" [ebuild])
(dependency required by "sage" [argument])

[cschwan]

Commit 1e4ac3f60bbb2af0637004bd584e483617a07361 adds cython-0.15.1-r1. Please tell me if it works.

[aymenbh]

Thanks. But it seems that I will need the old version of numpy too...

 These are the packages that would be merged, in order:

Calculating dependencies... done!

emerge: there are no ebuilds to satisfy "~dev-python/numpy-1.5.1".
(dependency required by "sci-mathematics/sage-4.8-r1" [ebuild])
(dependency required by "sage" [argument])

[cschwan]

OK, added in commit 8e4d3b9dd61b21ce8502dac6c43859e643db3569. Hope it works.

[aymenbh]

Well... This time is the turn of ipython... I will need the version 0.10.2 Should I tell the funtoo developers to include these old versions again ?

[cschwan]

You should try it for all three packages, since Sage 5.0 will not upgrade any of these ... In the meantime I will include ipython.

[cschwan]

Upgrade to numpy-1.6.x is WIP at http://trac.sagemath.org/sage_trac/ticket/11334

[cschwan]

Included in commit 191007c1a41348bc6408189da3fc6d49debbd92b

[aymenbh]

Thanks, I will try that when I'm back home. But just a question : from where you add these ebuilds ? I am asking because if I will need to add some other ones, I don't bother you with that :p.

[cschwan]

I added these from the portage tree which I have locally. But you can access it also on the web at http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/ . If you want to use git, look at http://anoncvs.gentoo.org/#git

[aymenbh]

There is some progress... At least, it can detect now all the packages that should be installed. The problem is that there are some conflict dependencies as it is shown here:

Total: 101 packages (4 downgrades, 94 new, 2 in new slots, 1 reinstall), Size of downloads: 391,045 kB

!!! Multiple package instances within a single package slot have been pulled
!!! into the dependency graph, resulting in a slot conflict:

dev-python/numpy:0

  (dev-python/numpy-1.5.1::sage-on-gentoo, ebuild scheduled for merge) pulled in by
    ~dev-python/numpy-1.5.1 required by (sci-mathematics/sage-4.8-r1::sage-on-gentoo, ebuild scheduled for merge)

  (dev-python/numpy-1.6.1-r2::gentoo, installed) pulled in by
    dev-python/numpy[python_abis_2.5?,python_abis_2.6?,python_abis_2.7?,python_abis_3.1?,python_abis_3.2?,python_abis_3.3?] required by (sci-libs/scipy-0.10.1::gentoo, installed)
    dev-python/numpy[python_abis_2.6?,python_abis_2.7?] required by (dev-python/pygtk-2.24.0-r2::gentoo, installed)
    dev-python/numpy[python_abis_2.6?,python_abis_2.7?] required by (dev-python/matplotlib-1.1.0::gentoo, installed)

It may be possible to solve this problem by using package.mask to
prevent one of those packages from being selected. However, it is also
possible that conflicting dependencies exist such that they are
impossible to satisfy simultaneously.  If such a conflict exists in
the dependencies of two different packages, then those packages can
not be installed simultaneously. You may want to try a larger value of
the --backtrack option, such as --backtrack=30, in order to see if
that will solve this conflict automatically.

For more information, see MASKED PACKAGES section in the emerge man
page or refer to the Gentoo Handbook.

I tried to mask numpy-1.6.1-r2, it didn't work. I come with same message. Trying with the --backtrack option does not work neither.

Does this mean that I should unmerge numpy first and the packages that depend on it ??

[cschwan]

First find out which package depends numpy-1.6. You can use equery for that (in app-portage/gentoolkit):

equery d numpy

[aymenbh]

