[sage-devel] Re: Making Sage-7.1 Fails

[Antonio Rojas]

Adetokunbo Arogbonlo wrote:

> Cleaning out old PolyBoRi and BRiAl installations
>  patching file Makefile.am
>  patching file Makefile.in
>  patching file groebner/src/Makefile.am
>  patching file groebner/src/Makefile.in
>  checking for a BSD-compatible install... /usr/bin/install -c

The patch cygwin-gnucpp.patch is not being applied... did you remove it from 
the source?

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[sage-devel] Re: Making Sage-7.1 Fails

[Antonio Rojas]

Antonio Rojas wrote:

> Adetokunbo Arogbonlo wrote:
> 
>> Cleaning out old PolyBoRi and BRiAl installations
>>  patching file Makefile.am
>>  patching file Makefile.in
>>  patching file groebner/src/Makefile.am
>>  patching file groebner/src/Makefile.in
>>  checking for a BSD-compatible install... /usr/bin/install -c
> 
> The patch cygwin-gnucpp.patch is not being applied... did you remove it
> from the source?
> 

Sorry, I just saw that the patch is not in 7.1. This should be fixed in 7.2 
with the aforementioned patch.

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[sage-devel] Re: notebook does not work

[Antonio Rojas]

Dima Pasechnik wrote:

> Is your Sage built from source, or you downloaded a binary installation?
> 
> Anyway, I see what happens. For some strange reason it picks up wrong
> Twisted, the one for Python 3.
> You can see it from the log below, and the error message is the one you
> get by trying to use Python 2 style print statements in Python 3.
> How could this have happened is a mystery to me.
> 
> Could you try (re)installing Sage's Twisted package, by running
> 
> sage -i twisted
> 
> and see if this helps?

>From the paths it looks like they're using distro packages, so sage -i won't 
work.
Have you (or Antergos) messed up with the python2-twisted package files? Do 
you have a custom twisted installation?
Please post the output of "cat $(which twistd)"


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[sage-devel] Re: Re: notebook does not work

[Antonio Rojas]

Sándor Czirbusz wrote:

> This is the answer
> 
> # Copyright (c) Twisted Matrix Laboratories.
> # See LICENSE for details.
> import os, sys
> 
> try:
> import _preamble
> except ImportError:
> try:
> sys.exc_clear()
> except AttributeError:
> # exc_clear() (and the requirement for it) has been removed from
> # Py3
> pass
> 
> sys.path.insert(0, os.path.abspath(os.getcwd()))
> 
> from twisted.scripts.twistd import run
> run()

Did you cut off the first line? (that's the important one)

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[sage-devel] Re: Re: Re: notebook does not work

[Antonio Rojas]

Sándor Czirbusz wrote:

> Ah, sorry
> #!/usr/bin/python2
> 
> 

That looks OK. Are you sure you don't have any other 'twistd' executable 
lying around on your system?

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[sage-devel] networkx BipartiteGraph

[Antonio Rojas]

Hi all,
 In Arch we have upgraded networkx to version 2. This comes with major 
API changes that affect Sage's interface, and I'm currently trying to fix 
these issues. I'm struggling with a particular issue with bipartite 
graphs. In pure ipython, this code gives:

In [1]: import networkx
In [2]: A=networkx.complete_bipartite_graph(2,3)
In [3]: list(A.edges())
Out[3]: [(0, 2), (0, 3), (0, 4), (1, 2), (1, 3), (1, 4)]

The exact same code in Sage gives:

sage: import networkx
sage: A=networkx.complete_bipartite_graph(2,3)
sage: list(A.edges())
[(0, 0), (0, 1), (0, 2), (1, 1), (1, 2)]

As you can see, Sage has shifted the second set of vertices to start at 0 
instead of 2, so of course this is not a bipartite graph anymore. This 
seems strange since there is no Sage code involved in these commands at 
first sight.
 Can someone point me to the Sage code that modifies networkx's output so 
I can look into it?

Thanks.

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[sage-devel] Re: networkx BipartiteGraph

[Antonio Rojas]

El Thu, 14 Dec 2017 11:09:17 +, Vincent Delecroix escribió:

> What about
> 
> sage: A = networkx.complete_bipartite_graph(2r, 3r)

That works correctly:

sage: A=networkx.complete_bipartite_graph(2r,3r)
sage: list(A.edges())
[(0, 2), (0, 3), (0, 4), (1, 2), (1, 3), (1, 4)]

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[sage-devel] Re: executable referenced in sagemath jupyter kernel

[Antonio Rojas]

El jueves, 17 de mayo de 2018, 6:46:11 (UTC+2), Nils Bruin escribió:
>
>
> Are there good reasons to refer to .../local/bin/sage rather than the 
> .../sage script? If not, then it might be more flexible to change it.
>
>
This would break distribution packages, where SAGE_LOCAL is generally set 
to /usr and SAGE_ROOT/sage doesn't exist. In general, references to 
SAGE_ROOT within the sage python library should be avoided as they cause 
issues when packaging.

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Re: [sage-devel] Re: executable referenced in sagemath jupyter kernel

[Antonio Rojas]

El sábado, 19 de mayo de 2018, 8:30:12 (UTC+2), Nils Bruin escribió:
>
> so, am I right in concluding that  distribution packages patch this anyway 
> and that we can therefore safely put $SAGE_ROOT/sage in kernel.json by 
> default?
>

No - this does "the right thing" out of the box currently. On Arch we are 
not patching it, we set SAGE_LOCAL=/usr and kernel.json points to 
/usr/bin/sage, as it should. 

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Re: [sage-devel] Re: executable referenced in sagemath jupyter kernel

[Antonio Rojas]

>
> OK, so how do we see whether the  $SAGE_ROOT/sage script needs to be used? 
> Can we just see if $SAGE_ROOT/sage is present and executable and if not, 
> use $SAGE_LOCAL/bin/sage? The remark by François seems quite to the point: 
> if sage is installed system-wide as a package of python2, then invoking 
> python via $SAGE_LOCAL/bin/sage --python is unnecessary overkill. Then just 
> calling python2 should be sufficient anyway.
>
> The thing is: the kernel.json does *not* do the right thing out of the box 
> if you present it to a system jupyter and$SAGE_LOCAL/bin/sage can't run 
> without help. It would be nice if we can get our jupyter kernel 
> installation to do the right thing in both cases.
>
>
IMO the right way to fix this would be to make $SAGE_LOCAL/bin/sage not 
complain if $SAGE_ROOT is not set (when used to simply launch sage, it 
would still be needed for build or install operations). But not sure if 
that would currently be possible without major changes.  

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Re: [sage-devel] Re: executable referenced in sagemath jupyter kernel

[Antonio Rojas]

ATM we're setting it to /usr (arbitrary choice) simply because at some 
point Sage refused to start if it wan't set. But setting it to anything 
else doesn't make any difference.

El miércoles, 23 de mayo de 2018, 0:02:24 (UTC+2), Nils Bruin escribió:
>
> On Saturday, May 19, 2018 at 12:08:22 AM UTC-7, Antonio Rojas wrote:
>>
>>
>>
>>> OK, so how do we see whether the  $SAGE_ROOT/sage script needs to be 
>>> used? Can we just see if $SAGE_ROOT/sage is present and executable and if 
>>> not, use $SAGE_LOCAL/bin/sage? The remark by François seems quite to the 
>>> point: if sage is installed system-wide as a package of python2, then 
>>> invoking python via $SAGE_LOCAL/bin/sage --python is unnecessary overkill. 
>>> Then just calling python2 should be sufficient anyway.
>>>
>>> The thing is: the kernel.json does *not* do the right thing out of the 
>>> box if you present it to a system jupyter and$SAGE_LOCAL/bin/sage can't run 
>>> without help. It would be nice if we can get our jupyter kernel 
>>> installation to do the right thing in both cases.
>>>
>>>
>> IMO the right way to fix this would be to make $SAGE_LOCAL/bin/sage not 
>> complain if $SAGE_ROOT is not set (when used to simply launch sage, it 
>> would still be needed for build or install operations). But not sure if 
>> that would currently be possible without major changes.  
>>
>
> So what value does SAGE_ROOT have in the Arch distribution? And what value 
> does it have in sage-on-gentoo? And where does it get its value? The 
> vanilla $SAGE_LOCAL/bin/sage-env only figures out a value if "." or "../.." 
> are good choices (and tests that by the presence of a "sage" file and a 
> "build" directory, so it really ends up depending on its relative location 
> to the "$SAGE_ROOT/sage" script again).
>

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[sage-devel] Re: Sage fails to build on Arch linux, possible recurrence of an old bug

[Antonio Rojas]

Replying to the repo package issues:


El domingo, 8 de julio de 2018, 11:10:01 (UTC+2), Amit Wolecki escribió:
>
> As for the packaged installation problem, two examples are:
> 1. sage --testall fails to start, returning:
>
>   File "/usr/lib/python2.7/site-packages/sage/doctest/control.py", line 
> 696, in add_files
> sagenb_loc = working_set.find(Requirement.parse('sagenb')).location
> AttributeError: 'NoneType' object has no attribute 'location'
>
> Install the sage-notebook package. Note that there are many other (expected) 
> test failures due to using newer versions of libraries and some tests relying 
> on specific installation paths. Most of those failures are caused by output 
> format changes and should not affect normal Sage usage, if you find one that 
> does please report it to bugs.archlinux.org

 

> 2. installation of packages fail due to some environment confusion, for 
> example:
> [amit@amit-desk sage-8.2]$ sage -pip install surface_dynamics
>
 
You can't mix and match different installations methods. If you use the 
repository package, then you should also install all optional packages from 
the Arch repositories. Sage-specific installation commands such as 'sage 
-i' and 'sage -pip' will **not** work with the repo provided Sage package 
and will quite possibly break your installation. 

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Re: [sage-devel] Sage fails to build on Arch linux, possible recurrence of an old bug

[Antonio Rojas]

El domingo, 8 de julio de 2018 10:39:34 (CEST), Amit Wolecki escribió:

Replying to the repo package issues:


As for the packaged installation problem, two examples are:
1. sage --testall fails to start, returning:
  File 
"/usr/lib/python2.7/site-packages/sage/doctest/control.py", line 
696, in add_files

sagenb_loc = working_set.find(Requirement.parse('sagenb')).location
AttributeError: 'NoneType' object has no attribute 'location'


Install the sage-notebook package. Note that there are many other 
(expected) test failures due to using newer versions of libraries and some 
tests relying on specific installation paths. Most of those failures are 
caused by output format changes and should not affect normal Sage usage, if 
you find one that does please report it to bugs.archlinux.org


2. installation of packages fail due to some environment 
confusion, for example:
Command "python setup.py egg_info" failed with error code 1 in 
/tmp/pip-install-kf5xxcpj/surface-dynamics/


You can't mix and match different installations methods. If you use the 
repository package, then you should also install all optional packages from 
the Arch repositories. Sage-specific installation commands such as 'sage 
-i' and 'sage -pip' will *not* work with the repo provided Sage package and 
will quite possibly break your installation.


