sage-6.6 depends on several old python packages (dev-python/numpy-1.8.2, dev-python/sphinx-1.2.2, dev-python/matplotlib-1.3.1, dev-python/ipython-3.0.0-r1). These dependencies introduce some slot conflicts, which blocks for some days 'emerge -uvDN world' for me. See e.g. https://bugs.gentoo.org/show_bug.cgi?id=546716 and https://bugs.gentoo.org/show_bug.cgi?id=546896. Is there any chance, that sage will work with the current python packages? root@impala:/home/rose(84)# emerge --update --newuse --deep --with-bdeps=y --backtrack=30 @world Calculating dependencies... done! [ebuild U ] dev-python/numpy-1.9.2 [1.8.2] [ebuild U ] app-emulation/wine-1.7.41 [1.7.40] [ebuild U ] dev-python/bottleneck-1.0.0 [0.8.0] [ebuild U ] media-video/vlc-2.2.1 [2.2.0] [ebuild rR ] media-gfx/freecad-0.14.3702-r1 !!! 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-1.9.2:0/0::gentoo, ebuild scheduled for merge) pulled in by >=dev-python/numpy-1.9.1[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-)] required by (dev-python/bottleneck-1.0.0:0/0::gentoo, ebuild scheduled for merge) ^^ ^^^^^ (dev-python/numpy-1.8.2:0/0::gentoo, installed) pulled in by =dev-python/numpy-1.8*[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] required by (sci-mathematics/sage-6.6:0/0::sage-on-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. For more information, see MASKED PACKAGES section in the emerge man page or refer to the Gentoo Handbook. root@impala:/home/rose(85)# or at the next system: root@gepard:/var/tmp/portage(49)# emerge --update --newuse --deep --with-bdeps=y --backtrack=30 @world Calculating dependencies... done! [ebuild U ] dev-python/numpy-1.9.2 [1.8.2] [ebuild U ] net-fs/openafs-kernel-1.6.11 [1.6.5-r2] [ebuild U ] net-fs/openafs-1.6.11 [1.6.5-r1] USE="modules%*" [ebuild U ] dev-python/bottleneck-1.0.0 [0.8.0] [ebuild N ] sci-geosciences/mapnik-2.2.0 USE="cairo doc gdal postgres python sqlite -debug" PYTHON_SINGLE_TARGET="python2_7 -python3_3" PYTHON_TARGETS="python2_7 python3_3" [ebuild U ] sci-geosciences/viking-1.6-r1 [1.5.1] USE="mapnik%* -libexif% -sqlite3%" [ebuild rR ] media-gfx/freecad-0.14.3702-r1 [ebuild U ] sci-mathematics/sage-doc-6.6 [6.5] LINGUAS="de%* en%* fr%* ru%* -ca% -hu% -it% -pt% -tr%" !!! 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-1.9.2:0/0::gentoo, ebuild scheduled for merge) pulled in by >=dev-python/numpy-1.9.1[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-)] required by (dev-python/bottleneck-1.0.0:0/0::gentoo, ebuild scheduled for merge) ^^ ^^^^^ (dev-python/numpy-1.8.2:0/0::gentoo, installed) pulled in by =dev-python/numpy-1.8*[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] required by (sci-mathematics/sage-6.6:0/0::sage-on-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. For more information, see MASKED PACKAGES section in the emerge man page or refer to the Gentoo Handbook. root@gepard:/var/tmp/portage(50)# At an other system, where I removed sage due to this slot conflicts 'emerge -vuND sage' fails now with: root@lynx2:/usr/local/portage/sci-mathematics(43)# emerge -vuND sage These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] sci-mathematics/sage-baselayout-6.6::sage-on-gentoo [6.5::sage-on-gentoo] USE="X testsuite -debug" PYTHON_TARGETS="python2_7" 