This is the result of

equery d numpy

* These packages depend on numpy:
dev-python/cython-0.16-r1000 (numpy ? dev-python/numpy[python_abis_2.5?,python_abis_2.6?,python_abis_2.7?,python_abis_3.1?,python_abis_3.2?,python_abis_3.3?])
dev-python/ipython-0.12.1-r1000 (python_abis_2.6 ? dev-python/numpy[python_abis_2.6])
                                (python_abis_2.7 ? dev-python/numpy[python_abis_2.7])
                                (python_abis_3.1 ? dev-python/numpy[python_abis_3.1])
                                (python_abis_3.2 ? dev-python/numpy[python_abis_3.2])
                                (python_abis_3.3 ? dev-python/numpy[python_abis_3.3])
dev-python/matplotlib-1.1.0 (dev-python/numpy[python_abis_2.6?,python_abis_2.7?])
dev-python/pygtk-2.24.0-r2 (dev-python/numpy[python_abis_2.6?,python_abis_2.7?])
media-gfx/inkscape-0.48.3.1 (dev-python/numpy)
sci-libs/scipy-0.10.1 (dev-python/numpy[python_abis_2.5?,python_abis_2.6?,python_abis_2.7?,python_abis_3.1?,python_abis_3.2?,python_abis_3.3?])

In Funtoo forums, one told me that normally portage supports multiple slots for packages and probably the package itself should support this. Do you know if this is the case for numpy or is it possible to make some modifications to the ebuild so that it can support it ?

Otherwise, I guess that I need to unmerge the listed packages, since they come anyways with sage (except for inkscape).

[cschwan]

Hm, none of these explicitly depend on >=numpy-1.6.x. So try to umerge those - SLOT deps shouldnt be a problem.

[aymenbh]

Well, I unmerged all these packages and numpy.1-6.1-r2. I verified with equery d numpy that there is no package which depend on numpy, and tried again to install sage. This is what I got :