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[sage-devel] Re: Sage fails to build on Arch linux, possible recurrence of an old bug

[Antonio Rojas]

El lunes, 9 de julio de 2018, 21:35:04 (UTC+2), Amit Wolecki escribió:
>
> Thank you all for the useful comments!
> Antonio, I wasn't aware of the somewhat limiting way a repo installation 
> works, this remark made me try to stick to building from source.
>
>>
>>
Actually, scratch that. 'sage -i' will definitely not work as it's tightly 
tied to the upstream Sage directory structure. However, 'sage -pip' should 
simply work by calling the system pip. The reason why it didn't work is 
that our python2 pip command is renamed to pip2 so it doesn't conflict with 
the python3 version. I've now fixed that in 8.2-10 and 'sage -pip' works 
properly with the distro package.
 Note that you should always call it with --user, installing system wide 
packages with pip on Arch is highly discouraged

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Re: [sage-devel] Re: Sage fails to build on Arch linux, possible recurrence of an old bug

[Antonio Rojas]

El martes, 10 de julio de 2018, 14:21:03 (UTC+2), Amit Wolecki escribió:
>
> I see, thanks Antonio for the fix! To make sure I get the big picture - 
> distro package will use system services (e.g. python and especially pip) 
> whereas the built from source installation has it's own compiled python env 
> and is thus independent of the system installed python env. Do I get that 
> right?
>
>
Yes, mostly right. Just note that sage uses a custom PYTHONUSERBASE, so 
packages installed with 'sage -pip --user' will only be available in sage 
and not in the system python. If you want a package to work both in sage 
and in regular python you should use 'pip2 install --user' directly 
instead. 

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[sage-devel] Re: Arch: error building Sage, rpy2 fails

[Antonio Rojas]

El viernes, 17 de agosto de 2018, 17:31:13 (UTC+2), Nicolás Sirolli 
escribió:
>
> Hello,
>
> I'm trying to build Sage 8.4.beta1 (following the develop branch from git) 
> on Arch Linux, and it fails when trying to build the rpy2-2.8.2.p0 package. 
> I'm attaching the corresponding log file.
>
> Please, let me know if any further information can be helpful to solve the 
> issue.
>
>
You need to rebuild R against the latest ICU version. 

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[sage-devel] Re: zn_poly status?

[Antonio Rojas]

El viernes, 7 de septiembre de 2018, 15:53:43 (UTC+2), Erik Bray escribió:
>
> Hi all, 
>
> Does anyone know what that current status is of the upstream zn_poly 
> package?  According to its website 
> http://cims.nyu.edu/~harvey/zn_poly/ it is "no longer maintained", 
> though it has been re-released under a BSD-compatible license. 
>
>
Given that the library has been unmaintained for years, has someone looked 
into whether its functionality can be provided by some other library 
nowadays? 

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[sage-devel] Re: Delaying 8.5 or fast-tracking 8.6?

[Antonio Rojas]

El martes, 18 de diciembre de 2018, 12:50:44 (UTC+1), E. Madison Bray 
escribió:
>
> As pointed out by Samuel last month [1] the transition freeze (i.e. 
> new package versions) for the next major Debian release (buster) is 
> coming up January 12 [2].  This is important for Sage and those 
> working to package Sage for Debian, as it will impact what version of 
> Sage is available in Debian, and by extension big name Debian-based 
> distributions such as Ubuntu and Mint that carry with them probably 
> the majority of users on Linux. 
>
>
Since the GAP 4.10 work is considered done, does it really make that much 
difference whether it is in a stable Sage release or not? Can't Debian 
packagers simply backport the patch to 8.5? (which is what I'm planning to 
do on Arch if it doesn't make it to 8.5) 

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[sage-devel] Where is sage/tests/parallel.pyx?

[Antonio Rojas]

Hi,
 In module_list.py there is reference to a sage/tests/parallel.pyx 
extension, but there is no such file in the sources. This breaks compiling 
the Sage library with cython 0.22, which seems to be stricter than previous 
versions in dealing with missing sources.

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[sage-devel] cached methods in cython

[Antonio Rojas]

Hi,
 Cached methods in cython modules don't work if the cython source is not 
available:

sage: K=GF(5)
sage: K.factored_order()
---
AttributeErrorTraceback (most recent call last)
[...]
AttributeError: 'FiniteField_prime_modn_with_category' object has no 
attribute 'factored_order'

Non-cached methods work correctly:

sage: K.factored_unit_order()
[2^2]

 Is that expected? IOW, does the cython source need to be available at 
runtime? 

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[sage-devel] Re: cached methods in cython

[Antonio Rojas]

Vincent Delecroix wrote:

> Which Sage version are you using? The following code is ok for me on
> sage-6.6.beta0
> 
> sage: K=GF(5)
> sage: K.factored_order()
> 5
> 
> Vincent
> 

Version 6.5. Note the "if the cython source is not available" part, it works 
OK if the .pyx source is installed (we currently package it separately in 
Arch)

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[sage-devel] Re: cached methods in cython

[Antonio Rojas]

Simon King wrote:

> 
> In two experiments with Sage-6.5.beta4, I can not replicate the
> problem.
> 

Hi,
 I tried with a downloaded binary package to make sure it's not caused by 
our packaging, and can still reproduce:

- Remove src/sage/rings/finite_rings/finite_field_base.pyx
- Run:
   sage: K=GF(5)
   sage: K.factored_order() 

doesn't work.



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[sage-devel] Re: Issues with GCC 5.x

[Antonio Rojas]

leif wrote:

>  * Sage library -- modules using Lcalc headers won't build for the
>same reason (build with '-fpermissive' in
>CFLAGS; distutils ignores CXXFLAGS)
> 

sage/libs/coxeter3 also fails:

In file included from /usr/include/coxeter/coxgroup.h:67:0,
 from build/cythonized/sage/libs/coxeter3/coxeter.cpp:363:
/usr/include/coxeter/files.h:115:38: error: redeclaration of ‘template 
void files::printHeckeElt(FILE*, const H&, const schubert::SchubertContext&, 
const 
interface::Interface&, files::OutputTraits&, const Length&)’ may not have 
default arguments [-fpermissive]
const Length& l = undef_length);
  ^


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[sage-devel] Sage 6.7 build failure

[Antonio Rojas]

Hi,
 I'm getting this error when trying to build sage-the-library 6.7 (against 
system NTL), with both GCC 4.9 and GCC 5:

build/cythonized/sage/rings/polynomial/pbori.cpp:1931:3: error: reference to 
'WrappedPtr' is ambiguous
   WrappedPtr _strat;
   ^
In file included from 
build/cythonized/sage/rings/polynomial/pbori.cpp:308:0:
sage/libs/polybori/pb_wrap.h:180:7: note: candidates are: template class WrappedPtr
 class WrappedPtr:
   ^
In file included from /usr/include/NTL/ZZ.h:19:0,
 from 
/build/sagemath/src/sage-01432cf19605c9534a6063d1d66f55d7b96a50d1/src/c_lib/include/ntl_wrap.h:2,
 from build/cythonized/sage/rings/polynomial/pbori.cpp:319:
/usr/include/NTL/tools.h:490:7: note: template class NTL::WrappedPtr
 class WrappedPtr {
   ^

I've bisected and it is caused by this commit:
https://github.com/sagemath/sage/commit/01432cf19605c9534a6063d1d66f55d7b96a50d1

Any idea how to fix this?

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[sage-devel] Re: Sage 6.7 build failure

[Antonio Rojas]

François Bissey wrote:

>>
>> Are you really really certain about the bisection?
>>
>> Which version of Cython (system or with Sage patches?)
>>
> I'll have to add, because I have no such problems in
> sage-on-gentoo, which version of ntl? ntl-8 and 9
> will certainly lead to some failures.
> 
> Francois
> 

Right, it seems the WrappedPtr class was added to NTL/tools.h in NTL 8. So I 
guess I'm on my own for now, but this will be an issue when Sage's version 
of NTL is updated.

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[sage-devel] Re: Sage 6.7 build failure

[Antonio Rojas]

Jeroen Demeyer wrote:

> On 2015-05-18 23:19, Antonio Rojas wrote:
>> I've bisected and it is caused by this commit:
>> 
https://github.com/sagemath/sage/commit/01432cf19605c9534a6063d1d66f55d7b96a50d1
> 
> Are you really really certain about the bisection?
> 
> Which version of Cython (system or with Sage patches?)
> 

Not absolutely certain, but it sounds reasonable to me. This commits adds a 
sage.misc.long import in pbori.pyx which could indirectly pull some NTL 
imports which weren't there before and produces the conflicting class 
definitions.
I'm using cython git master.

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[sage-devel] Re: Build failure on Arch Linux: conway_polynomials fails to build

[Antonio Rojas]

Perl 5.22 throws warnings for unescaped '{', and pari treats warnings as errors 
by default. I'm using this patch for system-wide pari:

https://projects.archlinux.org/svntogit/community.git/tree/trunk/no_warnings_fatal.patch?h=packages/pari-sage

Joshua Hunt wrote:

> Hi,
> 
> Perl is v5.22.0.
> 
> Did you pass any funny flags to make (apart from -j4)?
>>
> 
> Nope, only -j4.
> 
> Can you please try following and send me the output?
>>
> 
>> echo garbage > local/share/pari/pari.desc
>> ./sage -ba
>>
> 
> I get the following:
> 
> Deleting Sage library build artifacts...
>> rm -f c_lib/.sconsign.dblite
>> find c_lib -name '*.os' | xargs rm -f
>> find c_lib -name '*.so' | xargs rm -f
>> find c_lib -name '*.dylib' | xargs rm -f
>> rm -rf build
>> find . -name '*.pyc' | xargs rm -f
>> rm -f sage/libs/pari/auto_*
>> rm -rf sage/ext/interpreters
>> This looks like the first time you are running Sage.
>> Updating various hardcoded paths...
>> (Please wait at most a few minutes.)
>> DO NOT INTERRUPT THIS.
>> Done updating paths.
>> make csage
>> make[1]: Entering directory '/home/joshua/build/sage-6.7/src'
>> cd c_lib && scons -Q install
>> Install file: "include/interrupt.h" as
>> "/home/joshua/build/sage-6.7/local/include/csage/interrupt.h"
>> Install file: "include/ntl_wrap.h" as
>> "/home/joshua/build/sage-6.7/local/include/csage/ntl_wrap.h"
>> gcc -o src/interrupt.os -c -fPIC
>> -I/home/joshua/build/sage-6.7/local/include
>> -I/home/joshua/build/sage-6.7/local/include/python2.7
>> -I/home/joshua/build/sage-6.7/local/include/NTL -Iinclude src/interrupt.c
>> In file included from
>> /home/joshua/build/sage-6.7/local/include/python2.7/Python.h:8:0,
>>  from include/interrupt.h:58,
>>  from src/interrupt.c:43:
>> /home/joshua/build/sage-6.7/local/include/python2.7/pyconfig.h:1182:0:
>> warning: "_POSIX_C_SOURCE" redefined
>>  #define _POSIX_C_SOURCE 200112L
>>  ^
>> In file included from /usr/include/stdio.h:27:0,
>>  from src/interrupt.c:29:
>> /usr/include/features.h:225:0: note: this is the location of the previous
>> definition
>>  # define _POSIX_C_SOURCE 200809L
>>  ^
>> src/interrupt.c: In function ‘print_enhanced_backtrace’:
>> src/interrupt.c:411:5: warning: implicit declaration of function
>> ‘waitpid’
>> [-Wimplicit-function-declaration]
>>  waitpid(pid, NULL, 0);
>>  ^
>> g++ -o src/ntl_wrap.os -c -fPIC
>> -I/home/joshua/build/sage-6.7/local/include
>> -I/home/joshua/build/sage-6.7/local/include/python2.7
>> -I/home/joshua/build/sage-6.7/local/include/NTL -Iinclude
>> src/ntl_wrap.cpp In file included from
>> /home/joshua/build/sage-6.7/local/include/python2.7/Python.h:8:0,
>>  from include/ntl_wrap.h:33,
>>  from src/ntl_wrap.cpp:5:
>> /home/joshua/build/sage-6.7/local/include/python2.7/pyconfig.h:1182:0:
>> warning: "_POSIX_C_SOURCE" redefined
>>  #define _POSIX_C_SOURCE 200112L
>>  ^
>> In file included from
>> /usr/include/c++/5.1.0/x86_64-unknown-linux-gnu/bits/os_defines.h:39:0,
>>  from
>> /usr/include/c++/5.1.0/x86_64-unknown-linux-gnu/bits/c++config.h:482,
>>  from /usr/include/c++/5.1.0/iostream:38,
>>  from src/ntl_wrap.cpp:1:
>> /usr/include/features.h:225:0: note: this is the location of the previous
>> definition
>>  # define _POSIX_C_SOURCE 200809L
>>  ^
>> In file included from
>> /home/joshua/build/sage-6.7/local/include/python2.7/Python.h:8:0,
>>  from include/ntl_wrap.h:33,
>>  from src/ntl_wrap.cpp:5:
>> /home/joshua/build/sage-6.7/local/include/python2.7/pyconfig.h:1204:0:
>> warning: "_XOPEN_SOURCE" redefined
>>  #define _XOPEN_SOURCE 600
>>  ^
>> In file included from
>> /usr/include/c++/5.1.0/x86_64-unknown-linux-gnu/bits/os_defines.h:39:0,
>>  from
>> /usr/include/c++/5.1.0/x86_64-unknown-linux-gnu/bits/c++config.h:482,
>>  from /usr/include/c++/5.1.0/iostream:38,
>>  from src/ntl_wrap.cpp:1:
>> /usr/include/features.h:166:0: note: this is the location of the previous
>> definition
>>  # define _XOPEN_SOURCE 700
>>  ^
>> g++ -o libcsage.so -shared src/interrupt.os src/ntl_wrap.os
>> -L/home/joshua/build/sage-6.7/local/lib
>> -L/home/joshua/build/sage-6.7/local/lib/python2.7/config -lntl -lpari
>> -lgmp -lpython2.7
>> Install file: "libcsage.so" as
>> "/home/joshua/build/sage-6.7/local/lib/libcsage.so"
>> make[1]: Leaving directory '/home/joshua/build/sage-6.7/src'
>> make sage
>> make[1]: Entering directory '/home/joshua/build/sage-6.7/src'
>> python -c "from sage_setup.autogen.pari import rebuild; rebuild()"
>> Traceback (most recent call last):
>>   File "", line 1, in 
>>   File "sage_setup/autogen/pari/__init__.py", line 5, in rebuild
>> G()
>>   File "sage_setup/autogen/pari/generator.py", line 232, in __call__
>> D = read_pari_desc()
>>   File "sage_setup/autogen/pari/parser.py", line 87, in read_pari_desc
>> while lines[n].startswith(" "):
>> In

[sage-devel] Duplicate folders in docs

[Antonio Rojas]

Hi,
 The Sage docs ship 22(!) almost identical copies of the _static dir, the 
only difference being the translations.js files. This adds almost 200MB to 
the Sage installation. Any chance that these could be replaced by symlinks 
on supported platforms?

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[sage-devel] docbuild aborting on warnings

[Antonio Rojas]

Sage doc build currently aborts by default whenever sphinx emits a warning, 
and keeps a hardcoded whitelist of "admissible" warnings that needs to be 
kept up to date. This is very inconvenient for distros building Sage with 
system Sphinx, as every new version introduces new warnings: a fix was just 
committed for Sphinx 4.3 and now it is broken again with 4.4 due to new 
warnings.

This is equivalent to adding "-Werror" in C/C++ build flags of released 
software, which is widely regarded as bad practice, as there is a high 
change of breakage when updating the compiler. Can we please reconsider 
this policy? Fixing the warnings can still be a requirement for accepting 
tickets upgrading Sage's bundled Sphinx, but this would make things less 
painful for distributions.

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[sage-devel] Re: Memory Leak in canonical_label with bliss?

[Antonio Rojas]

El lunes, 16 de mayo de 2022 a las 17:34:14 UTC+2, Ricardo Buring escribió:

> Specifically bliss::AbstractGraph::canonical_form calls 
> bliss::AbstractGraph::search, which sometimes calls 
> bliss::Partition::cr_init without calling bliss::Partition::cr_free, due 
> to a (conditional) early return.
> This leak is fixed in the latest upstream release available from 
> https://users.aalto.fi/~tjunttil/bliss/
>

Updating bliss is tracked at #33010 (and needs help) 

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[sage-devel] Re: System upgrades breaking sage frequently

[Antonio Rojas]

El jueves, 21 de julio de 2022 a las 7:32:59 UTC+2, Nils Bruin escribió:

> In that case, shouldn't sagemath be linking to libflint.so instead of 
> libflint.so.16 then? That's the thing that seems to be available between 
> the different versions. Are they not ABI compatible? (or at least in one 
> direction)?
>

They are not, that's exactly the point of library soversions. The 
soversion, if correctly used, is bumped when a release contains some ABI 
incompatible change that requires a rebuild of consumers. So you can't just 
link to the .so symlink, that would just defeat the point. 

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[sage-devel] Re: PARI/GP upgrade to 2.15

[Antonio Rojas]

Specifically, help is needed from someone who understands genus2reduction 
code in order to solve the (almost) last remaining issue.

El jueves, 15 de septiembre de 2022 a las 20:58:19 UTC+2, vdelecroix 
escribió:

> Dear all,
>
> The PARI/GP team is about to release a new version. I opened a ticket
> for that purpose at https://trac.sagemath.org/ticket/34537. It went
> relatively smoothly with respect to building. However there are a lot
> of doctest failures in a lot of different files that I am not familiar
> about. Some of them involves the fact that they introduced a new LLL
> implementation. The list of failures appears in comment:5 on the
> ticket. Any help on understanding/fixing them would be appreciated.
>
> Best
> Vincent
>

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Re: [sage-devel] VOTE: move Sage development to Github

[Antonio Rojas]

+1 for GitHub

El jueves, 22 de septiembre de 2022 a las 18:43:02 UTC+2, 
martinr...@googlemail.com escribió:

> +1 for GitHub
>
> On Wed, Sep 21 2022, David Roe wrote:
> > Dear Sage developers,
> > Following extensive discussion, both recently
> >  
> (prompted
> > by issues upgrading the trac server) and over
> >  
> the
> >  
> last
> >  
> decade
> > , 
> we
> > are calling a vote on switching Sage development from Trac
> >  to Github . We've
> > created a summary of the pros and cons of each system
> > , a 
> description
> > of the development model to be used on github
> > , 
> and
> > a trac ticket  for coordinating
> > work on the transition. More work will need to be done to carry out the
> > actual transition once voting is complete.
> >
> > The voting will last until noon Eastern time (16:00 UTC) on Wednesday,
> > October 5. Please use this thread only for sending votes, to make it
> > easier to count them afterward; there is a parallel thread where you can
> > make arguments in favor of either system.
> >
> > Finally, I will close with a plea to be involved in this vote and
> > discussion even if you are not a core Sage developer. By definition, core
> > Sage developers have become comfortable with trac, and I think that one 
> of
> > the major arguments in favor of github is that it will help bring in new
> > contributors who are not familiar with Sage's development workfow
> > . Anyone who has
> > ever contributed to the Sage code base or who maintains a Sage user 
> package
> > is welcome to vote.
> > David
>
>
> -- 
>
> _pgp: https://keybase.io/martinralbrecht
> _www: https://malb.io
> _prn: he/him or they/them
>
>

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[sage-devel] Re: sagelib fails to build (9.8.beta5)

[Antonio Rojas]

That's the singular 4.3.1.p3 update. The patch [1] fixes the build, but 
there are some regressions in the asymptotics ring that need looked into. 

[1]  
https://github.com/archlinux/svntogit-community/blob/packages/sagemath/trunk/sagemath-singular-4.3.1.p3.patch

El miércoles, 14 de diciembre de 2022 a las 14:11:05 UTC+1, vdelecroix 
escribió:

> Hello,
>
> Building sage 9.8.beta5 on archlinux went fine up to sagelib which
> complains that setuptools is not there (see attached config and logs).
> Dependency issue?
>
> Best
> Vincent
>

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[sage-devel] Re: why is sagemath 9.8 rc1 still running old maxima build?

[Antonio Rojas]

El martes, 7 de febrero de 2023 a las 9:35:53 UTC+1, Nasser M. Abbasi 
escribió:

Any chance that 9.8 will use the latest version instead?

 
No. Upgrading maxima needs 
work, https://github.com/sagemath/sage/issues/33718 

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[sage-devel] Test failures in R interface

[Antonio Rojas]

Hi,
 I've been seeing these failures for a while when running the doctests. It 
is not reproducible when testing the file standalone, only when testing the 
full sage library, which makes it really hard to debug. Has anybody seen 
this or has any idea how to fix it?