0 KiB [ebuild UD ] dev-python/numpy-1.8.2::gentoo [1.9.2::gentoo] USE="doc lapack {-test}" PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 KiB [ebuild UD ] media-gfx/tachyon-0.98.9-r2::sage-on-gentoo [0.99_beta6::gentoo] USE="doc examples jpeg opengl png threads -mpi" 0 KiB [ebuild U ] sci-chemistry/sage-jmol-bin-14.2.11-r1::sage-on-gentoo [14.2.11::sage-on-gentoo] 0 KiB [ebuild N ] sci-mathematics/eclib-20150323:0/1::sage-on-gentoo USE="boost flint -static-libs" 0 KiB [ebuild U ] dev-python/bottleneck-1.0.0::gentoo [0.8.0::gentoo] PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 KiB [ebuild U ] sci-mathematics/pari-2.8_pre20150307-r1:0/0::sage-on-gentoo [2.7.1-r2:0/4::sage-on-gentoo] USE="X data doc fltk gmp qt4" 0 KiB [ebuild U ] sci-mathematics/sage-clib-6.6::sage-on-gentoo [6.5::sage-on-gentoo] 0 KiB [ebuild UD ] dev-python/sphinx-1.2.2::sage-on-gentoo [1.3.1::gentoo] USE="doc latex {-test}" PYTHON_TARGETS="python2_7 python3_3 -pypy -python3_4" 0 KiB [ebuild UD ] dev-python/matplotlib-1.3.1::sage-on-gentoo [1.4.3::gentoo] USE="cairo examples excel fltk gtk gtk3 latex tk wxwidgets -doc -pyside -qt4* {-test} (-qt5%*)" PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 KiB [ebuild UD ] dev-python/ipython-3.0.0-r1::sage-on-gentoo [3.1.0::gentoo] USE="examples matplotlib mongodb notebook octave qt4 smp wxwidgets -doc -nbconvert {-test}" PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 KiB [ebuild N ] sci-mathematics/sage-6.6::sage-on-gentoo USE="latex testsuite -arb -debug -modular_decomposition" PYTHON_TARGETS="python2_7" 0 KiB [ebuild U ] sci-mathematics/sage-doc-6.6::sage-on-gentoo [6.5::sage-on-gentoo] USE="html" LINGUAS="de%* en%* fr%* ru%* -ca% -hu% -it% -pt% -tr%" PYTHON_TARGETS="python2_7" 0 KiB Total: 13 packages (6 upgrades, 5 downgrades, 2 new), Size of downloads: 0 KiB !!! 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-1.8.2:0/0::gentoo, ebuild scheduled for merge) pulled in by =dev-python/numpy-1.8*[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] required by (sci-mathematics/sage-6.6:0/0::sage-on-gentoo, ebuild scheduled for merge) ^ ^^^^ (dev-python/numpy-1.9.2:0/0::gentoo, installed) pulled in by >=dev-python/numpy-1.9.1[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-)] required by (dev-python/bottleneck-1.0.0:0/0::gentoo, ebuild scheduled for merge) ^^ ^^^^^ sci-mathematics/pari:0 (sci-mathematics/pari-2.8_pre20150307-r1:0/0::sage-on-gentoo, ebuild scheduled for merge) pulled in by >=sci-mathematics/pari-2.8_pre20150307[data,gmp] required by (sci-mathematics/sage-6.6:0/0::sage-on-gentoo, ebuild scheduled for merge) ^^ ^^^^^^^^^^^^^^^ (and 1 more with the same problem) (sci-mathematics/pari-2.7.1-r2:0/4::sage-on-gentoo, installed) pulled in by sci-mathematics/pari:0/4= required by (sci-mathematics/lcalc-1.23-r7:0/0::sage-on-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.
sage-6.6 still blocks 'emerge -uvDN world' due to this slot conflict with numpy.
This slot conflict is really very nasty. I need now for about four weeks every day some hours to update manually my gentoo installation on my systems, because 'emerge -uvDN world' fails due to this slot conflict. Is there any possibility to solve this issue besides uninstalling sage?
