Re: [sage-devel] Re: Optional and experimental packages

[Samuel Lelièvre]

Tue 2019-10-29 11:57 UTC, kcrisman:
>
>> Perhaps should we simply remove the pseudo-packages whose type is "pip"
>> (since there is the "sage -pip install" command), that is:
>>
>> beautifulsoup
>> biopython
>> brian
>> guppy
>> mercurial
>> mpi4py
>> nibabel
>> pybtex
>> pyflakes
>> sqlalchemy
>> trac
>
>
> As long as we can test that this works properly with "our" Python
> and make sure to update any documentation, that would be okay.
>  brian for instance probably doesn't need too much doc change.

> beautifulsoup was (is?) used for sagenb -> rst conversion,
> if I recall correctly, and if it isn't used elsewhere would probably be
> reasonable to deprecate, much as one might mourn the loss of
> sagenb in the near future.  (Though there may still be some places
> in some tutorials where this is mentioned, beautifulsoup I mean.)

We should keep the ability to export sagenb ".sws" worksheets
to rst and to ipynb for a long time. There are many, really many
people still using SageNB, and many, really many sws worksheets
out there.

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[sage-devel] Re: Switch to Python 3 by default

[Travis Scrimshaw]

+1

On Sunday, October 27, 2019 at 9:58:23 AM UTC+10, Volker Braun wrote:
>
> Maybe I missed it, but I didn't find a ticket for that. I think now would 
> be a good time to flip the switch, though. Any thoughts?
>

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Re: [sage-devel] Re: OSX Catalina works

[Andrew]

Thanks everyone for their comments.

 > try explicitly adding "-stdlib=libc++" to CXXLAGS and LDFLAGS.

Adding these flags to the Makefile didn't change anything: the build again 
failed with givaro-4.1.1

> After installing Xcode, did you run Xcode? 

Yes, of course! Xcode and the command line tools are both fully installed, 
with the terms and conditions agreed. The build would fail much earlier if 
this was not the case.

Just for fun I tried reinstalling Xcode (and the command line tools and 
then accepting the xcode conditions etc) but this made no difference in the 
sense that the sage build died at exactly the same place. Perhaps I should 
winding back to xcode 11?

Andrew

On Wednesday, 30 October 2019 11:39:18 UTC+11, Samuel Lelievre wrote:
>
> Tue 2019-10-29 11:46 UTC, Andrew: 
> > 
> > Thanks Dima 
> > 
> > On Tuesday, 29 October 2019 17:51:02 UTC+11, Dima Pasechnik wrote: 
> >> 
> >> Did you  run 
> >> 
> >> xcode-select --install 
> >> 
> >> after Xcode upgrade? 
> > 
> > 
> > Yes, the command line tools are correctly installed but, as far as I can 
> see, 
> > xcode-select --install  is no longer the correct way to check this 
> > because it results in the error: 
> > 
> > xcode-select: error: command line tools are already installed, use 
> "Software Update" to install updates 
>
> It's still the correct way; the error message is for trying to install 
> while it's already installed. Sometimes one needs to start XCode 
> once, and agree to the terms and conditions. 
>

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[sage-devel] Re: [sage-support] optional packages and binder

[Vincent Delecroix]

Dear Enrique,

It would be helpful to have the complete error message and the log
of the failed build. And if you know how to do that, you can open
a trac ticket.

Also, it would be nice to have docker images for Sage with most (if
not all) optional packages installed.

Vincent

Le 29/10/2019 à 05:13, Enrique Artal a écrit :

I want to make available some of my notebooks in binder. I found very
useful sage-binder-env but I ran into problems in a case where I needed an
optional package, namely gap_packages. As stated I installed make package
using the Dockerfile but the installation stops with an error in make
all-toolchain. I guess I need to install more packages but I do not know
which ones. Best regards, Enrique.