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  N     ] sci-libs/ufconfig-3.7.0  USE="-static-libs" 9 kB
[ebuild  N     ] sci-mathematics/ratpoints-2.1.3-r3::sage-on-gentoo  USE="sse2 -doc" 203 kB
[ebuild  N     ] sci-mathematics/sage-baselayout-4.8::sage-on-gentoo  USE="X -debug -testsuite -tools" 1,185 kB                                                                           
[ebuild  N     ] sci-libs/symmetrica-2.0-r2::sage-on-gentoo  USE="-doc" 704 kB
[ebuild  N     ] sci-libs/libcliquer-1.2_p7::sage-on-gentoo  95 kB
[ebuild  N     ] sci-mathematics/flintqs-20070817_p5::sage-on-gentoo  53 kB
[ebuild  N     ] sci-mathematics/palp-1.1-r2::sage-on-gentoo  184 kB
[ebuild  N     ] sci-mathematics/sage-data-polytopes_db-20100210-r1::sage-on-gentoo  32 kB
[ebuild  N     ] sci-mathematics/cubex-20060128::sage-on-gentoo  20 kB
[ebuild  N     ] sci-mathematics/sage-extcode-4.8::sage-on-gentoo  11,902 kB
[ebuild  N     ] sci-mathematics/sage-data-graphs-20070722_p1-r1::sage-on-gentoo  250 kB
[ebuild  N     ] sci-mathematics/dikcube-20070912_p16::sage-on-gentoo  135 kB
[ebuild  N     ] sci-mathematics/sage-data-conway_polynomials-0.2-r1::sage-on-gentoo  518 kB
[ebuild  N     ] sci-mathematics/gap-4.4.12-r2::sage-on-gentoo  USE="-emacs -vim-syntax" 46,598 kB
[ebuild  N     ] sci-mathematics/optimal-20040603::sage-on-gentoo  22 kB
[ebuild  N     ] sci-mathematics/pari-data-20110727  45,753 kB
[ebuild  N     ] dev-libs/gf2x-1.0-r1  USE="-bindist -static-libs" 451 kB
[ebuild  N     ] sci-mathematics/mcube-20051209::sage-on-gentoo  32 kB
[ebuild  N     ] sci-mathematics/cu2-20060223::sage-on-gentoo  74 kB
[ebuild  N     ] sci-libs/givaro-3.2.16::sage-on-gentoo  USE="-static-libs" 615 kB
[ebuild  N     ] sci-libs/cddlib-094f-r2  USE="-doc -static-libs" 1,495 kB
[ebuild  N     ] dev-libs/ppl-0.12.1  USE="-doc -lpsol -pch -static-libs -test" 14,589 kB
[ebuild  N     ] sci-libs/mpfi-1.5.1  USE="-static-libs" 357 kB
[ebuild  N     ] sci-libs/fplll-3.0.12-r2::sage-on-gentoo  USE="-static-libs" 390 kB
[ebuild  N     ] sci-mathematics/gfan-0.5  1,109 kB
[ebuild  N     ] sci-libs/iml-1.0.3-r2::sage-on-gentoo  USE="-static-libs" 386 kB
[ebuild  N     ] app-misc/rlwrap-0.37  USE="-debug" 246 kB
[ebuild  N     ] sci-mathematics/pari-2.5.1  USE="X data gmp -doc -fltk" 2,656 kB
[ebuild  N     ] sci-mathematics/lcalc-1.23-r4::sage-on-gentoo  USE="pari" 626 kB
[ebuild  N     ] sci-mathematics/sympow-1.018.1_p8-r1::sage-on-gentoo  USE="-pari24" 2,159 kB
[ebuild  N     ] sci-mathematics/genus2reduction-0.3_p8-r1::sage-on-gentoo  52 kB
[ebuild  N     ] dev-libs/ntl-5.5.2  USE="-doc -static-libs -test" 691 kB
[ebuild  N     ] sci-mathematics/eclib-20100711::sage-on-gentoo  USE="-pari24" 1,589 kB
[ebuild  N     ] sci-libs/libsingular-3.1.3.3-r2::sage-on-gentoo  USE="-boost -debug" 19,581 kB
[ebuild  N     ] sci-libs/colamd-2.7.4  USE="-static-libs" 54 kB
[ebuild  N     ] dev-lisp/ecls-12.2.1  USE="X -debug -emacs -gengc -precisegc -threads -unicode" 8,765 kB                                                                                 
[ebuild  N     ] sci-libs/linbox-1.1.6-r7::sage-on-gentoo  USE="sage -ntl -static-libs" 1,215 kB
[ebuild  N     ] sci-mathematics/glpk-4.47  USE="-doc -examples -gmp -mysql -odbc -static-libs" 3,052 kB                                                                                  
[ebuild     UD ] dev-python/pexpect-2.0-r1::sage-on-gentoo [2.4::gentoo] USE="(-doc%) (-examples%)" PYTHON_ABIS="(-2.5%) (-2.5-jython%) (-2.6%) (-2.6-jython%) (-2.7%*) (-2.7-pypy-1.7%) (-2.7-pypy-1.8%)" 24 kB                                                                       
[ebuild  N     ] sci-libs/zn_poly-0.9-r3::sage-on-gentoo  113 kB
[ebuild  N     ] sci-libs/pynac-0.2.3::sage-on-gentoo  USE="-static-libs" 249 kB
[ebuild  N     ] dev-util/scons-2.1.0  USE="-doc" PYTHON_ABIS="2.7 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8" 562 kB                                                
[ebuild  N     ] sci-mathematics/sage-data-elliptic_curves-0.3::sage-on-gentoo  1,087 kB