Now I have the same issues with sage-6.7. 'emerge --update --newuse --deep --with-bdeps=y @world' still fails. The blocking of the sphinx-update creates a lot of other issues e.g. Bug 550720, Bug 549234, etc. Is there not any chance that sage works with current python-packages?
(In reply to Juergen Rose from comment #3) > Now I have the same issues with sage-6.7. 'emerge --update --newuse --deep > --with-bdeps=y @world' still fails. The blocking of the sphinx-update > creates a lot of other issues e.g. Bug 550720, Bug 549234, etc. > > Is there not any chance that sage works with current python-packages? Now sage-6.7 blocks the installation of more than 100 gnome-packages. I start to remove sage from my systems.
schwan@uni-mainz.de ? Do you still exist?
Sorry Juergen, I don't get notified on bugs filled in bugzilla. The other main sage developer, Christopher, should, except that bugzilla got his old email address. I must say I mainly target the sage ebuilds to people in `arch` and not `~arch` and yes that triggers some problems. numpy is at 1.8.2 because upstream still hasn't moved to matplotlib 1.4.x (partly my fault, I identified that problem ages ago). sphinx is more delicate, last time I check the 1.3 series it failed to build sage's documentation. However sphinx shouldn't be a problem if you use sage-doc-bin instead of sage-doc. Users in `arch` using our provided keywords files are getting sage-doc-bin by default. I am not sure I could make a comprehensive package.mask file for you. I can probably do something unilaterally for matplotlib independent of upstream so the numpy problem disappear.
(In reply to Francois Bissey from comment #6) ... > numpy is at 1.8.2 because upstream still hasn't moved to matplotlib 1.4.x > (partly my fault, I identified that problem ages ago). > > sphinx is more delicate, last time I check the 1.3 series it failed to build > sage's documentation. However sphinx shouldn't be a problem if you use > sage-doc-bin instead of sage-doc. Users in `arch` using our provided > keywords files are getting sage-doc-bin by default. I am not sure I could > make a comprehensive package.mask file for you. > > I can probably do something unilaterally for matplotlib independent of > upstream so the numpy problem disappear. The main problems for me seem to be numpy and sphinx. I just had again a slot conflict: root@condor:/root(14)# emerge -v --update --newuse --deep --with-bdeps=y --backtrack=30 @world These are the packages that would be merged, in order: ... [ebuild U ] dev-python/numpy-1.9.2::gentoo [1.8.2::gentoo] USE="doc lapack {-test}" PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 KiB ... Total: 45 packages (40 upgrades, 4 new, 1 in new slot), Size of downloads: 0 KiB !!! 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-1.9.2:0/0::gentoo, ebuild scheduled for merge) pulled in by >=dev-python/numpy-1.9.1[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-)] required by (dev-python/bottleneck-1.0.0:0/0::gentoo, ebuild scheduled for merge) ^^ ^^^^^ (dev-python/numpy-1.8.2:0/0::gentoo, installed) pulled in by =dev-python/numpy-1.8*[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] required by (sci-mathematics/sage-6.7:0/0::sage-on-gentoo, installed) ^ ^^^^ dev-python/sphinx:0 (dev-python/sphinx-1.3.1:0/0::gentoo, ebuild scheduled for merge) pulled in by >=dev-python/sphinx-1.3.1[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,python_targets_pypy(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-),-python_single_target_pypy(-)] required by (dev-python/pyxattr-0.5.5:0/0::gentoo, ebuild scheduled for merge) ^^ ^^^^^ (dev-python/sphinx-1.2.2:0/0::sage-on-gentoo, installed) pulled in by ~dev-python/sphinx-1.2.2[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] required by (sci-mathematics/sage-doc-6.7:0/0::sage-on-gentoo, installed) ^ ^^^^^ sage-6.7 and sage-doc-6.7 is intalled. But I can live with sage-doc-bin without any problems.