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Re: [sage-devel] Re: OSX Catalina works

[Samuel Lelièvre]

Tue 2019-10-29 11:46 UTC, Andrew:
>
> Thanks Dima
>
> On Tuesday, 29 October 2019 17:51:02 UTC+11, Dima Pasechnik wrote:
>>
>> Did you  run
>>
>> xcode-select --install
>>
>> after Xcode upgrade?
>
>
> Yes, the command line tools are correctly installed but, as far as I can see,
> xcode-select --install  is no longer the correct way to check this
> because it results in the error:
>
> xcode-select: error: command line tools are already installed, use "Software 
> Update" to install updates

It's still the correct way; the error message is for trying to install
while it's already installed. Sometimes one needs to start XCode
once, and agree to the terms and conditions.

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[sage-devel] Re: Symbolic Variables for Internal Use

[Nils Bruin]

Short answer: no.

Workaround: conceive some prefix to make a really unlikely name; something 
like _my_internal_symbol_t_ or so.

Ameliorating circumstance: for the most part, symbolic variables are just 
immutable place-holders, so it shouldn't matter who uses them. Probably the 
most serious case is when your code interacts with user-supplied symbolic 
expressions and you need to ensure that the variable you use is distinct 
from the ones that occur in the supplied expressions. A prefix should 
handle that (this is also how sage tries to avoid collisions when shipping 
symbols to maxima: it prefixes them with _sage_var_). There is some global 
state in the form of assumptions that can affect the meaning of symbols in 
SR.

If you need multiple "unique" expressions you could go with a symbol 
generating function. A very primitive one:

def gensym_generator():
i=1
while True:
yield SR.symbol("gensym%o"%i)
i+=1
gensym=gensym_generator().next

Every time you call gensym() you'll get a new symbol. Beware that these 
symbols are not unique across sessions, so if you intend to use parallel 
processing you already need to do something else (hash time in milliseconds 
plus process ID together or something like that)

Also: don't overuse that kind of thing: symbolic variable are leaky (they 
don't really get garbage collected).

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[sage-devel] Symbolic Variables for Internal Use

[Michael Jung]

I'd like to use symbolic expressions in the source code to compute taylor 
expansions of predefined functions. But this affects the use of variables 
named the same way on the level of the user. Is there a safe way to use the 
framework of symbolic calculus without affecting the variables globally?

Thanks in advance! :)

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Re: [sage-devel] Re: sage.plot.graphics.GraphicsArray no longer available?

[Eric Gourgoulhon]

Le mardi 29 octobre 2019 23:49:41 UTC+1, William a écrit :
>
> On Tue, Oct 29, 2019 at 1:37 PM Eric Gourgoulhon  > wrote:  
> > 
> > Do you think it's necessary to add a redirect import for GraphicsArray 
> from sage.plot.graphics? We can easily make a new ticket to fix this for 
> Sage 9.0. 
> > 
>
> I don't think it is strictly necessary, but I personally think it 
> would be nice since at least two people were explicitly importing 
> that:  (1) me -- for cocalc, and (2) the original poster, Pong, in 
> this thread.  There could easily be other people doing the same 
> thing... 
>
>
OK, this is now  https://trac.sagemath.org/ticket/28675

Eric.

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Re: [sage-devel] Re: sage.plot.graphics.GraphicsArray no longer available?

[William Stein]

On Tue, Oct 29, 2019 at 1:37 PM Eric Gourgoulhon  wrote:
>
> Le mardi 29 octobre 2019 21:17:02 UTC+1, Eric Gourgoulhon a écrit :
>>
>> Le mardi 29 octobre 2019 19:19:51 UTC+1, William a écrit :
>>>
>>>
>>> It's (obviously) likely that at least one person did that.   This is part 
>>> of the public API of Sage, so it would be good if it were deprecated before 
>>> removal (or just left in via a one-liner redirect import).
>>
>>
>> Sorry about that.  Since the user interface graphics_array() was left 
>> unchanged, I did not felt necessary to add a deprecation notice.
>
>
> Do you think it's necessary to add a redirect import for GraphicsArray from 
> sage.plot.graphics? We can easily make a new ticket to fix this for Sage 9.0.
>

I don't think it is strictly necessary, but I personally think it
would be nice since at least two people were explicitly importing
that:  (1) me -- for cocalc, and (2) the original poster, Pong, in
this thread.  There could easily be other people doing the same
thing...

William

-- 
William (http://wstein.org)

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[sage-devel] Re: sage.plot.graphics.GraphicsArray no longer available?

