There is really no good way to deal with this besides proper OS packages or rebuild sage from source when you do nontrivial system upgrades.
On Sat, Nov 26, 2016 at 11:27 AM Francois Bissey < francois.bis...@canterbury.ac.nz> wrote: > libvpx has stung before. When we upgraded linbox I made sure > it wouldn’t be linked to openCL for sage binaries but made no > provisions for regular builds. > In a way with Gentoo or arch (and SuSE tumbleweed and…) we are > in a unusual position compared to standard distro. Most binary > distros with releases that are not rolling will stick with > a version of the library unless forced to change. > So for them the problem is only when they upgrade to a new release. > For rolling release distro the problem is whenever. > > sage itself cannot really deal very well with the problem, especially > when it relies on some components of the base system. Unless you > go all gentoo-prefix style (and even then I am sure sometimes the base > system creeps in). > > François > > > On 27/11/2016, at 08:11, Steven Trogdon <steven.trog...@gmail.com> > wrote: > > > > So how is this sort of thing to be dealt with, in general, under Sage? > For example looking at files just under local/lib I see the following libs > that are linked to system libs which presumably would require a rebuild if > system libs were changed > > > > local/lib/libgd.so > > libvpx.so.3 => /usr/lib64/libvpx.so.3 (0x00007f7e40c3b000) > > libtiff.so.5 => /usr/lib64/libtiff.so.5 (0x00007f7e406cb000) > > libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00007f7e3fc95000) > > local/lib/libzmq.so > > libsodium.so.18 => /usr/lib64/libsodium.so.18 > (0x00007f3584ad9000) > > local/lib/liblinbox.so > > libOpenCL.so.1 => /usr/lib64/libOpenCL.so.1 (0x00007fd68e402000) > > local/lib/liblinboxsage.so > > libOpenCL.so.1 => /usr/lib64/libOpenCL.so.1 (0x00007f38cfceb000) > > > > There are lots more of these if local/lib/python2.7 and local/lib/R were > searched. > > > > On Saturday, November 26, 2016 at 12:54:05 AM UTC-6, François wrote: > > After inspection there is a configure switch. It is always on > > in Gentoo. We could configure zeromq in sage to never depend > > on it. Ticket time? > > > > François > > > > > On 26/11/2016, at 19:49, Francois Bissey <francoi...@canterbury.ac.nz> > wrote: > > > > > > I am guessing it is picked up automagically by zeromq. > > > Sage doesn’t provide it, it was detected from your system. > > > I’ll look into it. > > > > > > François > > > > > >> On 26/11/2016, at 19:46, Steven Trogdon <steven....@gmail.com> wrote: > > >> > > >> OK, after looking at the logs beta3 was built on 11/17. libsodium was > upgraded from libsodium.so.13 to libsodium.so.18 on 11/18. So there has > been a system update between the build of beta3 and beta4. The question is > 'is libsodium.so.18' really needed? > > >> > > >> On Saturday, November 26, 2016 at 12:31:04 AM UTC-6, François wrote: > > >> libsodium is not a sage package so it comes from Gentoo. > > >> libsodium.so.13 was provided by libsodium-1.0.2. > > >> All the other libsodium available in Gentoo provide > > >> libsodium.so.18. > > >> Would you have by chance been doing an upgrade rather > > >> than a build of sage from scratch - and upgraded > > >> libsodium just before the upgrade? > > >> > > >> François > > >> > > >>> On 26/11/2016, at 18:46, Steven Trogdon <steven....@gmail.com> > wrote: > > >>> > > >>> Fails here on Gentoo when building the docs: > > >>> > > >>> [dochtml] Traceback (most recent call last): > > >>> [dochtml] File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python/runpy.py", line > 162, in _run_module_as_main > > >>> [dochtml] "__main__", fname, loader, pkg_name) > > >>> [dochtml] File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python/runpy.py", line > 72, in _run_code > > >>> [dochtml] exec code in run_globals > > >>> [repl ] File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/zmq/__init__.py", > line 34, in <module> > > >>> [repl ] from zmq import backend > > >>> [repl ] File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/zmq/backend/__init__.py", > line 40, in <module> > > >>> [repl ] reraise(*exc_info) > > >>> [repl ] File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/zmq/backend/__init__.py", > line 27, in <module> > > >>> [repl ] _ns = select_backend(first) > > >>> [repl ] File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/zmq/backend/select.py", > line 26, in select_backend > > >>> [repl ] mod = __import__(name, fromlist=public_api) > > >>> [repl ] File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/zmq/backend/cython/__init__.py", > line 6, in <module> > > >>> [repl ] from . import (constants, error, message, context, > > >>> [repl ] ImportError: libsodium.so.13: cannot open shared object > file: No such file or directory > > >>> [polynomia] reading sources... [ 9%] sage/rings/fraction_field_FpT > > >>> Error building the documentation. > > >>> Traceback (most recent call last): > > >>> File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python/runpy.py", line > 162, in _run_module_as_main > > >>> "__main__", fname, loader, pkg_name) > > >>> File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python/runpy.py", line > 72, in _run_code > > >>> exec code in run_globals > > >>> File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py", > line 2, in <module> > > >>> main() > > >>> File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", > line 1667, in main > > >>> builder() > > >>> File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", > line 316, in _wrapper > > >>> getattr(get_builder(document), 'inventory')(*args, **kwds) > > >>> File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", > line 510, in _wrapper > > >>> build_many(build_ref_doc, L) > > >>> File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", > line 252, in build_many > > >>> ret = x.get(99999) > > >>> File > "/64bitdev/storage/sage-git_develop/sage/local/lib/python/multiprocessing/pool.py", > line 567, in get > > >>> raise self._value > > >>> OSError: [repl ] > /64bitdev/storage/sage-git_develop/sage/src/doc/en/reference/repl/sage/repl/ipython_kernel/kernel.rst:11: > WARNING: autodoc: failed to import module > u'sage.repl.ipython_kernel.kernel'; the following exception was raised: > > >>> > > >>> I have libsodium.so.18 install which is current. I don't know which > libsodium I had installed when beta3 was built, but no problem there. Is > libsodium.so.18 really needed? > > >>> > > >>> -- > > >>> You received this message because you are subscribed to the Google > Groups "sage-release" group. > > >>> To unsubscribe from this group and stop receiving emails from it, > send an email to sage-release...@googlegroups.com. > > >>> To post to this group, send email to sage-r...@googlegroups.com. > > >>> Visit this group at https://groups.google.com/group/sage-release. > > >>> For more options, visit https://groups.google.com/d/optout. > > >> > > >> > > >> -- > > >> You received this message because you are subscribed to the Google > Groups "sage-release" group. > > >> To unsubscribe from this group and stop receiving emails from it, > send an email to sage-release...@googlegroups.com. > > >> To post to this group, send email to sage-r...@googlegroups.com. > > >> Visit this group at https://groups.google.com/group/sage-release. > > >> For more options, visit https://groups.google.com/d/optout. > > > > > > -- > > > You received this message because you are subscribed to the Google > Groups "sage-release" group. > > > To unsubscribe from this group and stop receiving emails from it, send > an email to sage-release...@googlegroups.com. > > > To post to this group, send email to sage-r...@googlegroups.com. > > > Visit this group at https://groups.google.com/group/sage-release. > > > For more options, visit https://groups.google.com/d/optout. > > > > > > -- > > You received this message because you are subscribed to the Google > Groups "sage-release" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to sage-release+unsubscr...@googlegroups.com. > > To post to this group, send email to sage-release@googlegroups.com. > > Visit this group at https://groups.google.com/group/sage-release. > > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-release+unsubscr...@googlegroups.com. > To post to this group, send email to sage-release@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-release. > For more options, visit https://groups.google.com/d/optout. > -- Sent from my massive iPhone 6 plus. -- You received this message because you are subscribed to the Google Groups "sage-release" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-release+unsubscr...@googlegroups.com. To post to this group, send email to sage-release@googlegroups.com. Visit this group at https://groups.google.com/group/sage-release. For more options, visit https://groups.google.com/d/optout.
