Re: [sage-devel] vote on behaviour of is_similar for matrices

[Justin C. Walker]

> On Oct 27, 2016, at 10:47, William Stein  wrote:
> 
> Just curious:  what choice does magma (or maple or Mathematica etc) make 
> regarding this?

Magma acts as follows, when the matrices are square, but different sizes, or 
when one or both are non-square:

> M1:=Matrix(ZZ,2,2,[1,2,3,4]);
> M2:=Matrix(ZZ,3,3,[1,2,3,4,5,6,7,8,9]);
> IsSimilar(M1,M2);

>> IsSimilar(M1,M2);
^
Runtime error in 'IsSimilar': Arguments are not compatible
Argument types given: AlgMatElt[RngInt], AlgMatElt[RngInt]

That’s “sort of friendly”…

FWIW, I’d like it to blow up when deep in a computation (something is seriously 
borked at that point); at the prompt, ???

HTH

Justin

--
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Institute for the Absorption of Federal Funds
---
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Re: [sage-devel] Re: vote on behaviour of is_similar for matrices

[John H Palmieri]

On Thursday, October 27, 2016 at 2:42:56 PM UTC-7, Travis Scrimshaw wrote:
>
>
>
> On Thursday, October 27, 2016 at 2:12:01 PM UTC-5, William wrote:
>>
>> On Thu, Oct 27, 2016 at 11:25 AM, kcrisman  wrote: 
>> > 
>> > 
>> > On Thursday, October 27, 2016 at 2:11:58 PM UTC-4, John H Palmieri 
>> wrote: 
>> >> 
>> >> (1) Why should a nonsquare matrix even have an "is_similar" method? 
>> Can we 
>> >> get rid of that? (Same for "determinant" and some other methods.) 
>> > 
>> > 
>> > Those are not even the most annoying methods like this throughout Sage 
>> that 
>> > are not actually implemented but nonetheless appear in tab-completion, 
>> > thanks for the reminder - not sure how to fix it without putting in a 
>> bunch 
>> > of super-classes that don't have them. 
>>
>> We could change how tab completion works to have a hook/way to exclude 
>> a list of methods.  That's a simple backward compatible fix that does 
>> not require any new classes, and can be iteratively applied with 0 
>> change in efficiency. 
>>
>>The OOP way would be to have a mix-in class and subclasses for square 
> matrices that implement these methods. This would mean setting the Element 
> attribute in the initialization of the parent, but that's not so bad IMO. 
> This would be my fix; it just takes a bit more work.
>

Or plug (square) matrices into the category framework? Would that be too 
slow? I see that there is a file categories/matrix_algebras.py, but there 
is not much in it.

-- 
John

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Re: [sage-devel] Re: vote on behaviour of is_similar for matrices

[Travis Scrimshaw]

On Thursday, October 27, 2016 at 2:12:01 PM UTC-5, William wrote:
>
> On Thu, Oct 27, 2016 at 11:25 AM, kcrisman  > wrote: 
> > 
> > 
> > On Thursday, October 27, 2016 at 2:11:58 PM UTC-4, John H Palmieri 
> wrote: 
> >> 
> >> (1) Why should a nonsquare matrix even have an "is_similar" method? Can 
> we 
> >> get rid of that? (Same for "determinant" and some other methods.) 
> > 
> > 
> > Those are not even the most annoying methods like this throughout Sage 
> that 
> > are not actually implemented but nonetheless appear in tab-completion, 
> > thanks for the reminder - not sure how to fix it without putting in a 
> bunch 
> > of super-classes that don't have them. 
>
> We could change how tab completion works to have a hook/way to exclude 
> a list of methods.  That's a simple backward compatible fix that does 
> not require any new classes, and can be iteratively applied with 0 
> change in efficiency. 
>
>The OOP way would be to have a mix-in class and subclasses for square 
matrices that implement these methods. This would mean setting the Element 
attribute in the initialization of the parent, but that's not so bad IMO. 
This would be my fix; it just takes a bit more work.

Best,
Travis

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Re: [sage-devel] Re: sage's increasingly long startup time?

[Jeroen Demeyer]

Well, Python isn't exactly efficient when it comes to system calls...

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Re: [sage-devel] Re: sage's increasingly long startup time?

[William Stein]

This is more what concerns me:

~$  strace sage-7.4 -c pass 2>a
~$ wc -l a
35137
~$ grep stat a |wc -l
8712
~$ grep open a |wc -l
10289
~$ grep read a |wc -l
5645

etc.

I was wrong -- its "only" 8712 stats.

Anyway, I probably just need to tweak os caching parameters or the
disk, since of course with everything in cache the startup time is
less than 2s as others report.

William


On Thu, Oct 27, 2016 at 12:23 PM, Eric Gourgoulhon
 wrote:
>
>
> Le jeudi 27 octobre 2016 21:22:23 UTC+2, Eric Gourgoulhon a écrit :
>>
>> Hi,
>>
>> Which computer are you using? On my 5-years old laptop (Core i5-2410M + 4
>> GB memory), it takes "only" 22 seconds. Running a second time takes 1.4
>> second.
>>
>> Best regards,
>>
>> Eric.
>>
>>
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[sage-devel] Re: sage's increasingly long startup time?

[Eric Gourgoulhon]

Le jeudi 27 octobre 2016 21:22:23 UTC+2, Eric Gourgoulhon a écrit :
>
> Hi,
>
> Which computer are you using? On my 5-years old laptop (Core i5-2410M + 4 
> GB memory), it takes "only" 22 seconds. Running a second *time* takes 1.4 
> second.
>
> Best regards,
>
> Eric.
>
>
>

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Re: [sage-devel] sage's increasingly long startup time?

[John Cremona]

On 27 October 2016 at 20:08, William Stein  wrote:
> Does anybody else find this depressing?
>
> ⨯ time sage-7.4 -c pass
> 2.18user 0.99system 0:34.29elapsed 9%CPU (0avgtext+0avgdata 
> 170712maxresident)k
> 285672inputs+8outputs (628major+49021minor)pagefaults 0swaps
>
> 35 seconds?
>
> Yes, I know, doing it again is fast, since it can stat 100K files
> using the cache quickly.
>
> But seriously?

That is odd.  I just tried "time sage -c pass" on a machine I rebooted
today which had not yet run Sage since then, and which is 6 years old,
and I got

real 0m2.124s
user 0m1.960s
sys 0m1.028s

On another also recently rebooted, I have been washing some dirty cows) I get

real 0m2.458s
user 0m7.408s
sys 0m0.426s

John

>
>  -- William
>
>
> --
> William (http://wstein.org)
>
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[sage-devel] Re: sage's increasingly long startup time?

[Eric Gourgoulhon]

Hi,

Which computer are you using? On my 5-years old laptop (Core i5-2410M + 4 
GB memory), it takes "only" 22 seconds. Running a second takes 1.4 second.

Best regards,

Eric.


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[sage-devel] jsmol.js

[William Stein]

In case anybody cares, in Sage-7.4 this bug remains

   https://github.com/jupyterhub/jupyterhub/issues/401

which blocks 3d graphics in jupyter/sage working at all for sage and
jupyter hub:

   https://github.com/sagemathinc/smc/issues/159

It seems like according to
https://github.com/jupyterhub/jupyterhub/issues/401 the fix might be
an easy one liner for whoever maintains the sage jupyter jsmol 3d
graphics notebook extension.

Who is that?  Where is it?

-- 
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Re: [sage-devel] Re: vote on behaviour of is_similar for matrices

[William Stein]

On Thu, Oct 27, 2016 at 11:25 AM, kcrisman  wrote:
>
>
> On Thursday, October 27, 2016 at 2:11:58 PM UTC-4, John H Palmieri wrote:
>>
>> (1) Why should a nonsquare matrix even have an "is_similar" method? Can we
>> get rid of that? (Same for "determinant" and some other methods.)
>
>
> Those are not even the most annoying methods like this throughout Sage that
> are not actually implemented but nonetheless appear in tab-completion,
> thanks for the reminder - not sure how to fix it without putting in a bunch
> of super-classes that don't have them.

We could change how tab completion works to have a hook/way to exclude
a list of methods.  That's a simple backward compatible fix that does
not require any new classes, and can be iteratively applied with 0
change in efficiency.

>
>>
>>
>> (2) What is the definition of similar?
>>
>>   (a) Two matrices M and N, both square of the same size, are similar iff
>> there is an invertible matrix P so that M = PNP^{-1}.
>>
>> or
>>
>>   (b) Two matrices M and N are similar iff there is an invertible matrix P
>> so that ...
>
>
> I get that argument, but also like that we have an error for 1 / 0 == 3 as
> pointed out on that ticket.  Then again, we not only don't raise an error
> here, we actually have (again from the ticket)
>
> sage: identity_matrix(10) == 1
> True
>
> I land - slightly - on the BB side.
>
> --
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[sage-devel] sage's increasingly long startup time?