[Eric Gourgoulhon]

Le mardi 29 octobre 2019 21:17:02 UTC+1, Eric Gourgoulhon a écrit :
>
> Le mardi 29 octobre 2019 19:19:51 UTC+1, William a écrit :
>>
>>
>> It's (obviously) likely that at least one person did that.   This is part 
>> of the public API of Sage, so it would be good if it were deprecated before 
>> removal (or just left in via a one-liner redirect import).   
>>
>
> Sorry about that.  Since the user interface graphics_array() was left 
> unchanged, I did not felt necessary to add a deprecation notice. 
>

Do you think it's necessary to add a redirect import for GraphicsArray from 
sage.plot.graphics? We can easily make a new ticket to fix this for Sage 
9.0.

Eric.

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[sage-devel] Re: sage.plot.graphics.GraphicsArray no longer available?

[Eric Gourgoulhon]

Le mardi 29 octobre 2019 19:19:51 UTC+1, William a écrit :
>
>
> It's (obviously) likely that at least one person did that.   This is part 
> of the public API of Sage, so it would be good if it were deprecated before 
> removal (or just left in via a one-liner redirect import).   
>

Sorry about that.  Since the user interface graphics_array() was left 
unchanged, I did not felt necessary to add a deprecation notice. Actually 
the main reason why I moved GraphicsArray from graphics.py to the new file 
multi_graphics.py is that the former was already more than 3,500 lines 
long. I could of course have added the new class MultiGraphics in 
graphics.py, but this would have resulted in a file of ~ 4,700 lines... 
Currently (Sage 9.0.beta3) the situation in src/sage/plot is as follows:

- graphics.py (3,318 lines --> 3403 lines in 9.0.beta4): class Graphics
- multi_graphics.py (878 lines --> 1318 lines in 9.0.beta4): class 
MultiGraphics and the derived class GraphicsArray.

The user interface is via the following functions/methods:

- graphics_array(): creates a GraphicsArray
- multi_graphics(): creates a MultiGraphics from a list of Graphics objects 
and positions (to appear in Sage 9.0.beta4, cf #27866 
) 
- Graphics.inset(): creates an inset in a Graphics (returns a MultiGraphics)

Best wishes,

Eric.

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[sage-devel] Re: sage.plot.graphics.GraphicsArray no longer available?

[William]

On Friday, October 25, 2019 at 4:32:49 AM UTC-7, kcrisman wrote:
>
> I didn't think that this would break any code - is it a very likely thing 
> that people would have been importing this class explicitly instead of 
> using the wrapper?
>

It's (obviously) likely that at least one person did that.   This is part 
of the public API of Sage, so it would be good if it were deprecated before 
removal (or just left in via a one-liner redirect import).   As soon as I 
saw this code, I suspected this would happen, so I rewrote our client code 
(for cocalc) to be more robust... 
https://github.com/sagemathinc/cocalc/commit/bbe5ead182358e40427dc7884445099fdb4fc818#diff-a103ad80295a75843b8e11e34da98611

 

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Re: [sage-devel] Re: OSX Catalina works

[John H Palmieri]

On Tuesday, October 29, 2019 at 4:45:53 AM UTC-7, Andrew wrote:
>
> Thanks Dima
>
> On Tuesday, 29 October 2019 17:51:02 UTC+11, Dima Pasechnik wrote:
>>
>> Did you  run 
>>
>> xcode-select --install 
>>
>> after Xcode upgrade? 
>>
>
> Yes, the command line tools are correctly installed but, as far as I can 
> see, xcode-select --install  is no longer the correct way to check this 
> because it results in the error:
>
> xcode-select: error: command line tools are already installed, use 
> "Software Update" to install updates
>

After installing Xcode, did you run Xcode? Often it needs to be run once to 
install some components, and in particular the command line tools.