[ebuild  N     ] dev-python/gdmodule-0.56-r2  USE="jpeg png truetype -xpm" 48 kB
[ebuild  N     ] dev-python/pysqlite-2.6.3  USE="-examples" PYTHON_ABIS="2.7 -2.5 -2.6" 74 kB
[ebuild  N     ] sci-libs/flint-1.6::sage-on-gentoo  USE="ntl -doc -test" 2,354 kB
[ebuild  N     ] net-zope/namespaces-zope-0  USE="Products Shared Shared.DC five zope zope.app" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 0 kB
[ebuild  N     ] dev-python/cython-0.15.1-r1::sage-on-gentoo  USE="-doc -examples -numpy" 1,755 kB
[ebuild  N     ] dev-python/pycrypto-2.5  USE="gmp -doc" PYTHON_ABIS="2.7 3.2 -2.5 -2.6 -3.1 (-3.3)" 417 kB
[ebuild  N     ] dev-python/pyopenssl-0.13  USE="-doc" PYTHON_ABIS="2.7 3.2 -2.5 -2.6 -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 245 kB                                                     
[ebuild  N     ] net-zope/namespaces-zc-0  USE="zc zc.recipe" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 0 kB                      
[ebuild  N     ] virtual/python-sqlite-0  USE="external" PYTHON_ABIS="2.7 3.2 -2.5 -2.6 -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 0 kB                                                     
[ebuild  N     ] net-zope/zope-fixers-1.0  PYTHON_ABIS="3.2 -3.1 (-3.3)" 8 kB
[ebuild  N     ] net-zope/zconfig-2.9.2  USE="-test" PYTHON_ABIS="2.7 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8" 255 kB                                             
[ebuild  N     ] dev-python/sqlalchemy-0.7.7-r1000  USE="sqlite -doc -examples (-firebird) -mssql -mysql -postgres -test" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 2,542 kB                                                   
[ebuild  N     ] dev-python/networkx-1.2::sage-on-gentoo  USE="-examples" 573 kB
[ebuild  N     ] dev-python/roman-1.4.0  PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 3 kB                                           
[ebuild  N     ] dev-python/markupsafe-0.15  PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 12 kB                                      
[ebuild  N     ] net-zope/zope-event-3.5.2  USE="-doc -test" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 13 kB                      
[ebuild  N     ] net-zope/zc-lockfile-1.0.0  USE="-test" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 4 kB                           
[ebuild  N     ] dev-python/manuel-1.6.0  USE="-test" PYTHON_ABIS="2.7 3.2 -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 31 kB
[ebuild  N     ] net-zope/zope-interface-3.8.0  USE="-test" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 109 kB                      
[ebuild  N     ] dev-python/jinja-2.6  USE="-doc -examples -i18n -vim-syntax" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 381 kB    
[ebuild  N     ] dev-python/docutils-0.9-r1000  USE="-glep" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 1,499 kB                    
[ebuild  N     ] net-zope/zdaemon-2.0.4  PYTHON_ABIS="2.7 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8" 42 kB
[ebuild  N     ] dev-python/sphinx-1.1.3-r1000  USE="-doc -latex -test" PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 2,571 kB        
[ebuild  N     ] net-zope/transaction-1.2.0  USE="-test" PYTHON_ABIS="2.7 3.2 -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 42 kB                                           
[ebuild  N     ] net-zope/zope-exceptions-3.7.1  PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 10 kB                                  
[ebuild  N     ] sci-mathematics/sage-doc-4.8::sage-on-gentoo  USE="pdf -html" 80,236 kB
[ebuild  N     ] net-zope/zope-testing-4.1.1  PYTHON_ABIS="2.7 3.2 -2.5 -2.5-jython -2.6 (-2.6-jython) -2.7-pypy-1.7 -2.7-pypy-1.8 -3.1 (-3.3)" 50 kB                                     
[ebuild  N     ] net-zope/zodb-3.10.5  PYTHON_ABIS="2.7 -2.6" 690 kB
[ebuild  N     ] media-gfx/tachyon-0.98.9-r2::sage-on-gentoo  USE="jpeg opengl png -doc -examples -mpi -threads" 3,197 kB                                                                 