[William Stein]

Does anybody else find this depressing?

⨯ time sage-7.4 -c pass
2.18user 0.99system 0:34.29elapsed 9%CPU (0avgtext+0avgdata 170712maxresident)k
285672inputs+8outputs (628major+49021minor)pagefaults 0swaps

35 seconds?

Yes, I know, doing it again is fast, since it can stat 100K files
using the cache quickly.

But seriously?

 -- William


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Re: [sage-devel] Trac error on push

[John Cremona]

The machine hosting trac did change recently.

On 27 October 2016 at 19:17, jhonrubia6  wrote:
> After working on ticket #21052, I committed the changed file and tried to
> git trac push and get the error
>
> git_trac.git_error.GitError: git returned with non-zero exit code (128) when
> executing "git push trac
> HEAD:refs/heads/u/jhonrubia6/add_pictures_to_implicit_plot3d_py"
>
> STDERR: @@@
>
> STDERR: @WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @
>
> STDERR: @@@
>
> STDERR: IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
>
> STDERR: Someone could be eavesdropping on you right now
> (man-in-the-middle attack)!
>
> STDERR: It is also possible that a host key has just been changed.
>
> STDERR: The fingerprint for the ECDSA key sent by the remote host is
>
> STDERR: SHA256:4Op/q3b5792x+F1lHSKRi5UIORAPDlIFVA5cUq9YVXI.
>
> STDERR: Please contact your system administrator.
>
> STDERR: Add correct host key in /Users/J_Honrubia/.ssh/known_hosts to
> get rid of this message.
>
> STDERR: Offending ECDSA key in /Users/J_Honrubia/.ssh/known_hosts:4
>
> STDERR: ECDSA host key for trac.sagemath.org has changed and you have
> requested strict checking.
>
> STDERR: Host key verification failed.
>
> STDERR: fatal: Could not read from remote repository.
>
> STDERR:
>
> STDERR: Please make sure you have the correct access rights
>
> STDERR: and the repository exists.
>
>
> git trac config works fine without errors.
>
> but
>
> OnoSendaiII:sage J_Honrubia$ ssh g...@trac.sagemath.org info
>
> @@@
>
> @WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @
>
> @@@
>
> IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
>
> Someone could be eavesdropping on you right now (man-in-the-middle attack)!
>
> It is also possible that a host key has just been changed.
>
> The fingerprint for the ECDSA key sent by the remote host is
>
> SHA256:4Op/q3b5792x+F1lHSKRi5UIORAPDlIFVA5cUq9YVXI.
>
> Please contact your system administrator.
>
> Add correct host key in /Users/J_Honrubia/.ssh/known_hosts to get rid of
> this message.
>
> Offending ECDSA key in /Users/J_Honrubia/.ssh/known_hosts:4
>
> ECDSA host key for trac.sagemath.org has changed and you have requested
> strict checking.
>
> Host key verification failed.
>
>
> Any clue?
>
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Re: [sage-devel] vote on behaviour of is_similar for matrices

[John Cremona]

On 27 October 2016 at 18:47, William Stein  wrote:
> Just curious:  what choice does magma (or maple or Mathematica etc) make
> regarding this?

Using Magma V2.22-3 I am not impressed:

> A:=Matrix([[1,2],[3,4]]);
> B:=Matrix([[1,2],[3,4]]);
> Parent(A);
Full Matrix Algebra of degree 2 over Integer Ring
> Parent(B);
Full Matrix Algebra of degree 2 over Integer Ring
> IsSimilar(A,B);

>> IsSimilar(A,B);
^
Runtime error in 'IsSimilar': Coefficient ring of argument 1 is not an
exact field

I can get it to give true by replcing the first entries by 1/1.

If B has a different size it gives


> B:=Matrix([[1/1,2],[3,4],[5,6]]);
> IsSimilar(A,B);

>> IsSimilar(A,B);
^
Runtime error in 'IsSimilar': Bad argument types
Argument types given: AlgMatElt[FldRat], ModMatFldElt[FldRat]

which is a not very easy to understand error message.

>
>
> On Thursday, October 27, 2016, Dima Pasechnik  wrote:
>>
>> AA
>> (but make sure docs make sense after the change)
>>
>> On Thursday, October 27, 2016 at 4:21:02 PM UTC, Travis Scrimshaw wrote:
>>>
>>> I am for BB because:
>>>
>>> 1 - the definition (as even given in the docstring) still makes full
>>> sense if the matrices are not the same size or if they are not square. There
>>> does not exist such a matrix P.
>>
>>
>> this is an argument for changing the docs, yes.
>>
>>>
>>> 2 - It puts an unnecessary burden on the average user. They have to deal
>>> with errors on a true/false question. You then also have to explain why
>>> there is the error message to your linear algebra students, provided you
>>> were very careful with your definition of similar matrices.
>>
>>
>> Just as they have to deal with errors from multiplying matrices of
>> different sizes.
>>
>>>
>>> 3 - It is a backwards incompatible change that (IMO) is not a bug and we
>>> cannot deprecate.
>>>
>>
>>  well, a wrong decision was made at some point. Do you mean to say one has
>> to keep suffering from it forever? :-)
>>
>> Cheers,
>> Dima
>>
>>> Best,
>>> Travis
>>>
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>
>
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[sage-devel] Re: vote on behaviour of is_similar for matrices

[kcrisman]

On Thursday, October 27, 2016 at 2:11:58 PM UTC-4, John H Palmieri wrote:
>
> (1) Why should a nonsquare matrix even have an "is_similar" method? Can we 
> get rid of that? (Same for "determinant" and some other methods.)
>

Those are not even the most annoying methods like this throughout Sage that 
are not actually implemented but nonetheless appear in tab-completion, 
thanks for the reminder - not sure how to fix it without putting in a bunch 
of super-classes that don't have them.
 

>
> (2) What is the definition of similar?
>
>   (a) Two matrices M and N, both square of the same size, are similar iff 
> there is an invertible matrix P so that M = PNP^{-1}.
>
> or
>
>   (b) Two matrices M and N are similar iff there is an invertible matrix P 
> so that ...
>

I get that argument, but also like that we have an error for 1 / 0 == 3 as 
pointed out on that ticket.  Then again, we not only don't raise an error 
here, we actually have (again from the ticket)

sage: identity_matrix(10) == 1
True

I land - slightly - on the BB side.  

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[sage-devel] Trac error on push

[jhonrubia6]

After working on ticket #21052, I committed the changed file and tried to 
git trac push and get the error

git_trac.git_error.GitError: git returned with non-zero exit code (128) 
when executing "git push trac 
HEAD:refs/heads/u/jhonrubia6/add_pictures_to_implicit_plot3d_py"

STDERR: @@@

STDERR: @WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @

STDERR: @@@

STDERR: IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!

STDERR: Someone could be eavesdropping on you right now 
(man-in-the-middle attack)!

STDERR: It is also possible that a host key has just been changed.

STDERR: The fingerprint for the ECDSA key sent by the remote host is

STDERR: SHA256:4Op/q3b5792x+F1lHSKRi5UIORAPDlIFVA5cUq9YVXI.

STDERR: Please contact your system administrator.

STDERR: Add correct host key in /Users/J_Honrubia/.ssh/known_hosts to 
get rid of this message.

STDERR: Offending ECDSA key in /Users/J_Honrubia/.ssh/known_hosts:4

STDERR: ECDSA host key for trac.sagemath.org has changed and you have 
requested strict checking.

STDERR: Host key verification failed.

STDERR: fatal: Could not read from remote repository.

STDERR: 

STDERR: Please make sure you have the correct access rights

STDERR: and the repository exists.


git trac config works fine without errors.

but

OnoSendaiII:sage J_Honrubia$ ssh g...@trac.sagemath.org info

@@@

@WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @

@@@

IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!

Someone could be eavesdropping on you right now (man-in-the-middle attack)!

It is also possible that a host key has just been changed.

The fingerprint for the ECDSA key sent by the remote host is

SHA256:4Op/q3b5792x+F1lHSKRi5UIORAPDlIFVA5cUq9YVXI.

Please contact your system administrator.

Add correct host key in /Users/J_Honrubia/.ssh/known_hosts to get rid of 
this message.

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[kcrisman]

> So either they will stop distribute R or they will patch 
>> en-masse. 
>>
>
> Somehow, I doubt it.
>
>
Probably nobody even bothered to notice or notify e.g. Debian?

Thanks for working on this; how annoying. 