 

>  
>
>> By the way, why don't you use NTL from brew? 
>> https://formulae.brew.sh/formula/ntl#default 
>>
>> you can also make things easier by installing Flint and Arb into 
>> homebrew, by using formulas from 
>> https://github.com/dimpase/homebrew-science 
>>
>> Run 
>>
>> brew install dimpase/science/flint 
>> brew install dimpase/science/arb 
>>
>
> Thanks. I didn't know that there were homebrew formulas for any of these. 
> Unfortunately, neither of these work either, giving similar (but shorter) 
> messages to the compilation errors with sage. Installing flint results in:
>
> ==> Downloading http://flintlib.org/flint-2.5.2.tar.gz
>  
> 100.0%
> ==> ./configure --prefix=/usr/local/Cellar/flint/2.5.2_1 
> --with-gmp=/usr/local/opt/gmp --with-mpfr=/u
> ==> make
> Last 15 lines from /Users/andrew/Library/Logs/Homebrew/flint/02.make:
>   ~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:324:9:
>  
> error: no member named 'islessgreater' in the global namespace
> using ::islessgreater;
>   ~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:325:9:
>  
> error: no member named 'isunordered' in the global namespace
> using ::isunordered;
>   ~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:326:9:
>  
> error: no member named 'isunordered' in the global namespace
> using ::isunordered;
>   ~~^
> 13 errors generated.
> make[2]: *** [build/interfaces/NTL-interface.lo] Error 1
> clang: error: no such file or directory: 
> 'build/interfaces/NTL-interface.lo'
> make[1]: *** [libflint-13.5.2.dylib] Error 1
> make: *** [library] Error 2
>
>
> and arb fails in the same way because it first tries to install flint.
>
> Andrew
>
>
>
>> (these are source-only, so this will build packages from source) 
>>
>>
>> On Tue, Oct 29, 2019 at 2:01 AM Andrew  wrote: 
>> > 
>> > I (stupidly) upgraded to XCode 11.1 on catalina. I have succeeded in 
>> compiling sage with python2, not python 3, on an imac but can't get it to 
>> compile on a macbook pro with fairly similar specs.I am using homebrew and 
>> have: 
>> > 
>> > ProductName:Mac OS X 
>> > ProductVersion:10.15 
>> > BuildVersion:19A603 
>> > Xcode 11.1 
>> > Build version 11A1027 
>> > 
>> > with gcc --version returning 
>> > 
>> > Configured with: 
>> --prefix=/Applications/Xcode.app/Contents/Developer/usr 
>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
>>  
>>
>> > Apple clang version 11.0.0 (clang-1100.0.33.8) 
>> > Target: x86_64-apple-darwin19.0.0 
>> > Thread model: posix 
>> > InstalledDir: 
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>  
>>
>> > 
>> > When I try to compile sage is breaks with: 
>> > 
>> > * package: givaro-4.1.1 
>> >   log file: /usr/local/src/sage/logs/pkgs/givaro-4.1.1.log 
>> >   build directory: 
>> /usr/local/src/sage/local/var/tmp/sage/build/givaro-4.1.1 
>> > * package: ntl-11.3.2 
>> >   log file: /usr/local/src/sage/logs/pkgs/ntl-11.3.2.log 
>> >   build directory: 
>> /usr/local/src/sage/local/var/tmp/sage/build/ntl-11.3.2 
>> > 
>> > Sometimes I also get ntl failing to compile. I have compared the log 
>> files one the two machines but can't identify the problem. I attach the log 
>> files for givaro and ntl and the install.log from the machine that has the 
>> problem. Does anyone have any ideas how to fix this? 
>> > 
>> > Andrew 
>> > 
>> > -- 
>> > 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-...@googlegroups.com. 
>> > To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/sage-devel/695c9caa-6efe-49ad-a05f-100c49be7a93%40googlegroups.com.
>>  
>>
>>
>

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Re: [sage-devel] Re: OSX Catalina works

[Dima Pasechnik]

try explicitly adding "-stdlib=libc++" to CXXLAGS and LDFLAGS.