[ebuild  N     ] sci-libs/m4ri-20111004::sage-on-gentoo  USE="openmp sse2 -debug -static-libs" 444 kB
[ebuild  N     ] sci-mathematics/ecm-6.3-r1::sage-on-gentoo  USE="openmp sse2 -shellcmd -static-libs" 830 kB                                                                              
[ebuild  N     ] sci-libs/amd-2.2.3  USE="-doc -static-libs" 256 kB
[ebuild  N     ] sci-libs/m4rie-20111004::sage-on-gentoo  USE="openmp -debug -static-libs" 389 kB
[ebuild  N     ] sci-libs/umfpack-5.5.2  USE="-doc -metis -static-libs" 1,272 kB
[ebuild  N    #] dev-python/numpy-1.6.1-r2  USE="lapack -doc -test" PYTHON_ABIS="2.7 3.2 -2.5 -2.6 -3.1 (-3.3)" 0 kB
[ebuild  N     ] dev-python/numpy-1.5.1::sage-on-gentoo  USE="lapack -doc -test" 2,227 kB
[ebuild  N     ] sci-libs/cholmod-1.7.4  USE="supernodal -debug -doc -metis -minimal -static-libs" 1,148 kB                                                                               
[ebuild  N     ] sci-libs/scipy-0.10.1  USE="-doc -test -umfpack" PYTHON_ABIS="2.7 3.2 -2.5 -2.6 -3.1 (-3.3)" 0 kB                                                                        
[ebuild  N     ] dev-python/cvxopt-1.1.5  USE="glpk -doc -dsdp -examples -fftw -gsl" 3,356 kB
[ebuild  NS    ] dev-java/icedtea-bin-6.1.11.1-r1 [7.2.1-r1] USE="X alsa cups -cjk -doc -examples -nsplugin -source" 34,387 kB                                                            
[ebuild  N     ] dev-python/pygtk-2.24.0-r2  USE="-doc -examples -test" PYTHON_ABIS="2.7 -2.6" 0 kB
[ebuild  N     ] dev-lang/R-2.15.0  USE="X cairo jpeg nls openmp perl png readline tiff -bash-completion -doc -icu -java -lapack -minimal -profile -static-libs -tk" 23,629 kB            
[ebuild  NS    ] virtual/jdk-1.6.0-r1 [1.7.0] 0 kB
[ebuild  N     ] dev-python/twisted-12.0.0  USE="crypt gtk -serial" PYTHON_ABIS="2.7 -2.5 -2.6 -2.7-pypy-1.7 -2.7-pypy-1.8" 1,362 kB                                                      
[ebuild  N     ] dev-python/rpy-2.2.6  164 kB
[ebuild  N     ] dev-java/commons-cli-1.2  USE="-doc -source -test" 67 kB
[ebuild  N     ] sci-libs/jmol-acme-1.0  468 kB
[ebuild  N     ] sci-libs/vecmath-objectclub-1.14  74 kB
[ebuild  N     ] sci-mathematics/singular-3.1.3.3  USE="emacs readline -boost -doc -examples -test" 0 kB                                                                                  
[ebuild  N     ] dev-python/twisted-web2-8.1.0::sage-on-gentoo  131 kB
[ebuild  N     ] dev-python/twisted-names-12.0.0  PYTHON_ABIS="2.7 -2.5 -2.6 -2.7-pypy-1.7 -2.7-pypy-1.8" 54 kB                                                                           
[ebuild  N     ] dev-python/ipython-0.10.2::sage-on-gentoo  USE="emacs readline wxwidgets -doc -examples -gnuplot -smp -test" 5,706 kB                                                    
[ebuild  N     ] dev-python/twisted-mail-12.0.0  PYTHON_ABIS="2.7 -2.5 -2.6 -2.7-pypy-1.7 -2.7-pypy-1.8" 143 kB                                                                           
[ebuild  N     ] sci-mathematics/polybori-0.7.1-r2::sage-on-gentoo  USE="sage -doc -gd" 2,325 kB
[ebuild  N     ] sci-mathematics/sage-clib-4.8::sage-on-gentoo  0 kB
[ebuild  N     ] dev-java/itext-2.1.5  USE="-cjk -doc -rtf -rups -source" 1,272 kB
[ebuild  N     ] sci-chemistry/jmol-applet-12.0.45-r1::sage-on-gentoo  25,881 kB
[ebuild  N     ] sci-chemistry/jmol-12.0.45::sage-on-gentoo  USE="client-only -vhosts" 0 kB
[ebuild  N     ] dev-python/matplotlib-1.1.0  USE="cairo gtk latex qt4 wxwidgets -doc -examples -excel -fltk -tk" PYTHON_ABIS="2.7 -2.6" 0 kB                                             
[ebuild   R    ] sci-mathematics/maxima-5.27.0  USE="X clisp ecls* emacs latex nls unicode -clozurecl (-cmucl) (-gcl) -sbcl -tk -xemacs" LINGUAS="-es -pt -pt_BR" 0 kB                    
[ebuild  N     ] sci-mathematics/sage-4.8-r1::sage-on-gentoo  USE="-latex -testsuite" 0 kB
[ebuild  N     ] sci-mathematics/sage-notebook-0.8.26-r1::sage-on-gentoo  USE="java ssl -server" 18,462 kB                                                                                