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[sage-devel] Re: vote on behaviour of is_similar for matrices

[John H Palmieri]

(1) Why should a nonsquare matrix even have an "is_similar" method? Can we 
get rid of that? (Same for "determinant" and some other methods.)

(2) What is the definition of similar?

  (a) Two matrices M and N, both square of the same size, are similar iff 
there is an invertible matrix P so that M = PNP^{-1}.

or

  (b) Two matrices M and N are similar iff there is an invertible matrix P 
so that ...



I vote for version (b) of the definition, so I vote

BB

We don't raise an error when asking if M == N for matrices of different 
shapes, so why should we raise an error for M.is_similar(N)?

  John



On Thursday, October 27, 2016 at 1:48:17 AM UTC-7, Frédéric Chapoton wrote:
>
> Hello,
>
> on https://trac.sagemath.org/ticket/18505, we are trying to enhance the 
> *is_similar* method of matrices.
>
> Because we cannot agree, we require your vote on the following matter:
>
> 1) When M.is_similar(N) is called and either M or N is not square:
>
> A) raise an helpful specific error message
> B) return False
>
> 2) When M.is_similar(N) is called and M and N are square of different 
> sizes:
>
> A) raise an helpful specific error message
> B) return False
>
> Please vote. I am voting AA
>
> Frederic
>

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[sage-devel] coercion failure?

[kcrisman]

See https://trac.sagemath.org/ticket/21777 for a surprising (to me) relict 
of what appears to be coercion failure - I don't know who is around who is 
an expert in this and might be able to diagnose it, hopefully someone here 
is.

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[Travis Scrimshaw]

Mathematica doesn't seem to have such a function for checking similarity. 
Maple returns false. I don't know for magma.

Best,
Travis


On Thursday, October 27, 2016 at 12:47:29 PM UTC-5, William wrote:
>
> Just curious:  what choice does magma (or maple or Mathematica etc) make 
> regarding this?
>
> On Thursday, October 27, 2016, Dima Pasechnik  > wrote:
>
>> AA
>> (but make sure docs make sense after the change)
>>
>> On Thursday, October 27, 2016 at 4:21:02 PM UTC, Travis Scrimshaw wrote:
>>>
>>> I am for BB because:
>>>
>>> 1 - the definition (as even given in the docstring) still makes full 
>>> sense if the matrices are not the same size or if they are not square. 
>>> There does not exist such a matrix P.
>>>
>>
>> this is an argument for changing the docs, yes.
>>  
>>
>>> 2 - It puts an unnecessary burden on the average user. They have to deal 
>>> with errors on a true/false question. You then also have to explain why 
>>> there is the error message to your linear algebra students, provided you 
>>> were very careful with your definition of similar matrices.
>>>
>>
>> Just as they have to deal with errors from multiplying matrices of 
>> different sizes.
>>  
>>
>>> 3 - It is a backwards incompatible change that (IMO) is not a bug and we 
>>> cannot deprecate.
>>>
>>>
>>  well, a wrong decision was made at some point. Do you mean to say one 
>> has to keep suffering from it forever? :-)
>>
>> Cheers,
>> Dima
>>
>> Best,
>>> Travis
>>>
>>> -- 
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>
>
> -- 
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>

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[Michael Orlitzky]

On 10/27/2016 12:21 PM, Travis Scrimshaw wrote:
> I am for BB because:
> 

Both options have merit. If most people think we should have a
user-friendly error for a common mistake (mismatched dimensions), then
maybe it makes sense to add an ignore_dims (default: False) parameter
for the people who expect the dimensions to differ occasionally?

The alternative is to repeat the dimension checks yourself, and that's a
little annoying. And trying to catch the exception might catch the wrong
thing.

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[William Stein]

Just curious:  what choice does magma (or maple or Mathematica etc) make
regarding this?

On Thursday, October 27, 2016, Dima Pasechnik  wrote:

> AA
> (but make sure docs make sense after the change)
>
> On Thursday, October 27, 2016 at 4:21:02 PM UTC, Travis Scrimshaw wrote:
>>
>> I am for BB because:
>>
>> 1 - the definition (as even given in the docstring) still makes full
>> sense if the matrices are not the same size or if they are not square.
>> There does not exist such a matrix P.
>>
>
> this is an argument for changing the docs, yes.
>
>
>> 2 - It puts an unnecessary burden on the average user. They have to deal
>> with errors on a true/false question. You then also have to explain why
>> there is the error message to your linear algebra students, provided you
>> were very careful with your definition of similar matrices.
>>
>
> Just as they have to deal with errors from multiplying matrices of
> different sizes.
>
>
>> 3 - It is a backwards incompatible change that (IMO) is not a bug and we
>> cannot deprecate.
>>
>>
>  well, a wrong decision was made at some point. Do you mean to say one has
> to keep suffering from it forever? :-)
>
> Cheers,
> Dima
>
> Best,
>> Travis
>>
>> --
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Re: [sage-devel] Multivariate polynomial factoring and bug(?)

[Dima Pasechnik]

factorisation of multivariate polynomials is very slow. This is a fact of 
life.

On Thursday, October 27, 2016 at 9:38:48 AM UTC, Jori Mäntysalo wrote:
>
> On Thu, 27 Oct 2016, Vincent Delecroix wrote: 
>
> > Concerning your code, it got stuck on the first run? What is the 
> > degree of the polynomial you are trying to factorize? 
>
> It stucks in every run. You can run my test code, it does not take so 
> long. 
>
> Degree is 199. And I have no idea about the algorithm Singular uses, and 
> the memory requirements. So this may be just a feature. 
>
> (Actually there is at least a minor bug: at mimum I should have gotten an 
> error message about running out of memory.) 
>
> -- 
> Jori Mäntysalo 
>

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[Dima Pasechnik]

AA
(but make sure docs make sense after the change)

On Thursday, October 27, 2016 at 4:21:02 PM UTC, Travis Scrimshaw wrote:
>
> I am for BB because:
>
> 1 - the definition (as even given in the docstring) still makes full sense 
> if the matrices are not the same size or if they are not square. There does 
> not exist such a matrix P.
>

this is an argument for changing the docs, yes.
 

> 2 - It puts an unnecessary burden on the average user. They have to deal 
> with errors on a true/false question. You then also have to explain why 
> there is the error message to your linear algebra students, provided you 
> were very careful with your definition of similar matrices.
>

Just as they have to deal with errors from multiplying matrices of 
different sizes.
 

> 3 - It is a backwards incompatible change that (IMO) is not a bug and we 
> cannot deprecate.
>
>
 well, a wrong decision was made at some point. Do you mean to say one has 
to keep suffering from it forever? :-)

Cheers,
Dima

Best,
> Travis
>
>

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[Travis Scrimshaw]

I am for BB because:

1 - the definition (as even given in the docstring) still makes full sense 
if the matrices are not the same size or if they are not square. There does 
not exist such a matrix P.
2 - It puts an unnecessary burden on the average user. They have to deal 
with errors on a true/false question. You then also have to explain why 
there is the error message to your linear algebra students, provided you 
were very careful with your definition of similar matrices.
3 - It is a backwards incompatible change that (IMO) is not a bug and we 
cannot deprecate.

Best,
Travis

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 5:28:41 PM UTC+2, William wrote:
>
> On Thu, Oct 27, 2016 at 8:25 AM, Jean-Pierre Flori  > wrote: 
> > 
> > 
> > On Thursday, October 27, 2016 at 5:16:02 PM UTC+2, Jean-Pierre Flori 
> wrote: 
> >> 
> >> But you're right, by default Debian links to openssl: 
> >> https://packages.debian.org/sid/libcurl3 
> >> 
> >> And indeed curl is not GPL anyway: 
> >> https://curl.haxx.se/docs/copyright.html 
> >> Groumpf. 
> >> See https://curl.haxx.se/legal/distro-dilemma.html for more rumbling. 
> >> 
> > Apart from the linking issue, doesn't it apply that we cannot ship curl 
> > sources? 
> > 
> > I seem to remember that stuff about Sage already violating the GPL as it 
> is 
> > GPL v3+ and ships some GPL v2 only code. 
>
> Such as?  I don't think this is the case. 
>
> Indeed, it was a wrong souvenir:
https://groups.google.com/d/msg/sage-devel/amxAxHkmvbw/bgnBseSV_u8J

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[William Stein]

On Thu, Oct 27, 2016 at 8:25 AM, Jean-Pierre Flori  wrote:
>
>
> On Thursday, October 27, 2016 at 5:16:02 PM UTC+2, Jean-Pierre Flori wrote:
>>
>> But you're right, by default Debian links to openssl:
>> https://packages.debian.org/sid/libcurl3
>>
>> And indeed curl is not GPL anyway:
>> https://curl.haxx.se/docs/copyright.html
>> Groumpf.
>> See https://curl.haxx.se/legal/distro-dilemma.html for more rumbling.
>>
> Apart from the linking issue, doesn't it apply that we cannot ship curl
> sources?
>
> I seem to remember that stuff about Sage already violating the GPL as it is
> GPL v3+ and ships some GPL v2 only code.