Sage-doc-bin will take care of sphinx, I am working on the matplotlib problem that is blocking numpy 1.9.
Dropped a massive patch to support MPL 1.4 in sage 6.7 and 9999. Support for MPL 1.4 means we can also use numpy 1.9. So mask sage-doc to force the use of sage-doc-bin, sync the overlay and try to build.
(In reply to Francois Bissey from comment #9) > Dropped a massive patch to support MPL 1.4 in sage 6.7 and 9999. Support for > MPL 1.4 means we can also use numpy 1.9. So mask sage-doc to force the use > of sage-doc-bin, sync the overlay and try to build. Thank you Francois for your work. I tried to follow your hints, but it still does not work. I masked sage-doc: root@lynx:/root(86)# grep sage-doc /etc/portage/package.mask sci-mathematics/sage-doc I synced all overlays and tried to emerge sage, which failed with: root@lynx:/usr/share/applications/Rlogin/TECNETAIR(83)# emerge -pvD sage These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild UD ] dev-python/sphinx-1.2.2::sage-on-gentoo [1.3.1::gentoo] USE="doc latex {-test}" PYTHON_TARGETS="python2_7 python3_3 -pypy -python3_4" 0 KiB [ebuild UD ] sci-mathematics/maxima-5.35.1-r2::sage-on-gentoo [5.36.1::gentoo] USE="X ecls emacs latex nls sbcl tk unicode -clisp -clozurecl (-cmucl) -gcl -xemacs" LINGUAS="-es -pt -pt_BR" 0 KiB [ebuild N ] sci-mathematics/sage-6.7-r1::sage-on-gentoo USE="latex testsuite -arb -bliss -debug -modular_decomposition" PYTHON_TARGETS="python2_7" 0 KiB [ebuild N #] sci-mathematics/sage-doc-6.7::sage-on-gentoo USE="html" LINGUAS="de en fr ru -ca -hu -it -pt -tr" PYTHON_TARGETS="python2_7" 0 KiB Total: 4 packages (2 downgrades, 2 new), Size of downloads: 0 KiB The following mask changes are necessary to proceed: (see "package.unmask" in the portage(5) man page for more details) # required by sci-mathematics/sage-6.7-r1::sage-on-gentoo # required by sage (argument) # /etc/portage/package.mask: ... #>=sci-mathematics/pari-2.2 =sci-mathematics/sage-doc-6.7
This is pulled by the testsuite flag. I think it should be ok to use sage-doc-bin there as well, I will fix that in a few hours.
Note that I have discovered a few issues with sage using numpy 1.9. It mostly works but a few things in a few corner are broken.
OK I pushed a potential fix, can you try again?
(In reply to Francois Bissey from comment #13) > OK I pushed a potential fix, can you try again? Thank you Francois, for your work. At one system I could now install sage-6.7 with: sphinx-1.3.1 numpy-1.9.2 matplotlib-1.4.3 At the second system 'emerge -uvDN world' fails with: ... Cythonizing sage/categories/map.pyx Cythonizing sage/categories/morphism.pyx Cythonizing sage/coding/binary_code.pyx Error compiling Cython file: ------------------------------------------------------------ ... # as published by the Free Software Foundation; either version 2 of # the License, or (at your option) any later version. # http://www.gnu.org/licenses/ #***************************************************************************** from cpython.object cimport Py_TYPE, PyTypeObject ^ ------------------------------------------------------------ ./sage/ext/stdsage.pxd:13:0: 'Py_TYPE.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... # as published by the Free Software Foundation; either version 2 of # the License, or (at your option) any later version. ... ------------------------------------------------------------ ./sage/ext/stdsage.pxd:31:5: Cannot convert 'PyTypeObject *' to Python object Error compiling Cython file: ------------------------------------------------------------ ... cdef inline bint HAS_DICTIONARY(obj): """ Test whether the given object has a Python dictionary. """ return Py_TYPE(obj).tp_dictoffset != 0 ^ ------------------------------------------------------------ ./sage/ext/stdsage.pxd:38:18: undeclared name not builtin: Py_TYPE Traceback (most recent call last): File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 1003, in cythonize_one_helper return cythonize_one(*m[1:]) File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 985, in cythonize_one raise CompileError(None, pyx_file) CompileError: sage/categories/map.pyx Cythonizing sage/combinat/combinat_cython.pyx Traceback (most recent call last): File "setup.py", line 565, in <module> run_cythonize() File "setup.py", line 557, in run_cythonize 'profile': profile, File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 856, in cythonize result.get(99999) # seconds File "/usr/lib64/python2.7/multiprocessing/pool.py", line 567, in get raise self._value Cython.Compiler.Errors.CompileError: sage/categories/map.pyx * ERROR: sci-mathematics/sage-6.7-r1::sage-on-gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 93: Called src_compile * environment, line 4669: Called distutils-r1_src_compile * environment, line 1627: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile' * environment, line 624: Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 4073: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 3131: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 3129: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 1123: Called distutils-r1_run_phase 'distutils-r1_python_compile' * environment, line 1618: Called distutils-r1_python_compile * environment, line 1503: Called esetup.py 'build'
