[sage-devel] rpy2 fails to build when adding openssl to MacOS prebuilt sage 9 binary

[Zachary Scherr]

Hi,

   I recently tried adding openssl to the app.dmg prebuilt sage 9 binary 
via: sage -i openssl && sage -f python3.  During the rebuild, rpy2 failed 
with the message:

[rpy2-2.8.2.p1] dyld: lazy symbol binding failed: Symbol not found: 
_timespec_get
[rpy2-2.8.2.p1]   Referenced from: 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/lib/libR.dylib
[rpy2-2.8.2.p1]   Expected in: /usr/lib/libSystem.B.dylib
[rpy2-2.8.2.p1]
[rpy2-2.8.2.p1] dyld: Symbol not found: _timespec_get
[rpy2-2.8.2.p1]   Referenced from: 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/lib/libR.dylib
[rpy2-2.8.2.p1]   Expected in: /usr/lib/libSystem.B.dylib

   From Googling, it appears that the problem might be tied to changes made 
by Xcode 11.  I will try to downgrade to Xcode 10 to see if this fixes the 
problem.  For what it's worth I am currently able to build sage from 
scratch, it's just that rebuilding is a problem.

Thanks,
Zach

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Found local metadata for rpy2-2.8.2.p1
Attempting to download package rpy2-2.8.2.tar.gz from mirrors
http://mirrors.mit.edu/sage/spkg/upstream/rpy2/rpy2-2.8.2.tar.gz
[..]
rpy2-2.8.2.p1

Setting up build directory for rpy2-2.8.2.p1
Finished extraction
Applying patches from ../patches...
Applying ../patches/cygwin.patch
patching file rpy/rinterface/na_values.c
patching file rpy/rinterface/_rinterface.c
Hunk #1 succeeded at 1156 (offset -6 lines).
Hunk #2 succeeded at 3750 (offset 1 line).
Hunk #3 succeeded at 3760 (offset 1 line).
Hunk #4 succeeded at 3770 (offset 1 line).
Hunk #5 succeeded at 3780 (offset 1 line).
patching file setup.py
Hunk #1 succeeded at 200 (offset 40 lines).

Host system:
Darwin Zacharys-MBP.fios-router.home 18.7.0 Darwin Kernel Version 18.7.0: Sun 
Dec  1 18:59:03 PST 2019; root:xnu-4903.278.19~1/RELEASE_X86_64 x86_64

C compiler: gcc
C compiler version:
Configured with: --prefix=/Library/Developer/CommandLineTools/usr 
--with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Uninstalling existing 'rpy2'
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/__init__.cpython-37.pyc'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_dplyr.cpython-37.pyc'
 not found
Warning: Directory 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_ggplot2.cpython-37.pyc'
 not found
Warning: Directory 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_grdevices.cpython-37.pyc'
 not found
Warning: Directory 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/interactive/tests/__pycache__/__init__.cpython-37.pyc'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/ipython/tests/__pycache__/__init__.cpython-37.pyc'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/ipython/tests/__pycache__/test_rmagic.cpython-37.pyc'
 not found
Warning: Directory 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/ipython/tests/__pycache__'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/rinterface/tests/__pycache__/__init__.cpython-37.pyc'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-pa

[sage-devel] Re: drop python2 compatibility in 9.1 ?

[Volker Braun]

* I think its not too difficult to write code that is Python 2.7 + 3.x (for 
high enough x) compatible, so its not a super pressing issue
* We do have a Python 2 buildbot to test for regressions
* For semver reasons we should drop Python 2.7 support in Sage 10, not 9.1

Having said that, I'm fine with an accelerated Sage 9 -> Sage 10 schedule, 
maybe a month or two instead of the usual 3-4. Though first we should take 
the opportunity and see if there are any outstanding Python 3 bugs now that 
we have more data. For example it would be nice if a build with 
SAGE_DEBUG=yes would pass tests. There are a few more regressions, e.g. 
#28817


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[sage-devel] Porting .sage files to sage-9.0

[David Roe]

I had a recent discussion asking if there are any good tools for porting
Sage code to Python 3.  Given the recent discussion
 about how
long we support Python 2, it seems like one concrete step we can take to
help users is to provide some documentation for doing so.

The first step would seem to be to update our FAQ

to
reflect the current status (and probably the outcome of the discussion
about how long we support Python 2), with a pointer to the relevant
 wiki
 pages
.  But I don't see any discussion
on those pages about using any of the tools for porting from Python 2 to
Python 3 on .sage files.  Has anyone tried this yet?  Any
successes/failures?
David

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[sage-devel] Re: Removing reverse graph from CGraph

[David Coudert]

I'm in favor of this change. The code is faster and slightly easier to 
understand.

Extra opinions are more than welcome.
David.

Le mardi 7 janvier 2020 22:42:45 UTC+1, Jonathan Kliem a écrit :
>
> Dear all,
>
> currently the sparse graph backend keeps a reversed copy of the graph.
>
> However, the SparseGraph itself does not have access to it and thus the 
> reversed structure should be moved there for obvious optimizations. See 
> #28904 .
>
> As the sparse graph backend is the only backend actually using the 
> reversed structure, it would make sense to remove this.
>
> However, it is very well possible that people use the unsafe methods of 
> SparseGraph directly and code will break.
> E.g. in graphs/trees.py the undirected trees are generated by manually 
> adding an arc in each direction.
>
> I think, if we remove the reversed graph attribute in CGraph altogether, 
> people are more likely to catch on that something changed.
> But in an undirected graph it can very well happen that they add two edges 
> instead of one (as they used to add one arc for each direction).
>
> Any thoughts?
>
> Jonathan
>

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Re: [sage-devel] Adopting orphaned math packages

[E. Madison Bray]

On Thu, Jan 9, 2020 at 4:28 AM Michael Orlitzky  wrote:
>
> On 1/6/20 10:35 AM, E. Madison Bray wrote:
> >
> > Sorry for the delay; I went ahead and created an empty project under
> > our organization and added (I assume) you as a maintainer, so have at
> > it: https://gitlab.com/sagemath/symmetrica
> >
>
> Thanks, I've gotten it to a point where it's usable. Most sage and
> distro patches have been applied (see the issue list for some hand
> wringing), and there's now a real build system thanks mainly to the
> Debian maintainer.
>
> Please give it a try and see what I broke.

Great, I'll give it a try.  It's nice they were able to help you add a
proper autoconf-based build system.  I'm going to test it out on
Cygwin.

Maybe said Debian maintainer can help me out on my automake rework of
zn_poly's build system:
https://gitlab.com/sagemath/zn_poly/tree/autotooling  I started
working on it last year and it basically works for building the
library.  But I ran into some complications, mainly related to the
fact that it reuses source files in different combinations from
different directories to build different targets, in a way that is
normally incompatible with automake (I think I probably just need to
reorganize the sources a bit but I was trying to see how far I could
get without moving any files around; alas maybe that's just what needs
to be done).

I'll also see if I can add a .gitlab-ci.yml for symmetrica.

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