Such as?  I don't think this is the case.


-- 
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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 5:23:58 PM UTC+2, William wrote:
>
> Hi, 
>
>  
>
> We've been down this road before with Sage, and it's pretty annoying. 
> I've personally wasted hundreds of hours on it (GNUtls, openssl, etc.) 
>  Programmers playing lawyers have ended up with a broken and 
> inconsistent legal foundation. There is no easy way out, since only 
> copyright owners can change licenses.  Because this is volunteer open 
> source, much of the generation that got us into this mess is MIA (or 
> even dead in some cases).Sigh... 
>
>  
>

Yup it's a uselessly messy situation :/
I certainly do not want to play lawyers. 

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 5:16:02 PM UTC+2, Jean-Pierre Flori wrote:
>
> But you're right, by default Debian links to openssl: 
> https://packages.debian.org/sid/libcurl3
>
> And indeed curl is not GPL anyway: 
> https://curl.haxx.se/docs/copyright.html
> Groumpf.
> See https://curl.haxx.se/legal/distro-dilemma.html for more rumbling.
>
> Apart from the linking issue, doesn't it apply that we cannot ship curl 
sources?

I seem to remember that stuff about Sage already violating the GPL as it is 
GPL v3+ and ships some GPL v2 only code.
No idea about the implication for LGPL and other funny stuff.

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 5:18:40 PM UTC+2, Emmanuel Charpentier 
wrote:
>
>
>
> Le jeudi 27 octobre 2016 17:00:05 UTC+2, Jean-Pierre Flori a écrit :
>>
>>
>>
>> On Thursday, October 27, 2016 at 4:59:02 PM UTC+2, Jean-Pierre Flori 
>> wrote:
>>>
>>>
>>>
>>> On Thursday, October 27, 2016 at 4:49:23 PM UTC+2, Emmanuel Charpentier 
>>> wrote:



 Le jeudi 27 octobre 2016 16:04:52 UTC+2, Jean-Pierre Flori a écrit :
>
>
>
> On Thursday, October 27, 2016 at 3:59:26 PM UTC+2, Emmanuel 
> Charpentier wrote:
>>
>>
>>
>> Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :
>>>
>>> It is a most interesting point because it explain why 
>>> the R binary installed from epel for RH7.1 and family 
>>> isn’t linked to openssl. 
>>>
>>
>> How old is RH7.1 ? The introduction of the libcurl requirement dates 
>> from the R 3.3.0 release, (May 3, 2016).
>>
>> I note that Debian (notoriously twitchy about license issues) didn't 
>> seem to have any qualms packaging 3.3.0, nor 3.3.1. 
>>
>  
> I'd say Debian links curl to GnuTLS.
>

 Probably not : My system's curl-config --protocols says that HTTPS: is 
 supported. A trial of curl's configure --without-ssl --with-gnutls does 
 not 
 claim to support it (in the summary printed at th end of ./configure...).

 Are you sure you  installed the gnutls dev headers?
>>> GnuTLS provides an SSL implem, not just SSL.
>>>  
>>>
 However, I'm not sure : Debian's blurb about libcurl3-gnutls says that 
 it supports https, imaps, ldaps, smtps and pop3s.

 To be sure, I'll have to setup a virtual machine with a minimal 
 environment (no openssl, of course) and try to setup libcurl (and, if 
 successful, Sage) in that environment. This is time consuming, so not 
 quite 
 real soon...

>>> You mean with gnutls?
>>> Or with no ssl/tls at all?
>>>
>>> I already did the latter and it works (modulo hacking R's configure).
>>>
>>
>>  (sage-sh) jpflori@gcc1-power7:sage.git$ curl-config --protocols
>> DICT
>> FILE
>> FTP
>> GOPHER
>> HTTP
>> IMAP
>> POP3
>> RTSP
>> SCP
>> SFTP
>> SMTP
>> TELNET
>> TFTP
>> (sage-sh) jpflori@gcc1-power7:sage.git$ R --version
>> R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
>> Copyright (C) 2016 The R Foundation for Statistical Computing
>> Platform: powerpc64-unknown-linux-gnu (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under the terms of the
>> GNU General Public License versions 2 or 3.
>> For more information about these matters see
>> http://www.gnu.org/licenses/.
>>
>
> No HTTPS. Damn.. 
>
As far as installing packages goes, R suggest me 27 https mirrors and a 
28-th option "HTTP mirrors", if I go there it works. 

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[William Stein]

Hi,



We've been down this road before with Sage, and it's pretty annoying.
I've personally wasted hundreds of hours on it (GNUtls, openssl, etc.)
 Programmers playing lawyers have ended up with a broken and
inconsistent legal foundation. There is no easy way out, since only
copyright owners can change licenses.  Because this is volunteer open
source, much of the generation that got us into this mess is MIA (or
even dead in some cases).Sigh...



 -- William

On Thu, Oct 27, 2016 at 8:18 AM, Emmanuel Charpentier
 wrote:
>
>
> Le jeudi 27 octobre 2016 17:00:05 UTC+2, Jean-Pierre Flori a écrit :
>>
>>
>>
>> On Thursday, October 27, 2016 at 4:59:02 PM UTC+2, Jean-Pierre Flori
>> wrote:
>>>
>>>
>>>
>>> On Thursday, October 27, 2016 at 4:49:23 PM UTC+2, Emmanuel Charpentier
>>> wrote:



 Le jeudi 27 octobre 2016 16:04:52 UTC+2, Jean-Pierre Flori a écrit :
>
>
>
> On Thursday, October 27, 2016 at 3:59:26 PM UTC+2, Emmanuel Charpentier
> wrote:
>>
>>
>>
>> Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :
>>>
>>> It is a most interesting point because it explain why
>>> the R binary installed from epel for RH7.1 and family
>>> isn’t linked to openssl.
>>
>>
>> How old is RH7.1 ? The introduction of the libcurl requirement dates
>> from the R 3.3.0 release, (May 3, 2016).
>>
>> I note that Debian (notoriously twitchy about license issues) didn't
>> seem to have any qualms packaging 3.3.0, nor 3.3.1.
>
>
> I'd say Debian links curl to GnuTLS.


 Probably not : My system's curl-config --protocols says that HTTPS: is
 supported. A trial of curl's configure --without-ssl --with-gnutls does not
 claim to support it (in the summary printed at th end of ./configure...).

>>> Are you sure you  installed the gnutls dev headers?
>>> GnuTLS provides an SSL implem, not just SSL.
>>>

 However, I'm not sure : Debian's blurb about libcurl3-gnutls says that
 it supports https, imaps, ldaps, smtps and pop3s.

 To be sure, I'll have to setup a virtual machine with a minimal
 environment (no openssl, of course) and try to setup libcurl (and, if
 successful, Sage) in that environment. This is time consuming, so not quite
 real soon...
>>>
>>> You mean with gnutls?
>>> Or with no ssl/tls at all?
>>>
>>> I already did the latter and it works (modulo hacking R's configure).
>>
>>
>>  (sage-sh) jpflori@gcc1-power7:sage.git$ curl-config --protocols
>> DICT
>> FILE
>> FTP
>> GOPHER
>> HTTP
>> IMAP
>> POP3
>> RTSP
>> SCP
>> SFTP
>> SMTP
>> TELNET
>> TFTP
>> (sage-sh) jpflori@gcc1-power7:sage.git$ R --version
>> R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
>> Copyright (C) 2016 The R Foundation for Statistical Computing
>> Platform: powerpc64-unknown-linux-gnu (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under the terms of the
>> GNU General Public License versions 2 or 3.
>> For more information about these matters see
>> http://www.gnu.org/licenses/.
>
>
> No HTTPS. Damn..
>
> --
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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

But you're right, by default Debian links to openssl: 
https://packages.debian.org/sid/libcurl3

And indeed curl is not GPL anyway: https://curl.haxx.se/docs/copyright.html
Groumpf.
See https://curl.haxx.se/legal/distro-dilemma.html for more rumbling.

Now what if a GPL application links to libcurl?
Section 6 of https://curl.haxx.se/docs/faq.html tells its a legal issue and 
they cannot help you.