What is your version of cython?
BTW., ' MAKEOPTS=-j1 emerge -v1 sage' fails now also on the system , where it works three days again. Maybe it does not work with 'cython-0.22.1'. root@lynx:/root(19)# emerge --info '=sci-mathematics/sage-6.7-r1::sage-on-gentoo' Portage 2.2.20 (python 2.7.10-final-0, default/linux/amd64/13.0/desktop, gcc-4.9.2, glibc-2.20-r2, 4.1.0 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.1.0-x86_64-Intel-R-_Core-TM-_i7-3630QM_CPU_@_2.40GHz-with-gentoo-2.2 KiB Mem: 7860752 total, 4131372 free KiB Swap: 12582908 total, 12582908 free Timestamp of repository gentoo: Tue, 23 Jun 2015 07:00:01 +0000 sh bash 4.3_p39 ld GNU ld (Gentoo 2.25 p1.2) 2.25 distcc[23135] (dcc_trace_version) distcc 3.2rc1 x86_64-pc-linux-gnu; built Feb 28 2015 11:00:31 [disabled] app-shells/bash: 4.3_p39::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2-r1::gentoo dev-lang/python: 2.7.10::gentoo, 3.3.5-r1::gentoo, 3.4.3::gentoo dev-util/cmake: 3.2.3::gentoo dev-util/pkgconfig: 0.28-r3::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.17::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r1::gentoo sys-devel/automake: 1.9.6-r4::gentoo, 1.10.3-r1::gentoo, 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25-r1::gentoo sys-devel/gcc: 4.9.2::gentoo sys-devel/gcc-config: 1.8::gentoo sys-devel/libtool: 2.4.6-r1::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.0::gentoo (virtual/os-headers) sys-libs/glibc: 2.20-r2::gentoo Repositories: gentoo location: /usr/portage_lynx sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sage-on-gentoo location: /var/lib/layman/sage-on-gentoo masters: gentoo priority: 0 science location: /var/lib/layman/science masters: gentoo priority: 1 sunrise location: /var/lib/layman/sunrise masters: gentoo priority: 2 tlp location: /var/lib/layman/tlp masters: gentoo priority: 3 x11 location: /var/lib/layman/x11 masters: gentoo priority: 4 ago location: /var/lib/layman/ago masters: gentoo priority: 5 local location: /usr/local/portage masters: gentoo priority: 6 g-cpan location: /var/lib/cpan masters: gentoo priority: 7 g-octave location: /var/lib/g-octave masters: gentoo priority: 8 Installed sets: @system ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j9" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 amr ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples excel exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx ftp fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hdaps hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java java6 jbig jit john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libgda libkms libnotify libsamplerate lirc live lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 qt5 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 sse3 sse4 sse4_1 sse4_2 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l v4l2 vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx vtk wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog sensors thermal" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="nss" DVB_CARDS="usb-wt220u" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev synaptics void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd SureElec" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= sci-mathematics/sage-6.7-r1::sage-on-gentoo was built with the following: USE="latex testsuite -arb -bliss -debug -modular_decomposition" ABI_X86="64" PYTHON_TARGETS="python2_7" root@lynx:/root(20)# emerge -pqv '=sci-mathematics/sage-6.7-r1::sage-on-gentoo' [ebuild R ] sci-mathematics/sage-6.7-r1 USE="latex testsuite -arb -bliss -debug -modular_decomposition" PYTHON_TARGETS="python2_7"
Created attachment 405580 [details] build.log
I think that is the case. Sage developers (Ok just Jeroen Demeyer) have heavily patched cython during the development of sage 6.6 and 6.7. All the included patches have been included upstream but while some have made it into 0.22.1 it looks like most will only land in 0.23. Masking cython-0.22.1 is the safest course of action at this stage.