Total: 105 packages (1 downgrade, 101 new, 2 in new slots, 1 reinstall), Size of downloads: 391,045 kB

!!! Multiple package instances within a single package slot have been pulled
!!! into the dependency graph, resulting in a slot conflict:

dev-python/numpy:0

  (dev-python/numpy-1.5.1::sage-on-gentoo, ebuild scheduled for merge) pulled in by
    ~dev-python/numpy-1.5.1 required by (sci-mathematics/sage-4.8-r1::sage-on-gentoo, ebuild scheduled for merge)

  (dev-python/numpy-1.6.1-r2::gentoo, ebuild scheduled for merge) pulled in by
    dev-python/numpy[python_abis_2.6?,python_abis_2.7?] required by (dev-python/matplotlib-1.1.0::gentoo, ebuild scheduled for merge)                                                     
    dev-python/numpy[python_abis_2.6?,python_abis_2.7?] required by (dev-python/pygtk-2.24.0-r2::gentoo, ebuild scheduled for merge)                                                      
    dev-python/numpy[python_abis_2.5?,python_abis_2.6?,python_abis_2.7?,python_abis_3.1?,python_abis_3.2?,python_abis_3.3?] required by (sci-libs/scipy-0.10.1::gentoo, ebuild scheduled for merge)

It may be possible to solve this problem by using package.mask to
prevent one of those packages from being selected. However, it is also
possible that conflicting dependencies exist such that they are
impossible to satisfy simultaneously.  If such a conflict exists in
the dependencies of two different packages, then those packages can
not be installed simultaneously. You may want to try a larger value of
the --backtrack option, such as --backtrack=30, in order to see if
that will solve this conflict automatically.

For more information, see MASKED PACKAGES section in the emerge man
page or refer to the Gentoo Handbook.

The following mask changes are necessary to proceed:
#required by dev-python/rpy-2.2.6, required by sci-mathematics/sage-4.8-r1, required by sci-mathematics/sage-notebook-0.8.26-r1
# /etc/portage/package.mask:
=dev-python/numpy-1.6.1-r2

NOTE: The --autounmask-keep-masks option will prevent emerge
      from creating package.unmask or ** keyword changes.

Use --autounmask-write to write changes to config files (honoring CONFIG_PROTECT).

So, it seems that sage wants to install two versions of numpy... I tried to mask numpy-1.6.1-r2 but I got the same message telling me that I need to mask this package and I don't understand why... ?

Anyways, is it normal that sage wants to install two different versions of numpy that seem to conflict (1.6.1-r2 and 1.5.1)?

[cschwan]

Its not normal. How did you mask numpy?

[aymenbh]

I just added the line =dev-python/numpy-1.6.1-r2 to the file /etc/portage/package.mask

[strogdon]

scipy-(0.9/0.10) can't be built with python-3.2 and numpy-1.5.1. The same is probably true with python-3.3. See http://archives.gentoo.org/gentoo-science/msg_4053f0693abf94db08095fe338cd447b.xml, although the exact proposed fix didn't work here (this may be portage version dependent). It appears that funtoo is adding python_abis_PYTHON-VERSION use flags that may be controlling things. Perhaps these flags could be masked relative to scipy (and possibly numpy). So maybe in /etc/portage/package.use.mask put something like:

sci-libs/scipy python_abis_3.2 python_abis_3.3

and perhaps something similar, if needed, for numpy?? Of course, this doesn't address the need for matplotlib/pygtk, but who knows.

[aymenbh]

Package.use.mask or package.mask ? Anyways I tried both but it does not mask anything in scipy. Keep having scipy0.10 with PYTHON_ABIS="2.7 3.2 -2.5 -2.6 -3.1 (-3.3)". Trying to mask numpy in the same way doesn't do anything neither. But I'm wondering in the first place why I keep having numpy-1.6.1-r2 in the list of the packages to be emerged while I have masked it in /etc/portage/package.mask ??

[aymenbh]

I guess then that I will need versions of matplotlib, pygtk and scipy which use only numpy-1.5.1. Because it seems that these three packages which are planned to be emerged depend on numpy -1.6.1. Do you know which versions work well ?

[strogdon]

Dependence on numpy-1.6.1. Hmm, now I see. It appears that funtoo has the progress overlay merged into its main tree. Ebuilds from this overlay have EAPI="4-python"? Thus the "odd" useflags. Perhaps cschwan knows how deep this may run.

[cschwan]

I am sorry, but I dont know how to solve this.

[kiwifb]

I am back in town. I will try to work on numpy but the EAPI from the progress overlay is pretty much what stopped me using it. Martin Scholz (golodhrim) was looking at sage for funtoo, he used to merge our overlay to funtoo may be we should ask him about this.

[cschwan]

Welcome back!

[kiwifb]

Could we have an update on the "sage-on-funtoo" situation with sage 5.8?

[kiwifb]

Since we don't seem to have feed back from funtoo people I am closing. New or current problems in a new issue please.