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Emmanuel Charpentier]

Le jeudi 27 octobre 2016 17:00:05 UTC+2, Jean-Pierre Flori a écrit :
>
>
>
> On Thursday, October 27, 2016 at 4:59:02 PM UTC+2, Jean-Pierre Flori wrote:
>>
>>
>>
>> On Thursday, October 27, 2016 at 4:49:23 PM UTC+2, Emmanuel Charpentier 
>> wrote:
>>>
>>>
>>>
>>> Le jeudi 27 octobre 2016 16:04:52 UTC+2, Jean-Pierre Flori a écrit :



 On Thursday, October 27, 2016 at 3:59:26 PM UTC+2, Emmanuel Charpentier 
 wrote:
>
>
>
> Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :
>>
>> It is a most interesting point because it explain why 
>> the R binary installed from epel for RH7.1 and family 
>> isn’t linked to openssl. 
>>
>
> How old is RH7.1 ? The introduction of the libcurl requirement dates 
> from the R 3.3.0 release, (May 3, 2016).
>
> I note that Debian (notoriously twitchy about license issues) didn't 
> seem to have any qualms packaging 3.3.0, nor 3.3.1. 
>
  
 I'd say Debian links curl to GnuTLS.

>>>
>>> Probably not : My system's curl-config --protocols says that HTTPS: is 
>>> supported. A trial of curl's configure --without-ssl --with-gnutls does not 
>>> claim to support it (in the summary printed at th end of ./configure...).
>>>
>>> Are you sure you  installed the gnutls dev headers?
>> GnuTLS provides an SSL implem, not just SSL.
>>  
>>
>>> However, I'm not sure : Debian's blurb about libcurl3-gnutls says that 
>>> it supports https, imaps, ldaps, smtps and pop3s.
>>>
>>> To be sure, I'll have to setup a virtual machine with a minimal 
>>> environment (no openssl, of course) and try to setup libcurl (and, if 
>>> successful, Sage) in that environment. This is time consuming, so not quite 
>>> real soon...
>>>
>> You mean with gnutls?
>> Or with no ssl/tls at all?
>>
>> I already did the latter and it works (modulo hacking R's configure).
>>
>
>  (sage-sh) jpflori@gcc1-power7:sage.git$ curl-config --protocols
> DICT
> FILE
> FTP
> GOPHER
> HTTP
> IMAP
> POP3
> RTSP
> SCP
> SFTP
> SMTP
> TELNET
> TFTP
> (sage-sh) jpflori@gcc1-power7:sage.git$ R --version
> R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: powerpc64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under the terms of the
> GNU General Public License versions 2 or 3.
> For more information about these matters see
> http://www.gnu.org/licenses/.
>

No HTTPS. Damn.. 

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Emmanuel Charpentier]

Le jeudi 27 octobre 2016 16:59:02 UTC+2, Jean-Pierre Flori a écrit :
>
>
>
> On Thursday, October 27, 2016 at 4:49:23 PM UTC+2, Emmanuel Charpentier 
> wrote:
>>
>>
>>
>> Le jeudi 27 octobre 2016 16:04:52 UTC+2, Jean-Pierre Flori a écrit :
>>>
>>>
>>>
>>> On Thursday, October 27, 2016 at 3:59:26 PM UTC+2, Emmanuel Charpentier 
>>> wrote:



 Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :
>
> It is a most interesting point because it explain why 
> the R binary installed from epel for RH7.1 and family 
> isn’t linked to openssl. 
>

 How old is RH7.1 ? The introduction of the libcurl requirement dates 
 from the R 3.3.0 release, (May 3, 2016).

 I note that Debian (notoriously twitchy about license issues) didn't 
 seem to have any qualms packaging 3.3.0, nor 3.3.1. 

>>>  
>>> I'd say Debian links curl to GnuTLS.
>>>
>>
>> Probably not : My system's curl-config --protocols says that HTTPS: is 
>> supported. A trial of curl's configure --without-ssl --with-gnutls does not 
>> claim to support it (in the summary printed at th end of ./configure...).
>>
>> Are you sure you  installed the gnutls dev headers?
> GnuTLS provides an SSL implem, not just SSL.
>

Yep :
dpkg -l "*tls*" | grep ii
ii  libcurl3-gnutls:amd64 7.50.1-1 amd64easy-to-use 
client-side URL transfer library (GnuTLS flavour)
ii  libcurl4-gnutls-dev:amd64 7.50.1-1 amd64development files 
and documentation for libcurl (GnuTLS flavour)

However, on the very same machine :
dpkg -l "*open*ssl*" | grep ii
ii  libgnutls-openssl27:amd64 3.5.5-2  amd64GNU TLS library - 
OpenSSL wrapper
ii  openssl   1.0.2j-1 amd64Secure Sockets 
Layer toolkit - cryptographic utility
ii  python-openssl16.1.0-1 all  Python 2 wrapper 
around the OpenSSL library

(Don't tell me it's inconsistent; I know it : this machine has been updated 
for 5 years without any reinstallation ; since I follow "testing" a bit 
closely, I tend to accumulate cruft...).

Again, I'm not convinced that a serious test on a clean virtual machine is 
the only way to be sure...)

 
>
>> However, I'm not sure : Debian's blurb about libcurl3-gnutls says that it 
>> supports https, imaps, ldaps, smtps and pop3s.
>>
>> To be sure, I'll have to setup a virtual machine with a minimal 
>> environment (no openssl, of course) and try to setup libcurl (and, if 
>> successful, Sage) in that environment. This is time consuming, so not quite 
>> real soon...
>>
> You mean with gnutls?
> Or with no ssl/tls at all?
>

I mean a pristine machine (Debian gnome + a browser + minimal development 
utilities  + Sage's minimal requirements + gnutls). Given my pipe to the 
net and my (home) machine, that might take a while.

>
> I already did the latter and it works (modulo hacking R's configure).
>

Are you able to install a package from Sage's R ? 

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 4:59:02 PM UTC+2, Jean-Pierre Flori wrote:
>
>
>
> On Thursday, October 27, 2016 at 4:49:23 PM UTC+2, Emmanuel Charpentier 
> wrote:
>>
>>
>>
>> Le jeudi 27 octobre 2016 16:04:52 UTC+2, Jean-Pierre Flori a écrit :
>>>
>>>
>>>
>>> On Thursday, October 27, 2016 at 3:59:26 PM UTC+2, Emmanuel Charpentier 
>>> wrote:



 Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :
>
> It is a most interesting point because it explain why 
> the R binary installed from epel for RH7.1 and family 
> isn’t linked to openssl. 
>

 How old is RH7.1 ? The introduction of the libcurl requirement dates 
 from the R 3.3.0 release, (May 3, 2016).

 I note that Debian (notoriously twitchy about license issues) didn't 
 seem to have any qualms packaging 3.3.0, nor 3.3.1. 

>>>  
>>> I'd say Debian links curl to GnuTLS.
>>>
>>
>> Probably not : My system's curl-config --protocols says that HTTPS: is 
>> supported. A trial of curl's configure --without-ssl --with-gnutls does not 
>> claim to support it (in the summary printed at th end of ./configure...).
>>
>> Are you sure you  installed the gnutls dev headers?
> GnuTLS provides an SSL implem, not just SSL.
>  
>
>> However, I'm not sure : Debian's blurb about libcurl3-gnutls says that it 
>> supports https, imaps, ldaps, smtps and pop3s.
>>
>> To be sure, I'll have to setup a virtual machine with a minimal 
>> environment (no openssl, of course) and try to setup libcurl (and, if 
>> successful, Sage) in that environment. This is time consuming, so not quite 
>> real soon...
>>
> You mean with gnutls?
> Or with no ssl/tls at all?
>
> I already did the latter and it works (modulo hacking R's configure).
>

 (sage-sh) jpflori@gcc1-power7:sage.git$ curl-config --protocols
DICT
FILE
FTP
GOPHER
HTTP
IMAP
POP3
RTSP
SCP
SFTP
SMTP
TELNET
TFTP
(sage-sh) jpflori@gcc1-power7:sage.git$ R --version
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: powerpc64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 4:49:23 PM UTC+2, Emmanuel Charpentier 
wrote:
>
>
>
> Le jeudi 27 octobre 2016 16:04:52 UTC+2, Jean-Pierre Flori a écrit :
>>
>>
>>
>> On Thursday, October 27, 2016 at 3:59:26 PM UTC+2, Emmanuel Charpentier 
>> wrote:
>>>
>>>
>>>
>>> Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :

 It is a most interesting point because it explain why 
 the R binary installed from epel for RH7.1 and family 
 isn’t linked to openssl. 