** 
File "/usr/lib/python3.10/site-packages/sage/interfaces/r.py", line 697, in 
sage.interfaces.r.R.__reduce__ 
Failed example: 
   rlr, t = r.__reduce__()  # optional - rpy2 
Exception raised: 
   Traceback (most recent call last): 
 File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 
695, in _run 
   self.compile_and_execute(example, compiler, test.globs) 
 File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 
1093, in compile_and_execute 
   exec(compiled, globs) 
 File "", line 1, in 
 
   rlr, t = r.__reduce__()  # optional - rpy2 
 File "/usr/lib/python3.10/copyreg.py", line 76, in _reduce_ex 
   raise TypeError(f"cannot pickle {cls.__name__!r} object") 
   TypeError: cannot pickle 'LazyImport' object 
** 
File "/usr/lib/python3.10/site-packages/sage/interfaces/r.py", line 698, in 
sage.interfaces.r.R.__reduce__ 
Failed example: 
   rlr(*t)  # optional - rpy2 
Exception raised: 
   Traceback (most recent call last): 
 File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 
695, in _run 
   self.compile_and_execute(example, compiler, test.globs) 
 File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 
1093, in compile_and_execute 
   exec(compiled, globs) 
 File "", line 1, in 
 
   rlr(*t)  # optional - rpy2 
   NameError: name 'rlr' is not defined 
** 
File "/usr/lib/python3.10/site-packages/sage/interfaces/r.py", line 1265, 
in sage.interfaces.r.R.plot 
Failed example: 
   with TemporaryDirectory() as d: # optional - rpy2, rgraphics 
   _ = r.setwd(d) 
   r.plot("1:10") 
Exception raised: 
   Traceback (most recent call last): 
 File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 
695, in _run 
   self.compile_and_execute(example, compiler, test.globs) 
 File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 
1093, in compile_and_execute 
   exec(compiled, globs) 
 File "", line 2, in  
   _ = r.setwd(d) 
 File "/usr/lib/python3.10/site-packages/sage/interfaces/r.py", line 
1988, in __call__ 
   return self._parent.function_call(self._name, args=list(args), 
kwds=kwds) 
 File "/usr/lib/python3.10/site-packages/sage/interfaces/r.py", line 
1061, in function_call 
   args, kwds = self._convert_args_kwds(args, kwds) 
 File "/usr/lib/python3.10/site-packages/sage/interfaces/interface.py", 
line 572, in _convert_args_kwds 
   args[i] = self(arg) 
 File "/usr/lib/python3.10/site-packages/sage/interfaces/interface.py", 
line 298, in __call__ 
   return cls(self, x, name=name) 
 File "/usr/lib/python3.10/site-packages/sage/interfaces/interface.py", 
line 749, in __init__ 
   self._name = parent._create(value, name=name) 
 File "/usr/lib/python3.10/site-packages/sage/interfaces/interface.py", 
line 516, in _create 
   self.set(name, value) 
 File "/usr/lib/python3.10/site-packages/sage/interfaces/r.py", line 
1110, in set 
   out = self.eval(cmd) 
 File "/usr/lib/python3.10/site-packages/sage/interfaces/r.py", line 
1325, in eval 
   return str(robjects.r(code)).rstrip() 
 File "/usr/lib/python3.10/site-packages/rpy2/robjects/__init__.py", 
line 458, in __call__ 
   p = rinterface.parse(string) 
 File 
"/usr/lib/python3.10/site-packages/rpy2/rinterface_lib/conversion.py", line 
45, in _ 
   cdata = function(*args, **kwargs) 
 File "/usr/lib/python3.10/site-packages/rpy2/rinterface.py", line 110, 
in parse 
   res = _rinterface._parse(robj.__sexp__._cdata, num, rmemory) 
 File 
"/usr/lib/python3.10/site-packages/rpy2/rinterface_lib/_rinterface_capi.py", 
line 720, in _parse 
   raise RParsingError('Parsing status not OK', 
   rpy2.rinterface_lib._rinterface_capi.RParsingError: Parsing status not 
OK - PARSING_STATUS.PARSE_ERROR 
**

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[sage-devel] %display latex in Sage command line

[Antonio Rojas]

Hi all,

 In older versions of sage/ipython, one could use '%display latex' or 
'%display typeset' to force all output to be formatted in latex. This is 
used by some third party GUIs (such as Cantor [1]) to typeset the output in 
their UI.

 In recent versions of Sage (at least since 9.5), this no longer works. It 
does work on Jupyter, which suggests there is some sort of autodetection 
going on for deciding whether to display latex output or not. I tried 
manually changing the display manager backend to IPythonNotebook with no 
success.

What would be the current way to force latex output in the Sage command 
line? 

[1] 
https://invent.kde.org/education/cantor/-/blob/v23.04.1/src/backends/sage/sagesession.cpp?ref_type=tags#L480
 

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[sage-devel] Re: Something is up with normaliz

[Antonio Rojas]

El jueves, 13 de julio de 2023 a las 8:21:34 UTC+2, Max Kölbl escribió:

Does anyone else have that problem?
I installed updates this morning and now there seems to be an issue with 
normaliz.
I can't really tell what's going on, but before today, normaliz worked just 
fine.
Maybe other arch / Manjaro users have the same issue?


Fixed with pynormaliz 2.18-3. Unfortunately, like too many other math 
projects, normaliz doesn't follow the customary soversioning rules to 
notify ABI changes.
 

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Re: [sage-devel] Re: configure fails to find some packages (archlinux)

[Antonio Rojas]

> There is also something funny with Flint 2.6 build using cmake - not 
> sure if it's the case on your system, but it seems 
> that in this case there is no way to specify whether you want GC 
> support or not. 
> I guess it ends up without GC support (or, perhaps, with GC support, 
> no idea), while not setting the corresponding HAVE_GC define. See 
> https://github.com/wbhart/flint2/issues/837 - my question there is 
> unanswered. 
>
>
Indeed, there's no HAVE_GC in flint-config.h and flint is not linked to 
libgc.so 

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[sage-devel] Re: Making the package jmol optional

[Antonio Rojas]

El lunes, 7 de diciembre de 2020 a las 6:11:31 UTC+1, Matthias Koeppe 
escribió:

> In https://trac.sagemath.org/ticket/30315 I propose to make jmol 
> optional. To my understanding it has been replaced by generally better 
> options such as threejs and jsmol. But it's possible that I'm missing 
> something.
>
> The Javascript version of it, previously installed as part of jmol, is 
> switched on this ticket to come from the pip-installable package 
> jupyter-jsmol.
>

Is there any reason for not making jsmol optional too? Isn't three.js the 
default renderer these days?
 

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[sage-devel] Re: distro packaging, docbuilding and modularisation

[Antonio Rojas]

El miércoles, 10 de marzo de 2021 a las 10:21:07 UTC+1, François Bissey 
escribió:

> Instead of trying to fix the problem that you should be building the 
> documentation 
> before installing, the push to modularisation is currently used to 
> enshrine the 
> current situation. #30010 actually separate the bits needed to build the 
> sage 
> documentation in a completely separate package. 
> So the situation is now: 
> * install package A 
> * install package B 
> * make a package C that takes B and applies it to the install of A and 
> install 
> the documentation of A (not C). 
>
>
Hi,
 As long as everything is still shipped in the Sage source tarball, isn't 
it just a matter of changing a path in the build script? I've always run 
the doc build directly from the Sage source, without installing anything, 
and I hope to be able to keep doing it that way (after a quick test, it 
still seems to be possible after #30010). Of course, if the long term plan 
is to split this to a separate git repo, then I completely share your 
concerns. 

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Re: [sage-devel] distro packaging, docbuilding and modularisation

[Antonio Rojas]

El miércoles, 10 de marzo de 2021 a las 21:13:15 UTC+1, François Bissey 
escribió:

> I’d like to talk to you on another channel, I have to do a small 
> patch currently. It may reflect different packaging strategy or 
> something I could improve. 
>

Here is my current PKGBUILD (after some cleanup I did 
today) 
https://github.com/archlinux/svntogit-community/blob/packages/sagemath-doc/trunk/PKGBUILD
I'm building the docs in a separate package for practical purposes (sage 
requires frequent rebuilds for soname bumps in dependencies, and I don't 
want to have to build the docs every time), hence the 'rm -r src/sage' line 
so that it doesn't pick up the uncompiled sage module from the source tree, 
this shouldn't be necessary if you build sagelibs and the docs together.
After #30010, simply changing sage_setup.docbuild to sage_docbuild works 
for me. 

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[sage-devel] Re: Status of modularization and packaging in Sage 9.3.beta9

[Antonio Rojas]

El lunes, 15 de marzo de 2021 a las 1:44:19 UTC+1, Matthias Koeppe escribió:

> A quick overview of the status of the modularization effort of Meta-ticket 
> #29705  in Sage 9.3.beta9.
>
What are the plans for the top-level setup.py? I noticed that it no longer 
installs sagelib in beta9, just the executables and sage-ext. It would be 
nice if it could be turned into a sort of meta-script that installed 
everything or, better yet, if one could specify which parts to install (eg. 
'python setup.py build sagelib docbuild')

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[sage-devel] Re: Memory leak in integer multiplication in sage?

[Antonio Rojas]

On Arch, using system libraries:

0
0
memory usage 10k: 10.69921875
0
memory usage 20k: 21.40234375

El jueves, 18 de marzo de 2021 a las 11:56:33 UTC+1, m.derick...@gmail.com 
escribió:

>
>

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[sage-devel] Loading all GAP packages

[Antonio Rojas]

Hi,
 On a fresh run of the GAP interface, Sage caches a GAP workspace which 
loads every single GAP package on the system. While this might be OK with 
Sage's trimmed-down version of gap_packages, if using a system GAP install 
with all optional packages installed this can take a massive amount of 
memory (~1GB with all packages included in the 4.11.1 tarball), which in 
many casses surpasses the default gap_memory_pool_size value, causing 
crashes. This will become a common issue once #29644 is merged.
 I don't think it is realistic to expect a user to need every single 
optional package. Should this preloading be limited to a selected number of 
packages (eg. those loaded in GAP by default)? Or just let users load the 
packages they need on demand?

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Re: [sage-devel] Loading all GAP packages

[Antonio Rojas]

El viernes, 30 de abril de 2021 a las 9:21:11 UTC+2, vdelecroix escribió:

>
> Does your remark applies to both the pexpect GAP interface and libgap? 
>
>
AFAIK this only affects the pexpect interface

https://git.sagemath.org/sage.git/tree/src/sage/interfaces/gap.py#n1549 

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[sage-devel] Re: Loading all GAP packages

[Antonio Rojas]

El viernes, 30 de abril de 2021 a las 9:05:41 UTC+2, Antonio Rojas escribió:

> Hi,
>  On a fresh run of the GAP interface, Sage caches a GAP workspace which 
> loads every single GAP package on the system. While this might be OK with 
> Sage's trimmed-down version of gap_packages, if using a system GAP install 
> with all optional packages installed this can take a massive amount of 
> memory (~1GB with all packages included in the 4.11.1 tarball), which in 
> many casses surpasses the default gap_memory_pool_size value, causing 
> crashes. This will become a common issue once #29644 is merged.
>  I don't think it is realistic to expect a user to need every single 
> optional package. Should this preloading be limited to a selected number of 
> packages (eg. those loaded in GAP by default)? Or just let users load the 
> packages they need on demand?
>

Opened #31761 for this 

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[sage-devel] Re: Proposal: Making cmake a standard package

[Antonio Rojas]

El viernes, 16 de julio de 2021 a las 22:44:22 UTC+2, Matthias Koeppe 
escribió:

> cmake is an advanced build system and currently an optional package, as it 
> is only used for building optional or experimental packages.
> I propose to make cmake a standard package (
> https://trac.sagemath.org/ticket/32213). (It is available as a system 
> package on all supported platforms/distributions.) This will allow us to 
> switch the standard package flint from its traditional build system to its 
> new cmake build system, which will be more robust.
>
> Any objections?
>
>
This is also required for the matplotlib update, cf #31580

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[sage-devel] Pushing to trac with openssh 8.8

[Antonio Rojas]

Hi all,
 I'm unable to push to git-trac since updating to openssh 8.8, getting a 
permission denied error. This version disables RSA/SHA1 signatures by 
default [1], is it possible that the server is using that to chack the keys?

[1] https://www.openssh.com/txt/release-8.8

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[sage-devel] Trac emails

[Antonio Rojas]

Hi all,
 I'm having an issue for a long time where many of the email notifications 
I should be receiving from trac are getting lost (many being over 50%). I 
thougt it might be a problem with my mail provider, but the same thing 
happens after changing to a different address. Is anybody else experiencing 
this?