After masking >dev-python/cython-0.22-r3, reemerging cython-0.22-r3 'MAKEOPTS=-j1 emerge -uvDN --backtrack=30 sage' worked. I am only afraid that there will be soon the next conflict due to the masking.
I know what you mean. cython 0.22.1 is a minor revision the worst thing that can happen to me is it being stabilized which would mean I would have to lock the dependencies until 0.23 comes out. Depending on how long it takes for 0.23 to come out I may have to provide a patched 0.22.1 in sage-on-gentoo.
I still tried install sage on a third system, beside of the expected downgrade of maxima, 'emerge -uvDN sage' want also to downgrade sci-mathematics/singular and dev-libs/ntl. And these downgrades seems to be huge downgrades: root@condor:/root(47)# emerge -pvuDN sage These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild r U ] dev-lang/ocaml-4.02.2:0/4.02.2::gentoo [4.02.1:0/4.02.1::gentoo] USE="X emacs latex ncurses ocamlopt -xemacs" 2,014 KiB [ebuild UD ] dev-libs/ntl-6.2.1::sage-on-gentoo [9.0.2::gentoo] USE="doc -static-libs {-test}" 0 KiB [ebuild UD ] sci-mathematics/singular-3.1.7_p1-r2::sage-on-gentoo [4.0.2::gentoo] USE="boost doc emacs examples python readline -flint% {-test%}" PYTHON_TARGETS="python2_7%*" 0 KiB [ebuild U ] dev-python/psycopg-2.6.1:2::gentoo [2.6:2::gentoo] USE="doc examples -debug" PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 KiB [ebuild N ] sci-mathematics/sage-doc-bin-6.7::sage-on-gentoo USE="html" LINGUAS="de en fr ru -ca -hu -it -pt -tr" 0 KiB [ebuild rR ] sys-devel/llvm-3.6.1:0/3.6::gentoo USE="clang doc gold libffi ncurses ocaml python static-analyzer xml -debug -libedit -multitarget {-test}" ABI_X86="32 (64) (-x32)" PYTHON_TARGETS="python2_7 -pypy" VIDEO_CARDS="-radeon" 0 KiB [ebuild UD ] sci-mathematics/maxima-5.35.1-r2::sage-on-gentoo [5.36.1::gentoo] USE="X ecls emacs latex nls sbcl tk unicode -clisp -clozurecl (-cmucl) -gcl -xemacs" LINGUAS="-es -pt -pt_BR" 0 KiB [ebuild N ] sci-mathematics/sage-6.7-r1::sage-on-gentoo USE="latex testsuite -arb -bliss -debug -modular_decomposition" PYTHON_TARGETS="python2_7" 0 KiB
They are expected. ntl had a recent growth spurt but I checked with tomka and sage currently cannot move from these two specific package versions. On the plus side there are very few dependencies for these two besides sage, fewer still have moved to those newer versions.