>>>
>>> How old is RH7.1 ? The introduction of the libcurl requirement dates 
>>> from the R 3.3.0 release, (May 3, 2016).
>>>
>>> I note that Debian (notoriously twitchy about license issues) didn't 
>>> seem to have any qualms packaging 3.3.0, nor 3.3.1. 
>>>
>>  
>> I'd say Debian links curl to GnuTLS.
>>
>
> Probably not : My system's curl-config --protocols says that HTTPS: is 
> supported. A trial of curl's configure --without-ssl --with-gnutls does not 
> claim to support it (in the summary printed at th end of ./configure...).
>
> Are you sure you  installed the gnutls dev headers?
GnuTLS provides an SSL implem, not just SSL.
 

> However, I'm not sure : Debian's blurb about libcurl3-gnutls says that it 
> supports https, imaps, ldaps, smtps and pop3s.
>
> To be sure, I'll have to setup a virtual machine with a minimal 
> environment (no openssl, of course) and try to setup libcurl (and, if 
> successful, Sage) in that environment. This is time consuming, so not quite 
> real soon...
>
You mean with gnutls?
Or with no ssl/tls at all?

I already did the latter and it works (modulo hacking R's configure).

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Emmanuel Charpentier]

Le jeudi 27 octobre 2016 16:04:52 UTC+2, Jean-Pierre Flori a écrit :
>
>
>
> On Thursday, October 27, 2016 at 3:59:26 PM UTC+2, Emmanuel Charpentier 
> wrote:
>>
>>
>>
>> Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :
>>>
>>> It is a most interesting point because it explain why 
>>> the R binary installed from epel for RH7.1 and family 
>>> isn’t linked to openssl. 
>>>
>>
>> How old is RH7.1 ? The introduction of the libcurl requirement dates from 
>> the R 3.3.0 release, (May 3, 2016).
>>
>> I note that Debian (notoriously twitchy about license issues) didn't seem 
>> to have any qualms packaging 3.3.0, nor 3.3.1. 
>>
>  
> I'd say Debian links curl to GnuTLS.
>

Probably not : My system's curl-config --protocols says that HTTPS: is 
supported. A trial of curl's configure --without-ssl --with-gnutls does not 
claim to support it (in the summary printed at th end of ./configure...).

However, I'm not sure : Debian's blurb about libcurl3-gnutls says that it 
supports https, imaps, ldaps, smtps and pop3s.

To be sure, I'll have to setup a virtual machine with a minimal environment 
(no openssl, of course) and try to setup libcurl (and, if successful, Sage) 
in that environment. This is time consuming, so not quite real soon...

--
Emmanuel Charpentier
 

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 3:59:26 PM UTC+2, Emmanuel Charpentier 
wrote:
>
>
>
> Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :
>>
>> It is a most interesting point because it explain why 
>> the R binary installed from epel for RH7.1 and family 
>> isn’t linked to openssl. 
>>
>
> How old is RH7.1 ? The introduction of the libcurl requirement dates from 
> the R 3.3.0 release, (May 3, 2016).
>
> I note that Debian (notoriously twitchy about license issues) didn't seem 
> to have any qualms packaging 3.3.0, nor 3.3.1. 
>
 
I'd say Debian links curl to GnuTLS.

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

Building R against a ssl-less libcurl works (modulo patching configure) and 
does not seem to add errors into R's test suite.
So I suggest the following:
[123]:
* add curl as a standard package and let it use ssl if present except when 
making dist tarballs (ticket needs some tweaking in case of dist tarballs).
* patch R unconditionally and build it against the potentially ssl-free 
curl (patch is ready).

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Emmanuel Charpentier]

Le jeudi 27 octobre 2016 13:10:17 UTC+2, François a écrit :
>
> It is a most interesting point because it explain why 
> the R binary installed from epel for RH7.1 and family 
> isn’t linked to openssl. 
>

How old is RH7.1 ? The introduction of the libcurl requirement dates from 
the R 3.3.0 release, (May 3, 2016).

I note that Debian (notoriously twitchy about license issues) didn't seem 
to have any qualms packaging 3.3.0, nor 3.3.1. 
 

> If they don’t have a rock solid argument, and even if they 
> have, there may not be anymore official R packages from big 
> league binary distros. Unless they patch R, their legal arm 
> will forbid it. 
>

I'm not aware of any such move on Debian. 

>
> So either they will stop distribute R or they will patch 
> en-masse. 
>

Somehow, I doubt it.

Again, why not ask the R core team how they reconcile OpenSSL and GPL'd R ? 
They are a much larger group than we are ; I doubt that the "IANAL" holds 
in their case : if they had any doubts, they probably have consulted people 
who AAL. 

--
Emmanuel Charpentier

>
> If they don’t patch, you may still be able to find a R 
> package for your distro but it won’t be approved by the 
> distro. 
>
> François 
>
> > On 27/10/2016, at 23:22, Emmanuel Charpentier  > wrote: 
> > 
> > So, before coming to these extremities, I'd like to explore two avenues 
> : 
> > Question the R Core Team to know how they reconcile their DPL 2-3 
> license and teir use of OpenSSL, and discuss if we can use the same 
> loophole as they did. In which case, all is fine and dandy... 
> > Excise R proprio dictu and keep the R interface(s) as optional, 
> reworking them to use an externally-installed R. And get rid of the damn 
> beast... 
>
>

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[Florent Hivert]

+1 on AA.

Florent

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[sage-devel] Re: [sage-support] sage-7.4-Ubuntu_16.04-x86_64.tar.bz2 fails to install correctly

[Volker Braun]

https://trac.sagemath.org/ticket/21772

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[David Joyner]

On Thu, Oct 27, 2016 at 4:48 AM, Frédéric Chapoton  wrote:
> Hello,
>
> on https://trac.sagemath.org/ticket/18505, we are trying to enhance the
> is_similar method of matrices.
>
> Because we cannot agree, we require your vote on the following matter:
>
> 1) When M.is_similar(N) is called and either M or N is not square:
>
> A) raise an helpful specific error message
> B) return False
>
> 2) When M.is_similar(N) is called and M and N are square of different sizes:
>
> A) raise an helpful specific error message
> B) return False
>
> Please vote. I am voting AA
>

AA

> Frederic
>
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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Francois Bissey]

It is a most interesting point because it explain why
the R binary installed from epel for RH7.1 and family 
isn’t linked to openssl.
If they don’t have a rock solid argument, and even if they
have, there may not be anymore official R packages from big 
league binary distros. Unless they patch R, their legal arm
will forbid it.

So either they will stop distribute R or they will patch 
en-masse. 

If they don’t patch, you may still be able to find a R 
package for your distro but it won’t be approved by the 
distro.

François

> On 27/10/2016, at 23:22, Emmanuel Charpentier  
> wrote:
> 
> So, before coming to these extremities, I'd like to explore two avenues :
> Question the R Core Team to know how they reconcile their DPL 2-3 license and 
> teir use of OpenSSL, and discuss if we can use the same loophole as they did. 
> In which case, all is fine and dandy...
> Excise R proprio dictu and keep the R interface(s) as optional, reworking 
> them to use an externally-installed R. And get rid of the damn beast...

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[David Roe]

Agreed: AA.

On Oct 27, 2016 04:53, "Vincent Delecroix" <20100.delecr...@gmail.com>
wrote:

> me too: AA
>
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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 12:22:37 PM UTC+2, Emmanuel Charpentier 
wrote:
>
> I'm afraid that we don't have much say in the matter : the R core 
> development team has choosen to rely on curl, and their build system will 
> fail without it. Furthermore, among those 9402 packages, a lot of them may 
> have choosen to follow R "guidance" an use CURL.
>
> If we choose to use another library, we are effectively forking R and a 
> $#!+load of those packages. Somehow, I doubt that we have the workforce to 
> do that credibly...
>
> So, before coming to these extremities, I'd like to explore two avenues :
> Question the R Core Team to know how they reconcile their DPL 2-3 license 
> and teir use of OpenSSL, and discuss if we can use the same loophole as 
> they did. In which case, all is fine and dandy...
>
I don't know how much they thought about it, or rather how many lawyers 
they did pay, but if they ship binaries including the libcurl and openssl 
that might be risky.
Some people invoke the special exception clause of the GPL...
See:
* https://people.gnome.org/~markmc/openssl-and-the-gpl.html
* 
https://groups.google.com/forum/#!searchin/sage-devel/openssl|sort:relevance/sage-devel/mbGbpRz96q0/8nsKRNyLs3oJ
 
(OpenSSL license issue) 
* 
https://groups.google.com/forum/#!searchin/sage-devel/openssl|sort:relevance/sage-devel/Jl11JxIb2E8/-1NrQmjbMKIJ
 
(why GnuTLS which is GPL is not a drop in replacement

If they rely on the user having its own libcurl and openssl then there is 
no problem.
 