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Re: [sage-devel] Trac emails

[Antonio Rojas]

I had already checked, but after a closer look it might have something to 
do. I had disabled automatic notifications for the tickets I have commented 
on, assuming that setting it would simply stop automatically adding me to 
the notification list of those tickets. But apparently what it does is 
explicitly blacklist my address from those tickets, *even* if I am on the 
CC list. And, to make it even more confusing, this is only for comments. 
Notifications about ticket changes or git commits are still sent.

I have now added an explicit rule to always email me when I'm CC'd, let's 
see if this fixes the problem. Thanks all for the help.

El lunes, 11 de octubre de 2021 a las 19:57:48 UTC+2, Nils Bruin escribió:

> You've probably already checked, but since at the moment there doesn't 
> seem to be a good lead for resolving this problem:
>
> Was an email *supposed* to be sent according to the trac preferences of 
> the account? In https://trac.sagemath.org/prefs/notification there are 
> quite a few options to select/deselect the sending of emails. If trac 
> didn't even send a message then the first explanation that comes to mind is 
> that trac determined it didn't have to; and these preferences could explain 
> that. So it's worth a check.
>

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[sage-devel] Re: BUG: Si(pi).n() throws error in sage 9.2-2

[Antonio Rojas]

This is not a Sage problem, it's a mpmath 1.2 issue, which broke Sage 
detection when using distro packages. You either need to revert commit [1] 
or set the MPMATH_SAGE env variable.

[1] https://github.com/fredrik-johansson/mpmath/commit/84ca137f

El domingo, 17 de octubre de 2021 a las 0:26:16 UTC+2, dlmin...@gmail.com 
escribió:

> Hi there,
>
> I am using sagemath 9.2-2 installed with apt on PopOs 21.04. When I try to 
> evaluate `Si(pi).n()` I get the following error:
> --- 
> TypeError Traceback (most recent call last) 
> /usr/lib/python3/dist-packages/sage/symbolic/expression.pyx in 
> sage.symbolic.expression.Expression.numerical_approx 
> (build/cythonized/sage/symbolic/expression.cpp:35783)() 6069 try: -> 6070 x 
> = x._convert(kwds) 6071 except TypeError: # numerical approximation for 
> real number failed 
> /usr/lib/python3/dist-packages/sage/symbolic/expression.pyx in 
> sage.symbolic.expression.Expression._convert 
> (build/cythonized/sage/symbolic/expression.cpp:10297)() 1464 """ -> 1465 cdef 
> GEx res = self._gobj.evalf(0, kwds) 1466 return new_Expression_from_GEx(
> self._parent, res) 
> /usr/lib/python3/dist-packages/sage/functions/exp_integral.py in 
> _evalf_(self, 
> z, parent, algorithm) 868 import mpmath --> 869 return mpmath_utils_call(
> mpmath.si, z, parent=parent) 870 
> /usr/lib/python3/dist-packages/sage/libs/mpmath/utils.pyx in 
> sage.libs.mpmath.utils.call 
> (build/cythonized/sage/libs/mpmath/utils.c:7121)() 438 mp.prec = orig --> 
> 439 y = mpmath_to_sage(y, prec) 440 if parent is None: 
> /usr/lib/python3/dist-packages/sage/libs/mpmath/utils.pyx in 
> sage.libs.mpmath.utils.mpmath_to_sage 
> (build/cythonized/sage/libs/mpmath/utils.c:5511)() 271 y = RealField(prec)
> () --> 272 mpfr_from_mpfval(y.value, x._mpf_) 273 return y 
> /usr/lib/python3/dist-packages/sage/libs/mpmath/utils.pyx in 
> sage.libs.mpmath.utils.mpfr_from_mpfval 
> (build/cythonized/sage/libs/mpmath/utils.c:4695)() 166 cdef long bc --> 
> 167 sign, man, exp, bc = x 168 if man: TypeError: Cannot convert mpz to 
> sage.rings.integer.Integer During handling of the above exception, another 
> exception occurred: TypeError Traceback (most recent call last) 
>  in  > 1 Si(pi).n() 
> /usr/lib/python3/dist-packages/sage/structure/element.pyx in 
> sage.structure.element.Element.n 
> (build/cythonized/sage/structure/element.c:8382)() 883 0.667 
> 884 """ --> 885 return self.numerical_approx(prec, digits, algorithm) 886 
> 887 def _mpmath_(self, prec=53, rounding=None): 
> /usr/lib/python3/dist-packages/sage/symbolic/expression.pyx in 
> sage.symbolic.expression.Expression.numerical_approx 
> (build/cythonized/sage/symbolic/expression.cpp:35856)() 6072 pass # try 
> again with complex 6073 kwds['parent'] = R.complex_field() -> 6074 x = x.
> _convert(kwds) 6075 6076 # we have to consider constants as well, since 
> infinity is a constant 
> /usr/lib/python3/dist-packages/sage/symbolic/expression.pyx in 
> sage.symbolic.expression.Expression._convert 
> (build/cythonized/sage/symbolic/expression.cpp:10297)() 1463 0 1464 """ -> 
> 1465 cdef GEx res = self._gobj.evalf(0, kwds) 1466 return 
> new_Expression_from_GEx(self._parent, res) 1467 
> /usr/lib/python3/dist-packages/sage/functions/exp_integral.py in 
> _evalf_(self, 
> z, parent, algorithm) 867 """ 868 import mpmath --> 869 return 
> mpmath_utils_call(mpmath.si, z, parent=parent) 870 871 def _derivative_(
> self, z, diff_param=None): 
> /usr/lib/python3/dist-packages/sage/libs/mpmath/utils.pyx in 
> sage.libs.mpmath.utils.call 
> (build/cythonized/sage/libs/mpmath/utils.c:7121)() 437 finally: 438 mp.prec 
> = orig --> 439 y = mpmath_to_sage(y, prec) 440 if parent is None: 441 
> return y /usr/lib/python3/dist-packages/sage/libs/mpmath/utils.pyx in 
> sage.libs.mpmath.utils.mpmath_to_sage 
> (build/cythonized/sage/libs/mpmath/utils.c:5511)() 270 if hasattr(x, 
> "_mpf_"): 271 y = RealField(prec)() --> 272 mpfr_from_mpfval(y.value, x.
> _mpf_) 273 return y 274 elif hasattr(x, "_mpc_"): 
> /usr/lib/python3/dist-packages/sage/libs/mpmath/utils.pyx in 
> sage.libs.mpmath.utils.mpfr_from_mpfval 
> (build/cythonized/sage/libs/mpmath/utils.c:4695)() 165 cdef long exp 166 
> cdef long bc --> 167 sign, man, exp, bc = x 168 if man: 169 mpfr_set_z(res
> , man.value, MPFR_RNDZ) TypeError: Cannot convert mpz to 
> sage.rings.integer.Integer
> --- 
>
> I believe this should be able to be approximated numerically and should 
> return approximately 1.851937
>

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[sage-devel] Re: `sage -t --log=file.log` broken in 9.5.beta5

[Antonio Rojas]

El lunes, 1 de noviembre de 2021 a las 17:36:18 UTC+1, Sébastien Labbé 
escribió:

> Bonjour,
>
> I just noticed that providing a log file to the `sage -t` command is 
> currently broken with the most recent version:
>
>
This is caused by https://trac.sagemath.org/ticket/32332. All arguments 
must go before the file name now. 

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[sage-devel] Re: Gap pexpect error when most Gap packages are installed

[Antonio Rojas]

I just noticed this yesterday after updating GAP to 4.10.2 in Arch. 
SymmetricGroup(n).conjugacy_classes_subgroups() works fine for n<=4, and 
fails for n>=5. Same as you, it works after removing all additional GAP 
packages.

Additionally, after the update (and with all GAP packages installed) some 
tests started failing due to using more memory than the default 330 
maximum. Running them with -m0 makes them pass. Again, no issue if I remove 
the additional packages. 

El domingo, 23 de junio de 2019, 16:25:45 (UTC+2), Isuru Fernando escribió:
>
> In the conda package for gap, we packaged almost all of the gap packages 
> (136 of 145) and sage pexpect gives an error for the following,
>
> sage: SymmetricGroup(7).conjugacy_classes_subgroups()
>
> saying,
> RuntimeError: Gap produced error output
> Error, sorry, the GAP Tables Of Marks Library is not installed
>
> I checked gap separately and tomlib imports fine and also running the 
> equivalent command on gap runs fine. When I run the command in gap with the 
> sage created workspace I get the same issue.
>
> I removed all gap packages except for the 18 packages that sage installs, 
> cleared the cache and it works. So, this is clearly an issue with a package 
> that sage doesn't install.
>
> Has anyone seen such an error before?
>
> Isuru
>
>
>

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[sage-devel] About python2 vs python3 package versions

[Antonio Rojas]

Hi all, 
 Today I tested building Sage on Arch against our python3 packages. Not 
surprisingly, it failed to even start. This is due to our python3 ipython 
package being at version 7 already, with includes some API changes that 
require some porting in Sage. 
 More and more python modules are completely dropping python2 support: 
ipython, sphinx, networkx, scipy, matplotlib... These packages can't be 
upgraded in sage-the-distribution and are therefore stuck to an old version 
until python2 support is dropped in Sage, which presumably won't happen for 
at least a couple of years. This is going to be a big problem for 
distributions in the period when Sage defaults to Python3 but still 
supports Python 2: much patching will probably be needed to support the 
newer versions of python3 modules with are still not upgraded in Sage due 
to not supporting python2. 
 My first question is: would Sage accept patches to support this newer 
version of python modules (while still keeping compatibility with the older 
versions shipped by Sage)?. That would allow to reduce the patching 
required by distros. 
 However, this would still not be completely satisfactory - the updated 
version code path would not be tested so the risk of regressions would be 
quite high. Ideally, Sage should allow to ship different versions for the 
python2 and python3 versions of these modules, so when compiling with 
python3 it would use the latest versions. Are there any plans in this 
direction, or are these packages going to be stuck to old versions until 
python2 support is dropped? 

--Antonio 

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[sage-devel] Re: [Debian-science-sagemath] name of arb library in Debian and adjustments needed

[Antonio Rojas]

El lunes, 15 de julio de 2019, 14:49:54 (UTC+2), Dima Pasechnik escribió:
>
>
>
> A quick way would be  to create src/sage/env.py.in, with a template for, 
> say, 
> `aliases["ARB_LIBRARIES"]` in `cython_aliases` 
> filled in by a call to AC_CONFIG_FILES. 
>
> This would be setting a precedent for sagelib (there are so far no 
> Python files treated this way). 
>
> I wonder whether this might create extra issues for packaging. 
>
> Dima 
>
>
Yes, it does. This makes sagelib compilation depend on sage's own build 
system which is a big step back for distro packaging. In fact with this 
patch I can no longer build standalone sagelib, trying to run configure 
fails with 

aclocal: error: m4/sage_spkg_collect.m4:57: file 
'm4/sage_spkg_configures.m4' does not exist


 

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[sage-devel] Re: maxima 5.43.0

[Antonio Rojas]

El jueves, 1 de agosto de 2019, 2:00:02 (UTC+2), François Bissey escribió:
>
> Hi all, 
>
> I am giving a shot at getting maxima-5.43.0 working for sage-on-gentoo 
> and it looks good overall but there are couple of things that needs 
> attention. 
> ** 
> File 
> "/usr/lib64/python2.7/site-packages/sage/symbolic/integration/integral.py", 
>
> line 829, in sage.symbolic.integration.integral.integrate 
> Failed example: 
>  abs(N(a - pi*log(2)/8)) < 1e-15  # long time 
> Expected: 
>  True 
> Got: 
>  False 
> **


This one is caused 
by 
https://sourceforge.net/p/maxima/code/ci/47a6afd1d4691b83bedd197dea322dfd64f4f0f9/

Note that this same commit broke some of maxima's own tests, which they 
'fixed' by skipping them. So it might make sense to do the same here.
 