> Excise R *proprio dictu* and keep the R interface(s) as optional, 
> reworking them to use an externally-installed R. And get rid of the damn 
> beast...
>
> What do you think ?
>
> Le jeudi 27 octobre 2016 12:11:43 UTC+2, François a écrit :
>>
>> My own examination of R-3.3.1 configure script is that configure will 
>> fail if libcurl 7.28+ is not present or present with ssl disabled 
>> [m4/R.m4 line 4215 thereafter]. 
>> Unless the code for `install.package` has significantly changed between 
>> 3.2.x and 3.3.x it is an unnecessary failure dictated by an unwillingness 
>> to have to support the alternatives. i.e.. not needing to explain what to 
>> do in when libcurl is not present or without ssl support. 
>> I doubt that 
>> install.package(“$some_package”,method=“$somemethod”) 
>> where $somemethod is CURL (command line) or WGET has disappeared. 
>> The R-3.2.1 package for RH7.1/centos7.1 is not compiled against libcurl 
>> or lack https support for example. An interesting experience I had at 
>> work 
>> today with a user. 
>>
>> François 
>>   
>> > On 27/10/2016, at 22:49, Jean-Pierre Flori  wrote: 
>> > 
>> > 
>> > 
>> > On Thursday, October 27, 2016 at 11:41:20 AM UTC+2, Jeroen Demeyer 
>> wrote: 
>> > On 2016-10-27 11:29, Francois Bissey wrote: 
>> > > R package system include downloading facility from repositories. 
>> > 
>> > That's fine but it should be possible to just run R without it's 
>> > packaging system. 
>> > Then I suggest a new solution: 
>> > [666] : 
>> > * patch R if curl (with https support) is not there and make curl an 
>> optional package, 
>> > * not patch R if curl (with https support) is ther. 
>> > 
>> > -- 
>> > You received this message because you are subscribed to the Google 
>> Groups "sage-devel" group. 
>> > To unsubscribe from this group and stop receiving emails from it, send 
>> an email to sage-devel+...@googlegroups.com. 
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>> > For more options, visit https://groups.google.com/d/optout. 
>>
>>

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Francois Bissey]

While not configurable by the user in R-3.2.x it would build if
libcurl wasn’t found or missing https support.
The change to bail out if you don’t fulfil all the condition appear 
deliberate to me. And I see the point from a support point of view.

My conclusion is that R developers would fill it as "not a bug".
We really want this.

François

> On 27/10/2016, at 23:18, Jean-Pierre Flori  wrote:
> 
> Upstream R devs might be somewhat uncooperative.

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Emmanuel Charpentier]

I'm afraid that we don't have much say in the matter : the R core 
development team has choosen to rely on curl, and their build system will 
fail without it. Furthermore, among those 9402 packages, a lot of them may 
have choosen to follow R "guidance" an use CURL.

If we choose to use another library, we are effectively forking R and a 
$#!+load of those packages. Somehow, I doubt that we have the workforce to 
do that credibly...

So, before coming to these extremities, I'd like to explore two avenues :
Question the R Core Team to know how they reconcile their DPL 2-3 license 
and teir use of OpenSSL, and discuss if we can use the same loophole as 
they did. In which case, all is fine and dandy...
Excise R *proprio dictu* and keep the R interface(s) as optional, reworking 
them to use an externally-installed R. And get rid of the damn beast...

What do you think ?

Le jeudi 27 octobre 2016 12:11:43 UTC+2, François a écrit :
>
> My own examination of R-3.3.1 configure script is that configure will 
> fail if libcurl 7.28+ is not present or present with ssl disabled 
> [m4/R.m4 line 4215 thereafter]. 
> Unless the code for `install.package` has significantly changed between 
> 3.2.x and 3.3.x it is an unnecessary failure dictated by an unwillingness 
> to have to support the alternatives. i.e.. not needing to explain what to 
> do in when libcurl is not present or without ssl support. 
> I doubt that 
> install.package(“$some_package”,method=“$somemethod”) 
> where $somemethod is CURL (command line) or WGET has disappeared. 
> The R-3.2.1 package for RH7.1/centos7.1 is not compiled against libcurl 
> or lack https support for example. An interesting experience I had at work 
> today with a user. 
>
> François 
>   
> > On 27/10/2016, at 22:49, Jean-Pierre Flori  > wrote: 
> > 
> > 
> > 
> > On Thursday, October 27, 2016 at 11:41:20 AM UTC+2, Jeroen Demeyer 
> wrote: 
> > On 2016-10-27 11:29, Francois Bissey wrote: 
> > > R package system include downloading facility from repositories. 
> > 
> > That's fine but it should be possible to just run R without it's 
> > packaging system. 
> > Then I suggest a new solution: 
> > [666] : 
> > * patch R if curl (with https support) is not there and make curl an 
> optional package, 
> > * not patch R if curl (with https support) is ther. 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
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> an email to sage-devel+...@googlegroups.com . 
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> > For more options, visit https://groups.google.com/d/optout. 
>
>

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 12:02:42 PM UTC+2, Jeroen Demeyer wrote:
>
> On 2016-10-27 11:49, Jean-Pierre Flori wrote: 
> > 
> > 
> > On Thursday, October 27, 2016 at 11:41:20 AM UTC+2, Jeroen Demeyer 
> wrote: 
> > 
> > On 2016-10-27 11:29, Francois Bissey wrote: 
> >  > R package system include downloading facility from repositories. 
> > 
> > That's fine but it should be possible to just run R without it's 
> > packaging system. 
> > 
> > Then I suggest a new solution: 
> > [666] : 
> > * patch R if curl (with https support) is not there and make curl an 
> > optional package, 
> > * not patch R if curl (with https support) is ther. 
>
> Conditionally patching is really bad because it cannot be pushed upstream. 
>
> Instead, in proper autoconfig style, we should conditionally build the 
> parts requiring curl. That is, change the logic in the R build system to 
> build R without the packaging system if curl is not available. 
>
Upstream R devs might be somewhat uncooperative.
I don't plan on pushing anything upstream. 

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Emmanuel Charpentier]

Le jeudi 27 octobre 2016 11:29:12 UTC+2, François a écrit :
>
> R package system include downloading facility from repositories. 
> That’s why you need curl. At least in theory. 
>

In practice, web access to (a lot of) data repositories, databases, etc... 
is more and more used : there is no point to force users to download a 
whole (WHO|CDC|WTO| I’ll have to check for 3.3.x but there was alternatives in 3.2.x. 
>
> François 
>
> > On 27/10/2016, at 22:26, Jeroen Demeyer  > wrote: 
> > 
> > This is the obvious answer: 
> > 
> >> [6] or patch R not to use curl 
> > 
> > Why should I need a web download tool to do calculations in statistics? 
> > 
> > -- 
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> > For more options, visit https://groups.google.com/d/optout. 
>
>

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Francois Bissey]

My own examination of R-3.3.1 configure script is that configure will
fail if libcurl 7.28+ is not present or present with ssl disabled
[m4/R.m4 line 4215 thereafter].
Unless the code for `install.package` has significantly changed between
3.2.x and 3.3.x it is an unnecessary failure dictated by an unwillingness
to have to support the alternatives. i.e.. not needing to explain what to
do in when libcurl is not present or without ssl support.
I doubt that 
install.package(“$some_package”,method=“$somemethod”)
where $somemethod is CURL (command line) or WGET has disappeared.
The R-3.2.1 package for RH7.1/centos7.1 is not compiled against libcurl
or lack https support for example. An interesting experience I had at work 
today with a user.

François
 
> On 27/10/2016, at 22:49, Jean-Pierre Flori  wrote:
> 
> 
> 
> On Thursday, October 27, 2016 at 11:41:20 AM UTC+2, Jeroen Demeyer wrote:
> On 2016-10-27 11:29, Francois Bissey wrote: 
> > R package system include downloading facility from repositories. 
> 
> That's fine but it should be possible to just run R without it's 
> packaging system. 
> Then I suggest a new solution:
> [666] :
> * patch R if curl (with https support) is not there and make curl an optional 
> package,
> * not patch R if curl (with https support) is ther.
> 
> -- 
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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Emmanuel Charpentier]

As of this morning, CRAN offered 9402 packages... These packages offer 
practical implementations for a tremendous list of applied statistics 
problems (and more...).

Using R "without its packaging system" is about as useful as using Python 
without pip or any other Python packaging system...

--
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Le jeudi 27 octobre 2016 11:41:20 UTC+2, Jeroen Demeyer a écrit :
>
> On 2016-10-27 11:29, Francois Bissey wrote: 
> > R package system include downloading facility from repositories. 
>
> That's fine but it should be possible to just run R without it's 
> packaging system. 
>

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jeroen Demeyer]

On 2016-10-27 11:49, Jean-Pierre Flori wrote:



On Thursday, October 27, 2016 at 11:41:20 AM UTC+2, Jeroen Demeyer wrote:

On 2016-10-27 11:29, Francois Bissey wrote:
 > R package system include downloading facility from repositories.