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[sage-devel] Re: error building barvinok (sage 8.9.beta8 + system NTL)

[Antonio Rojas]

El martes, 27 de agosto de 2019, 16:25:12 (UTC+2), Victor Shoup escribió:
>
> I reviewed some comments which mentioned a problem with ntl and threads. 
> I’m happy to fix that, but I don’t think I understand what the issue is. 
> Can anyone explain? Thanks.


Hi Victor,
 IIRC I reported this to you about a year ago. The problem is that you are 
using libtool as a build command, which calls the compiler with the 
-nostdlib flag, which in turn overrides the -pthread flag, so the binaries 
end up not being linked to libpthread. See eg. [1][2] for more info.

[1] https://bugzilla.redhat.com/show_bug.cgi?id=661333
[2] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=25460  

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[sage-devel] Re: error building barvinok (sage 8.9.beta8 + system NTL)

[Antonio Rojas]

El miércoles, 28 de agosto de 2019, 15:15:18 (UTC+2), Victor Shoup escribió:
>
> Thanks. I guess what I'm asking for is a solution.  From what you say 
> here, and what is said in the links, the problem seems to be a bug in 
> libtool, not NTL.  So a solution would be, either:
> 1) a patch other type of libtool workaround, or
> 2) an alternative to libtool.
> I though the whole point of libtool was to take care of all this nonsense, 
> and if it's not doing that, then
> it seems kind of pointless.
>
>
I'd say the easiest fix would be to treat libpthread just like any other 
library and link to it by passing -lpthread to the linker instead of 
relying on the -pthread gcc flag (I don't speak perl so I can't help with a 
patch, sorry) 

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Re: [sage-devel] Re: error building barvinok (sage 8.9.beta8 + system NTL)

[Antonio Rojas]

El miércoles, 28 de agosto de 2019, 23:47:43 (UTC+2), Dima Pasechnik 
escribió:
>
> Victor, 
> as you ship libtool, you can just patch it, essentially as in 
> https://lists.gnu.org/archive/html/libtool-patches/2013-11/msg00015.html 
> It needs to be moved to a slightly different place, but it works, 
> you'd get a properly linked libntl.so with the patch (attached), I 
> checked this on Linux at 
> least. 
>
>
Relying on patched bundled copies of dependencies is very much frowned upon 
by distros. It would be much preferable to make this work with unmodified 
libtool, which may be provided by the distribution. 

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Re: [sage-devel] Re: error building barvinok (sage 8.9.beta8 + system NTL)

[Antonio Rojas]

El jueves, 29 de agosto de 2019, 0:06:49 (UTC+2), Dima Pasechnik escribió:
>
>
> > Relying on patched bundled copies of dependencies is very much frowned 
> upon by distros. It would be much preferable to make this work with 
> unmodified libtool, which may be provided by the distribution. 
>
> Well, libtool is just a shell script, more or less. NTL isn't unique 
> in shipping its own version. 
> Does Arch use its own libtool when building NTL, or the bundled one? 
>
>
Regardless of how simple if may be, bundling dependencies increases the 
risk of introducing bugs and inconsistencies between distro packages. On 
Arch we are building ntl using system's libtool.
Anyway, whatever solution is adopted is not such a big deal since there is 
an easy workaround (pass LDLIBS='-lpthread' to configure) that distros can 
keep using - It would just be nicer to fix it without resorting to patched 
dependencies IMO. 

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[sage-devel] Re: [sage-packaging] About python2 vs python3 package versions

[Antonio Rojas]

El sábado, 13 de julio de 2019, 19:33:50 (UTC+2), Samuel Lelievre escribió:
>
> One thing we could do for a start, given that for now we build 
> both Python 2 and Python 3 in any case, would be to transition 
> the Jupyter part of Sage-the-distribution to be python3-based, 
> allowing us to upgrade all the Jupyter stack to current versions. 
>
> I don't know if there are any obstacles to that. 
>


Although this doesn't help much to solve the issue I tried to raise up in 
this thread, I've opened #28438 for this, which is an easy change.
 

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Re: [sage-devel] Re: error building barvinok (sage 8.9.beta8 + system NTL)

[Antonio Rojas]

El jueves, 5 de septiembre de 2019, 6:07:13 (UTC+2), Victor Shoup escribió:
 

> So, based on that comment, it seems that there is no problem if you link 
> with g++
> rather than libtool.  But who or what uses libtool to link?
> I would never have thought of doing that, as I thought libtool was a tool
> for creating libraries, not linking programs
>

But you do! This is from your mfile:

ntl.a: $(OBJ)
[...]
@{LSHAR} $(LIBTOOL) --tag=CXX --mode=link $(LINK) $(LIBTOOL_LINK_FLAGS) -o 
libntl.la $(OBJ:.o=.lo) $(GMP_OPT_LIBDIR) $(GMP_OPT_LIB) $(GF2X_OPT_LIBDIR) 
$(GF2X_OPT_LIB) $(LDLIBS) -rpath $(LIBDIR) -version-info `cat VERSION_INFO` 
#LSHAR

If you check the compilation output, this is the line where this is called:

libtool --tag=CXX --mode=link g++ -I../include -I.  -march=x86-64 
-mtune=generic -O2 -pipe -fno-plt -pthread 
-Wl,-O1,--sort-common,--as-needed,-z,relro,-z
,now  -o libntl.la FFT.lo FacVec.lo GF2.lo GF2E.lo GF2EX.lo 
GF2EXFactoring.lo GF2X.lo GF2X1.lo GF2XFactoring.lo GF2XVec.lo GetTime.lo 
GetPID.lo HNF.lo cto
ols.lo LLL.lo LLL_FP.lo LLL_QP.lo LLL_RR.lo LLL_XD.lo RR.lo WordVector.lo 
ZZ.lo ZZVec.lo ZZX.lo ZZX1.lo ZZXCharPoly.lo ZZXFactoring.lo ZZ_p.lo 
ZZ_pE.lo ZZ
_pEX.lo ZZ_pEXFactoring.lo ZZ_pX.lo ZZ_pX1.lo ZZ_pXCharPoly.lo 
ZZ_pXFactoring.lo fileio.lo lip.lo lzz_p.lo lzz_pE.lo lzz_pEX.lo 
lzz_pEXFactoring.lo lzz_pX
.lo lzz_pX1.lo lzz_pXCharPoly.lo lzz_pXFactoring.lo mat_GF2.lo mat_GF2E.lo 
mat_RR.lo mat_ZZ.lo mat_ZZ_p.lo mat_ZZ_pE.lo mat_lzz_p.lo mat_lzz_pE.lo 
mat_pol
y_ZZ.lo mat_poly_ZZ_p.lo mat_poly_lzz_p.lo quad_float.lo quad_float1.lo 
tools.lo vec_GF2.lo vec_GF2E.lo vec_RR.lo vec_ZZ.lo vec_ZZ_p.lo 
vec_ZZ_pE.lo vec_l
zz_p.lo vec_lzz_pE.lo xdouble.lo G_LLL_FP.lo G_LLL_QP.lo G_LLL_XD.lo 
G_LLL_RR.lo thread.lo BasicThreadPool.lo MatPrime.lo pd_FFT.lo -L/usr/lib 
 -lgmp  -L/
usr/lib  -lgf2x  -lpthread -rpath /usr/lib -version-info `cat VERSION_INFO` 
#LSHAR

And, right below it, you have the g++ command that libtool actually runs:

libtool: link: g++  -fPIC -DPIC -shared -nostdlib 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../lib/crti.o 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/crt
beginS.o  .libs/FFT.o .libs/FacVec.o .libs/GF2.o .libs/GF2E.o .libs/GF2EX.o 
.libs/GF2EXFactoring.o .libs/GF2X.o .libs/GF2X1.o .libs/GF2XFactoring.o 
.libs/
GF2XVec.o .libs/GetTime.o .libs/GetPID.o .libs/HNF.o .libs/ctools.o 
.libs/LLL.o .libs/LLL_FP.o .libs/LLL_QP.o .libs/LLL_RR.o .libs/LLL_XD.o 
.libs/RR.o .li
bs/WordVector.o .libs/ZZ.o .libs/ZZVec.o .libs/ZZX.o .libs/ZZX1.o 
.libs/ZZXCharPoly.o .libs/ZZXFactoring.o .libs/ZZ_p.o .libs/ZZ_pE.o 
.libs/ZZ_pEX.o .libs
/ZZ_pEXFactoring.o .libs/ZZ_pX.o .libs/ZZ_pX1.o .libs/ZZ_pXCharPoly.o 
.libs/ZZ_pXFactoring.o .libs/fileio.o .libs/lip.o .libs/lzz_p.o 
.libs/lzz_pE.o .libs
/lzz_pEX.o .libs/lzz_pEXFactoring.o .libs/lzz_pX.o .libs/lzz_pX1.o 
.libs/lzz_pXCharPoly.o .libs/lzz_pXFactoring.o .libs/mat_GF2.o 
.libs/mat_GF2E.o .libs/m
at_RR.o .libs/mat_ZZ.o .libs/mat_ZZ_p.o .libs/mat_ZZ_pE.o .libs/mat_lzz_p.o 
.libs/mat_lzz_pE.o .libs/mat_poly_ZZ.o .libs/mat_poly_ZZ_p.o 
.libs/mat_poly_lz
z_p.o .libs/quad_float.o .libs/quad_float1.o .libs/tools.o .libs/vec_GF2.o 
.libs/vec_GF2E.o .libs/vec_RR.o .libs/vec_ZZ.o .libs/vec_ZZ_p.o 
.libs/vec_ZZ_pE
.o .libs/vec_lzz_p.o .libs/vec_lzz_pE.o .libs/xdouble.o .libs/G_LLL_FP.o 
.libs/G_LLL_QP.o .libs/G_LLL_XD.o .libs/G_LLL_RR.o .libs/thread.o 
.libs/BasicThre
adPool.o .libs/MatPrime.o .libs/pd_FFT.o   -L/usr/lib -lgmp -lgf2x 
-lpthread -L/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0 
-L/usr/lib/gcc/x86_64-pc-linux-gnu/9
.1.0/../../../../lib -L/lib/../lib -L/usr/lib/../lib 
-L/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../.. -lstdc++ -lm -lc -lgcc_s 
/usr/lib/gcc/x86_64-pc-lin
ux-gnu/9.1.0/crtendS.o 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../lib/crtn.o 
 -march=x86-64 -mtune=generic -O2 -pthread -Wl,-O1 -Wl,--sort-common 
-Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now   -pthread -Wl,-soname 
-Wl,libntl.so.40 -o .libs/libntl.so.40.0.0

As you can see, libtool has added the -nostdlib flag to g++, which in turn 
invalidates all subsequent -pthread flags. Change that line in mfile to 
call $(LINK) directly and everything will work fine.
 

>  Again, when I build and install a shared NTL on a linux system, 
> everything works fine.

So I'm not even sure what the problem is:
>

What do you mean by "everything works fine"? Is libntl.so linked to 
libpthread? Because if not, it's not fine, it's underlinked, which is what 
is causing these issues that are being reported. 

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Re: [sage-devel] Re: error building barvinok (sage 8.9.beta8 + system NTL)

[Antonio Rojas]

El jueves, 5 de septiembre de 2019, 15:51:34 (UTC+2), Victor Shoup escribió:
>
> We seem to be talking past each other.
>

Unfortunately it seems so.

It is also true that when I run ldd on libntl.so, I do not see anything 
> related to pthread.
> From the comments I'm reading in  https://trac.sagemath.org/ticket/28406 
> ,
>  
> that seems
> to be what is "wrong".
>

Do you seriously not see why this is wrong? This is a textbook case of 
underlinking. Your library is calling functions from the libpthread 
library, so it *must* link to it. This is not a matter of "conventions" or 
"choices", this is how dynamic linking works. If you refuse to acknowledge 
that this is a problem then there's certainly nothing else to discuss.

When I actually build a program, either in the build directory using NTL's 
> makefile with libtool,
> or in another directory using a different makefile that uses g++, it works 
> fine.
>

And we already have two programs that don't work: latte-integrale (al least 
the old version which I reported to you a  year ago) and barvinok. And no, 
building those programs with -pthread is definitely not the solution: If a 
library A uses a function from library B and a program C uses a function 
from library A but nothing from library B then C does not have to and 
should not link to B: it's A's job to link to B. 

So my understanding is that whenever you compile a multi-threaded program
> you should pass -pthread to gcc. 
>

Correct. But you should *not* have to pass -pthread when you compile a 
single-threaded program and happens to use a multi-threaded library, which 
is the case here. 

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Re: [sage-devel] Adopting orphaned math packages

[Antonio Rojas]

El miércoles, 18 de diciembre de 2019, 11:19:54 (UTC+1), E. Madison Bray 
escribió:
>
>
> Looking in the latest source tarball for SYMMETRICA there are 
> absolutely zero license or copyright notifications.  And if the author 
> is deceased, does that mean it's public domain?  I don't know. 
>
>
>From http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/:

"Symmetrica is public domain"

which links to:

/*
Copyright (c) 1987-2010 , symmetrica (at) symmetrica.de

Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHORS DISCLAIM ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

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

[Antonio Rojas]

El lunes, 6 de enero de 2020, 8:43:14 (UTC+1), Nils Bruin escribió:
>
>
> You could say: there is such a way: just check out 9.0 and build that with 
> py2. Perhaps that's enough. However, I would err at the side of caution and 
> make a slightly bigger gesture here and still include 9.1 as well -- that 
> was published as a definite promise already. Once again, for any piece of 
> code where this turns out to be a bother, just wait with the merge until 
> 9.2. I don't think it needs to put a very large load on developers. It will 
> mainly be a pain for the release manager, so he/she should actually get to 
> have a significant voice in this
>

It's not as simple as waiting for 9.2 to merge them. Some of the pending 
changes (ipython 7 and python 3.8 support) require huge patches that touch 
lots of files. This means that they will probably need rebasing for every 
single beta release (this has been the case until now), which makes it not 
really practical to start working on them on trac until the 9.2 cycle 
starts. Until then the burden of maintaining the patches falls on the 
downstream packagers - and the situation is only going to get worse as new 
python3-only versions of dependencies are released and updated on distros. 

>  
>

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

[Antonio Rojas]

El viernes, 10 de enero de 2020, 14:54:24 (UTC+1), E. Madison Bray escribió:
>
> That seems like the obvious approach to me.  As it is I've long felt 
> that Sage should be more flexible in its dependencies where 
> possible/necessary.  With most Python packages it's easy as most have 
> a .__version__ and its not so hard to define some variable 
> like IS_RPY_2 and just have two separate branches.  I have things like 
> that all over the place in other packages to support e.g. different 
> Numpy versions or work around version-specific bugs. 
>

I've opened https://trac.sagemath.org/ticket/28988 for rpy. But at this 
point the major issues are python 3.8 and ipython 7, and I don't see how 
one could support several versions of them without forking hundreds of 
doctests. Both updates require multi-thousand-lines patches, due to changes 
in dict sorting and hashes.

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Re: [sage-devel] 9.1.beta0 build failure on Arch

[Antonio Rojas]

I don't think so - I'm pretty sure I've built it successfully after that 
commit. 

El sábado, 11 de enero de 2020, 9:25:04 (UTC+1), Dima Pasechnik escribió:
>
> isn't it due to https://trac.sagemath.org/ticket/27444 - which removed 
> --disable-openmp from fflas-ffpack flags ? 
> see https://trac.sagemath.org/ticket/27444#comment:34 
>
> On Sat, Jan 11, 2020 at 7:53 AM Antonio Rojas  > wrote: 
> > 
> > Build fails at fflas-ffpack, log attached. Seems related to FS#27870 
> > 
> > -- 
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>  
>
>

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Re: [sage-devel] 9.1.beta0 build failure on Arch

[Antonio Rojas]

openblas is not being built in Sage, the system one is detected and used 
after FS#27870. FWIW, building our distro fflas-ffpack package with our 
system openblas works fine.

El sábado, 11 de enero de 2020, 10:00:43 (UTC+1), Dima Pasechnik escribió:
>
> On Sat, Jan 11, 2020 at 8:57 AM Antonio Rojas  > wrote: 
> > 
> > I don't think so - I'm pretty sure I've built it successfully after that 
> commit. 
> > 
> please compare the system openblas linkage with the one you build in 
> Sage, and post the outputs of ldd here. 
> I am pretty sure there is an interesting 
> difference, I only don't know which way. 
>
>
> > El sábado, 11 de enero de 2020, 9:25:04 (UTC+1), Dima Pasechnik 
> escribió: 
> >> 
> >> isn't it due to https://trac.sagemath.org/ticket/27444 - which removed 
> >> --disable-openmp from fflas-ffpack flags ? 
> >> see https://trac.sagemath.org/ticket/27444#comment:34 
> >> 
> >> On Sat, Jan 11, 2020 at 7:53 AM Antonio Rojas  
> wrote: 
> >> > 
> >> > Build fails at fflas-ffpack, log attached. Seems related to FS#27870 
> >> > 
> >> > -- 
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>  
>
> > 
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Re: [sage-devel] 9.1.beta0 build failure on Arch

[Antonio Rojas]

El jueves, 23 de enero de 2020, 18:11:51 (UTC+1), Dima Pasechnik escribió:
>
> On Wed, Jan 22, 2020 at 5:20 PM Isuru Fernando  > wrote: 
> > 
> > [root@50586643ff22 /]# pkg-config --modversion blas 
> > 0.3.7 
> > [root@50586643ff22 /]# pkg-config --modversion cblas 
> > 3.9.0 
> > [root@50586643ff22 /]# pkg-config --modversion lapack 
> > 3.9.0 
> > [root@50586643ff22 /]# pkg-config --modversion openblas 
> > 0.3.7 
>
> To make it robust, I'd only allow cblas.pc to be used if it really is 
> based on openblas 
> and the same for lapack.pc 
>
> One way to do this is to  test openblas for a symbol that is on Arch 
> in cblas, not in openblas, 
> and the same for lapack. 
>
> Could someone figure out these symbols, or give me access to an Arch box? 
>
>
fflas-fflack configure tests need cblas_dgemm, so you should check for that 
function.
 

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[sage-devel] sagenb dependencies

[Antonio Rojas]

sagenb was made optional, but its dependencies (such as flask-* packages) 
are still standard and installed by default as of 9.1.beta7. Shouldn't they 
be made optional too?

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[sage-devel] Re: archlinux: some system package not recognized

[Antonio Rojas]

El jueves, 19 de marzo de 2020, 14:52:46 (UTC+1), vdelecroix escribió:
>
> Dear all, 
>
> Thanks to hard work it is now possible to use some package from 
> the system! That is great! But on my archlinux computer that also 
> has sage installed from the package manager the following 
> packages are still detected has "to be installed" 
>
> * eclib-20190909 
> * givaro-4.1.1 
> * lcalc-1.23.p19 
> * pari-2.11.2 
> * pari_galdata-20080411.p0 
> * pari_seadata_small-20090618.p0 
>
> The relevant package in archlinux I have are 
>
> * community/eclib 20190909-8 
> * community/givaro 4.1.1-1 
> * community/lcalc 1.23-19 
> * community/pari 2.11.3-2 
> * community/pari-galdata 20080411-2 
> * community/pari-seadata-small 20090618-2 
>
> Should I suspect that something is wrong with the Sage 
> configure scripts? Or that something is wrong with the packages 
> from archlinux? 
>
> Best 
> Vincent 
>

The pari spkg-configure also checks for galpol, elldata and (big) seadata. 
You need to have these installed for Sage to use the system package. 

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Re: [sage-devel] 9.1.beta0 build failure on Arch

[Antonio Rojas]

I'm missing some context here... flint does certainly link to ntl already, 
i don't see how it could work otherwise.


El martes, 14 de abril de 2020, 15:23:08 (UTC+2), Dima Pasechnik escribió:
>
> Hi Antonio, 
> can Arch's Flint be fixed so that it links against NTL, like in Sage? 
> Then we won't have to build Flint (and Arb) on Arch... 
>
>

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Re: [sage-devel] 9.1.beta0 build failure on Arch

[Antonio Rojas]

That's osx, not Arch

El martes, 14 de abril de 2020, 15:38:27 (UTC+2), Dima Pasechnik escribió:
>
> On Tue, Apr 14, 2020 at 9:28 PM Antonio Rojas  > wrote: 
> > 
> > I'm missing some context here... flint does certainly link to ntl 
> already, i don't see how it could work otherwise. 
>
> David just posted a message here claiming this not to be the case on 
> his Arch installation. 
> Perhaps he has an odd version of Flint conflicting with the system one? 
> (or just an old installation?) 
>
> > 
> > 
> > El martes, 14 de abril de 2020, 15:23:08 (UTC+2), Dima Pasechnik 
> escribió: 
> >> 
> >> Hi Antonio, 
> >> can Arch's Flint be fixed so that it links against NTL, like in Sage? 
> >> Then we won't have to build Flint (and Arb) on Arch... 
> >> 
> > -- 
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>  
>
>

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[sage-devel] Re: SingularError in rational_parameterization

[Antonio Rojas]

Works fine with system singular 4.3.2.p16 too, so this may be a bug in that 
particular Singular version.

El jueves, 18 de abril de 2024 a las 6:02:53 UTC+2, Kwankyu Lee escribió:

> No problem with Singular 4.3.2 included in sage (on mac).