That's fine but it should be possible to just run R without it's
packaging system.

Then I suggest a new solution:
[666] :
* patch R if curl (with https support) is not there and make curl an
optional package,
* not patch R if curl (with https support) is ther.


Conditionally patching is really bad because it cannot be pushed upstream.

Instead, in proper autoconfig style, we should conditionally build the 
parts requiring curl. That is, change the logic in the R build system to 
build R without the packaging system if curl is not available.


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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

On Thursday, October 27, 2016 at 11:41:20 AM UTC+2, Jeroen Demeyer wrote:
>
> On 2016-10-27 11:29, Francois Bissey wrote: 
> > R package system include downloading facility from repositories. 
>
> That's fine but it should be possible to just run R without it's 
> packaging system. 
>
Then I suggest a new solution:
[666] :
* patch R if curl (with https support) is not there and make curl an 
optional package,
* not patch R if curl (with https support) is ther.

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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jeroen Demeyer]

On 2016-10-27 11:29, Francois Bissey wrote:

R package system include downloading facility from repositories.


That's fine but it should be possible to just run R without it's 
packaging system.


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Re: [sage-devel] Multivariate polynomial factoring and bug(?)

[Jori Mäntysalo]

On Thu, 27 Oct 2016, Vincent Delecroix wrote:


Concerning your code, it got stuck on the first run? What is the
degree of the polynomial you are trying to factorize?


It stucks in every run. You can run my test code, it does not take so 
long.


Degree is 199. And I have no idea about the algorithm Singular uses, and 
the memory requirements. So this may be just a feature.


(Actually there is at least a minor bug: at mimum I should have gotten an 
error message about running out of memory.)


--
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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Francois Bissey]

R package system include downloading facility from repositories.
That’s why you need curl. At least in theory.
I’ll have to check for 3.3.x but there was alternatives in 3.2.x.

François

> On 27/10/2016, at 22:26, Jeroen Demeyer  wrote:
> 
> This is the obvious answer:
> 
>> [6] or patch R not to use curl
> 
> Why should I need a web download tool to do calculations in statistics?
> 
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Re: [sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jeroen Demeyer]

This is the obvious answer:


[6] or patch R not to use curl


Why should I need a web download tool to do calculations in statistics?

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Re: [sage-devel] Multivariate polynomial factoring and bug(?)

[Vincent Delecroix]

On 27 October 2016 at 11:21, Jori Mäntysalo  wrote:
> On Thu, 27 Oct 2016, Vincent Delecroix wrote:
>
>> 1) What is [a, b, c, d, e]?
>
>
> Arghs, forgot the definition list:
>
> R. = QQ['a, b, c, d, e']
>
>> 2) Your would better replace
>>
>>  [a, b, c, d, e][randint(0,4)]
>>
>> by
>>
>>  choice([a,b,c,d,e])
>
>
> That means using plain Python function to get a random number. I don't know
> if it plays well with Sage random state.

choice is pure Python

>>> import random
>>> random.choice
>

> But in any case, this is just a test code to see how well Singular works.

It helps if it is easier to read.



Concerning your code, it got stuck on the first run? What is the
degree of the polynomial you are trying to factorize?

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Re: [sage-devel] Multivariate polynomial factoring and bug(?)

[Jori Mäntysalo]

On Thu, 27 Oct 2016, Vincent Delecroix wrote:


1) What is [a, b, c, d, e]?


Arghs, forgot the definition list:

R. = QQ['a, b, c, d, e']


2) Your would better replace

 [a, b, c, d, e][randint(0,4)]

by

 choice([a,b,c,d,e])


That means using plain Python function to get a random number. I don't 
know if it plays well with Sage random state.


But in any case, this is just a test code to see how well Singular works.

--
Jori Mäntysalo

Re: [sage-devel] Multivariate polynomial factoring and bug(?)

[Vincent Delecroix]

1) What is [a, b, c, d, e]?

2) Your would better replace

  [a, b, c, d, e][randint(0,4)]

by

  choice([a,b,c,d,e])


On 27 October 2016 at 10:00, Jori Mäntysalo  wrote:
> As we now have Singular 4, I just made a little random test:
>
> set_random_seed(0)
> for i in range(1000):
> P = 1
> while random() < 0.9:
> M = (randint(1, 5) * ([a, b, c, d, e][randint(0, 4)])^randint(1, 5))
> A = (randint(1, 5) * ([a, b, c, d, e][randint(0, 4)])^randint(1, 5))
> P = P*M + A
> Q = 1
> while random() < 0.9:
> M = (randint(1, 5) * ([a, b, c, d, e][randint(0, 4)])^randint(1, 5))
> A = (randint(1, 5) * ([a, b, c, d, e][randint(0, 4)])^randint(1, 5))
> Q = Q*M + A
> if i == 112:
> print(P)
> print()
> print(Q)
> F = factor(P*Q)
>
> and this got stuck. Might be that it just needs more memory than I have; I
> don't know how much it normally uses.
>
> --
> Jori Mäntysalo

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Re: [sage-devel] vote on behaviour of is_similar for matrices

[Vincent Delecroix]

me too: AA

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[sage-devel] vote on behaviour of is_similar for matrices

[Frédéric Chapoton]

Hello,

on https://trac.sagemath.org/ticket/18505, we are trying to enhance the 
*is_similar* method of matrices.

Because we cannot agree, we require your vote on the following matter:

1) When M.is_similar(N) is called and either M or N is not square:

A) raise an helpful specific error message
B) return False

2) When M.is_similar(N) is called and M and N are square of different sizes:

A) raise an helpful specific error message
B) return False

Please vote. I am voting AA

Frederic

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Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet

[Luca De Feo]

Here's a quite popular service to share Jupyter notebooks together
with a preset environment (e.g., a SageMath kernel) :

  http://mybinder.org/

Quite a different workflow compared to sharing a notebook on a SageNB
server, though.

Luca




On Thu, Oct 27, 2016 at 7:11 AM, Jori Mäntysalo  wrote:
> On Sun, 23 Oct 2016, Luca De Feo wrote:
>
>> When I want to share a notebook with the students, I share a static
>> .ipynb file via gist, and visualize it via nbviewer. e.g.:
>>
>>  http://nbviewer.jupyter.org/gist/defeo/4adb727f7608dfd2c75eb7699d670fb7
>>
>> When I want to see the student's work, I ask them to send me the
>> .ipynb by mail, or directly access their notebooks using my admin
>> account.
>>
>> Works like a charm.
>
>
> OK, sounds possible to do. But document sharing between researchers still
> does not work. (But to be honest, only sharing so far here has been me
> replying to request like "Can you test this hypothesis?". Maybe some day...)
>
> --
> Jori Mäntysalo

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[sage-devel] R 3.3.1 depends on a SSL/TLS implementation

[Jean-Pierre Flori]

Hi all,

The latest R versions depends on libcurl and actually more than that: on a 
libcurl with https support.
So we might want to build our own libcurl with https support (see #21767) 
but we then need an SSL/TLS implementation which Sage curretnly provides 
only optionally through openSSL because of license issues so we can:
[1] either make R depend on libcurl depend on openssl and they all become 
optional,
[2] or make R depend on libcurl and make them standard and add an SSL/TLS 
implementation and its development headers a prereq,
[3] or make libcurl with https support (and development headers) a prereq, 
which basically means adding an SSL/TLS implementation as a prereq as well,
[4] or make R a prereq,
[5] or drop R support,
[6] or patch R not to use curl,
[7] or patch R to use curl but without https support,
[8] or wait until the end of times,
[9] or a mix of all of this,
[10] or do something else.

What do you think?

Best,
JPF

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[sage-devel] Multivariate polynomial factoring and bug(?)

[Jori Mäntysalo]

As we now have Singular 4, I just made a little random test:

set_random_seed(0)
for i in range(1000):
P = 1
while random() < 0.9:
M = (randint(1, 5) * ([a, b, c, d, e][randint(0, 4)])^randint(1, 5))
A = (randint(1, 5) * ([a, b, c, d, e][randint(0, 4)])^randint(1, 5))
P = P*M + A
Q = 1
while random() < 0.9:
M = (randint(1, 5) * ([a, b, c, d, e][randint(0, 4)])^randint(1, 5))
A = (randint(1, 5) * ([a, b, c, d, e][randint(0, 4)])^randint(1, 5))
Q = Q*M + A
if i == 112:
print(P)
print()
print(Q)
F = factor(P*Q)

and this got stuck. Might be that it just needs more memory than I have; I 
don't know how much it normally uses.


--
Jori Mäntysalo