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Re: [sage-devel] Re: [debian-science] Modularized sagemath packages: proof of concept

[Antonio Rojas]

El miércoles, 20 de noviembre de 2024 a las 15:37:32 UTC+1, 
dim...@gmail.com escribió:



On 20 November 2024 01:06:39 GMT-06:00, "'tobia...@gmx.de' via sage-devel" <
sage-...@googlegroups.com> wrote: 
>The new version of cysignals, released just a couple of hours ago, now 
>builds using Meson and works fine on Windows. Thanks Dima and Frédéric for 
>the quick reviews and the new release! 

I still need to figure out how to automatically publish releases on PyPI, 
so for the time being get a release on GitHub. 


I don't see any release (or tag) on GitHub either.
 

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[sage-devel] Re: Error with package during build on linux

[Antonio Rojas]

The missing header is provided by the brial package, which you don't seem 
to have installed. Looks like you will also 
need https://github.com/sagemath/sage/pull/39291

El jueves, 30 de enero de 2025 a las 21:10:39 UTC+1, aliat...@gmail.com 
escribió:

> Hi Antonio,
>
> I've switched to installing version 10.5 and it worked! However, I've been 
> trying to setup sagemath for use within Python, and if I'm correct I need 
> to install the sagemath-standard package. When trying to install said 
> package, I get an error message, attached below. Additionally, I've 
> attached the error log file.
>
> Thanks,
>
> Kareem
>
> On Tuesday, January 28, 2025 at 1:58:29 PM UTC Antonio Rojas wrote:
>
>> Are you really trying to build the 3-years-old version 9.5, or is that 
>> just the name of the dir? In the latter case, please post the full 
>> config.log
>>
>> El martes, 28 de enero de 2025 a las 14:41:18 UTC+1, aliat...@gmail.com 
>> escribió:
>>
>>> Hi,
>>>
>>> After running ./configure then make, I get greeted with this error 
>>> message.
>>>
>>> The log file is also attached to the message.
>>>
>>> Thanks,
>>>
>>> Kareem
>>>
>>

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[sage-devel] Re: Problem re-installing sage-10.5

[Antonio Rojas]

This is a bug in the Debian nauty package. Apparently they patch it to 
build against system libcliquer but don't actually link to it. Disable 
system nauty in configure.

El lunes, 3 de febrero de 2025 a las 7:44:35 UTC+1, tdumont escribió:

> I apologize if this problem as already be solved (I was far from my 
> computer for some time).
>
> I maintain two versions of Sage the 10.5 stable, and the 10.6 beta*.
>
> I am using a Debian testing amd-64 distribution.
>
> After upgrading my Debian system, both versions could not start.
>
> So, I made:
>
> make distclean
> ./configure
> make reconfigure
> make
>
> -> Everything went well for the 10.6 beta5 version,
>
> -> But for the 10.5 stable it crashes when compiling giac:
>
> 
> giac-1.9.0.15p0] [spkg-install] /usr/bin/ld: 
> /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/libnauty.so: 
> undefined reference to `clique_unweighted_find_single@CLIQUER_1'
> [giac-1.9.0.15p0] [spkg-install] /usr/bin/ld: 
> /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/libnauty.so: 
> undefined reference to `graph_free@CLIQUER_1'
> [giac-1.9.0.15p0] [spkg-install] /usr/bin/ld: 
> /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/libnauty.so: 
> undefined reference to `graph_new@CLIQUER_1'
> .
>
> 
> [giac-1.9.0.15p0] [spkg-install] Error building giac-1.9.0.15p0
> 
> Is a library missing ? The giac version installed on my system is 
> 1.9.0.93+dfsg2-3
>
> Yours,
> Thierry.
>
>

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[sage-devel] Re: Error with package during build on linux

[Antonio Rojas]

Are you really trying to build the 3-years-old version 9.5, or is that just 
the name of the dir? In the latter case, please post the full config.log

El martes, 28 de enero de 2025 a las 14:41:18 UTC+1, aliat...@gmail.com 
escribió:

> Hi,
>
> After running ./configure then make, I get greeted with this error message.
>
> The log file is also attached to the message.
>
> Thanks,
>
> Kareem
>

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[sage-devel] Re: Problems compiling sagemath 10.5.

[Antonio Rojas]

See the several reports about this on sage-support.

El martes, 28 de enero de 2025 a las 14:41:25 UTC+1, ssimon...@gmail.com 
escribió:

> I tried to compile from sagemath 10.5 source, but I get an error at some 
> point that stops the compilation: "Error installing package sagelib-10.5".
> The computer has a Debian distribution  testing (trixie) with a Linux 
> kernel installed 
> (Linux debsim 6.11.9-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.9-1 
> (2024-11-17) x86_64 GNU/Linux). 
> I attach the files as recommended by the compilation messages.
> Have you encountered this problem before?
> Thank you.
> Best regards
> Stefano Simonucci
>

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Re: [sage-devel] Re: Linker failure for gap_packages on arm64 macOS 15.3

[Antonio Rojas]

See 
https://web.archive.org/web/20201218114127/https://trac.sagemath.org/ticket/27372
 
for some previous discussion about this

El miércoles, 29 de enero de 2025 a las 21:43:36 UTC+1, marc@gmail.com 
escribió:

> On Wed, Jan 29, 2025 at 1:33 PM Dima Pasechnik  wrote:
>
>>
>>  libgap is not really involved here;
>>
> cypring's GAP kernel module
>> (that's what's compiled here) can be loaded either in libgap, or in
>> gap executable - and the latter
>> isn't linked to libgap.
>
>  
> I am no expert in GAP.  But the code in crypting.c references symbols 
> which are defined in libgap.  So to build crypting.so from crypting.o you 
> have to link against libgap or something else which defines those same 
> symbols.  After building with my patch, if I run the gap executable 
> $SAGE_ROOT/local/bin/gap then I am able to load the crypting module:
>
> % 
> /Applications/SageMath-10-6.app/Contents/Frameworks/Sage.framework/Versions/Current/local/bin/gap
>  ┌───┐   GAP 4.13.1 of 2024-06-11
>  │  GAP  │   https://www.gap-system.org
>  └───┘   Architecture: aarch64-apple-darwin24-default64-kv9
>  Configuration:  gmp 6.3.0, GASMAN, readline
>  Loading the library and packages ...
>  Packages:   AClib 1.3.2, Alnuth 3.2.1, AtlasRep 2.1.8, AutPGrp 1.11, 
>  CRISP 1.4.6, Cryst 4.1.27, CrystCat 1.1.10, CTblLib 1.3.9, 
>  FactInt 1.6.3, FGA 1.5.0, GAPDoc 1.6.7, IO 4.8.2, 
>  IRREDSOL 1.4.4, LAGUNA 3.9.6, Polenta 1.3.10, Polycyclic 
> 2.16, 
>  PrimGrp 3.4.4, RadiRoot 2.9, ResClasses 4.7.3, SmallGrp 
> 1.5.3, 
>  Sophus 1.27, TomLib 1.2.11, TransGrp 3.6.5, utils 0.85
>  Try '??help' for help. See also '?copyright', '?cite' and '?authors'
> gap> LoadPackage("crypting");
>
> 
> Loading crypting 0.10.4 (Hashes and Crypto in GAP)
> by Markus Pfeiffer (http://www.morphism.de/~markusp/).
> maintained by:
>Markus Pfeiffer (http://www.morphism.de/~markusp/) and
>The GAP Team (sup...@gap-system.org).
> Homepage: https://gap-packages.github.io/crypting/
> Report issues at https://github.com/gap-packages/crypting/issues
>
> 
> true
>
> That is all that I know about this.
>
> - Marc 
>

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[sage-devel] Re: Error installing package symmetrica-3.0.1

[Antonio Rojas]

Install the Arch symmetrica package. (And, unless you are planning to do 
sage development, it is highly recommended to use the sagemath distro 
package instead of building from source in Arch)

El domingo, 2 de marzo de 2025 a las 16:23:37 UTC+1, prito...@gmail.com 
escribió:

> Hi,
> New here. When building Sage I got an error stating, "Error installing 
> package symmetrica-3.0.1".  I have the following config:
> OS: Arch Linux x86_64
> Kernel: 6.13.4-arch1-1
> CPU: 12th Gen Intel i5-12400 (12) @ 4.400GHz
> GPU: Intel Alder Lake-S GT1 [UHD Graphics 730]
> Memory: 5834MiB / 15765MiB
>
> I have attached the log files.
> Thank you,
> Pritom
>

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[sage-devel] Re: Error building cypari 2.2.1

[Antonio Rojas]

Force disabling system pari for now in configure, should be fixed 
with https://github.com/sagemath/sage/pull/39700

El viernes, 14 de marzo de 2025 a las 2:45:37 UTC+1, Trevor Karn escribió:

> Hi all,
>
> I'm trying to build 10.6.beta9 from source on a Apple M3 Pro running 
> Sequoia 15.3.1 using Python 3.13, and when I try to build, it fails on 
> cypari 2.2.1, apparently with an error that there are an incorrect number 
> of arguments to the function `qfcvp0`.
>
> I see that PR #38749 bumped the cypari version from 2.2.0 since beta8, so 
> maybe that is related to this problem? Does anyone have any advice on how 
> to resolve this issue?
>
> My build process is to run the short shell script I wrote from a directory 
> containing SAGE_ROOT. The shell script is attached in addition to the logs 
> config.log and cypari-2.2.1.log.
>
> Thanks!
> Best,
> Trevor
>

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Re: [sage-devel] gap_packages

[Antonio Rojas]

The browse package is also causing trouble, simply having it installed 
makes doctesting hang (as it is automatically loaded by the standard 
ctbllib package if present).

El jueves, 27 de marzo de 2025 a las 1:22:09 UTC+1, François Bissey 
escribió:

> the xgap package was the guilty party causing trouble if my memory serves 
> me right from all those years ago. It was automatically loaded too.
> I cannot remember how I figured it out now. xgap would not load by itself 
> these days, if it still exists.
>
> François
>
>
> On 27/03/2025 09:19, enriqu...@gmail.com wrote:
>
> I have opened https://github.com/sagemath/sage/pull/39783. The immediate 
> goal is to add a recent gap package. There are several points tangentially 
> related with this PR that I wanted to share to the community: 
>
>1. Is there a reason to do not add some other packages? Long time ago, 
>I think someone told me that they may interfere with other sage packages, 
>but it is not clear to me since they must be loaded explicitely. 
>2. The compilation of gap_packages takes quite a while. Taking out 
> sdh_make 
>-j1 in spkg-install.in allows to compile in parallel each packages, 
>but I wonder if there was a reason to avoid parallelism. In the same 
> ideas, 
>since there are several packages to be built, it could be a good idea to 
>allow parallelism at the level of packages, but I do not how to do it.
>3. The third one is related with the use of gap functions. One option 
>is to add more functions to gap_functions.py, but I do not know if adding 
>too much functions may affect to the memory. A second option is to use 
>libgap.function_factory; it is OK. My issue is how to pass options to gap 
>functions. I have not found how to do it. In order to use libgap.eval, I 
> do 
>not know for example how to produce a gap string from a sage group. 
>
> Thanks, Enrique.
>
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>  
> 
> .
>
>
>

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