On Tue, 29 Oct 2019, 13:45 Andrew,  wrote:

> Thanks Dima
>
> On Tuesday, 29 October 2019 17:51:02 UTC+11, Dima Pasechnik wrote:
>>
>> Did you  run
>>
>> xcode-select --install
>>
>> after Xcode upgrade?
>>
>
> Yes, the command line tools are correctly installed but, as far as I can
> see, xcode-select --install  is no longer the correct way to check this
> because it results in the error:
>
> xcode-select: error: command line tools are already installed, use
> "Software Update" to install updates
>
>
>> By the way, why don't you use NTL from brew?
>> https://formulae.brew.sh/formula/ntl#default
>>
>> you can also make things easier by installing Flint and Arb into
>> homebrew, by using formulas from
>> https://github.com/dimpase/homebrew-science
>>
>> Run
>>
>> brew install dimpase/science/flint
>> brew install dimpase/science/arb
>>
>
> Thanks. I didn't know that there were homebrew formulas for any of these.
> Unfortunately, neither of these work either, giving similar (but shorter)
> messages to the compilation errors with sage. Installing flint results in:
>
> ==> Downloading http://flintlib.org/flint-2.5.2.tar.gz
> 
> 100.0%
> ==> ./configure --prefix=/usr/local/Cellar/flint/2.5.2_1
> --with-gmp=/usr/local/opt/gmp --with-mpfr=/u
> ==> make
> Last 15 lines from /Users/andrew/Library/Logs/Homebrew/flint/02.make:
>   ~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:324:9:
> error: no member named 'islessgreater' in the global namespace
> using ::islessgreater;
>   ~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:325:9:
> error: no member named 'isunordered' in the global namespace
> using ::isunordered;
>   ~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:326:9:
> error: no member named 'isunordered' in the global namespace
> using ::isunordered;
>   ~~^
> 13 errors generated.
> make[2]: *** [build/interfaces/NTL-interface.lo] Error 1
> clang: error: no such file or directory:
> 'build/interfaces/NTL-interface.lo'
> make[1]: *** [libflint-13.5.2.dylib] Error 1
> make: *** [library] Error 2
>
>
> and arb fails in the same way because it first tries to install flint.
>
> Andrew
>
>
>
>> (these are source-only, so this will build packages from source)
>>
>>
>> On Tue, Oct 29, 2019 at 2:01 AM Andrew  wrote:
>> >
>> > I (stupidly) upgraded to XCode 11.1 on catalina. I have succeeded in
>> compiling sage with python2, not python 3, on an imac but can't get it to
>> compile on a macbook pro with fairly similar specs.I am using homebrew and
>> have:
>> >
>> > ProductName:Mac OS X
>> > ProductVersion:10.15
>> > BuildVersion:19A603
>> > Xcode 11.1
>> > Build version 11A1027
>> >
>> > with gcc --version returning
>> >
>> > Configured with:
>> --prefix=/Applications/Xcode.app/Contents/Developer/usr
>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
>>
>> > Apple clang version 11.0.0 (clang-1100.0.33.8)
>> > Target: x86_64-apple-darwin19.0.0
>> > Thread model: posix
>> > InstalledDir:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>
>> >
>> > When I try to compile sage is breaks with:
>> >
>> > * package: givaro-4.1.1
>> >   log file: /usr/local/src/sage/logs/pkgs/givaro-4.1.1.log
>> >   build directory:
>> /usr/local/src/sage/local/var/tmp/sage/build/givaro-4.1.1
>> > * package: ntl-11.3.2
>> >   log file: /usr/local/src/sage/logs/pkgs/ntl-11.3.2.log
>> >   build directory:
>> /usr/local/src/sage/local/var/tmp/sage/build/ntl-11.3.2
>> >
>> > Sometimes I also get ntl failing to compile. I have compared the log
>> files one the two machines but can't identify the problem. I attach the log
>> files for givaro and ntl and the install.log from the machine that has the
>> problem. Does anyone have any ideas how to fix this?
>> >
>> > Andrew
>> >
>> > --
>> > 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-...@googlegroups.com.
>> > To view this discussion on the web visit
>> https://groups.google.com/d/msgid/sage-devel/695c9caa-6efe-49ad-a05f-100c49be7a93%40googlegroups.com.
>>
>>
> --
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> "sage-devel" group.
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> 

Re: [sage-devel] Re: Optional and experimental packages

[kcrisman]

> > 
> > Sage-wise, I believe Mercurial is a remnant of the time 
> > before we switched to Git. I think we should remove it. 
>
>
I'm surprised it hadn't been long before.  Even I would approve that.

 

>
> Perhaps should we simply remove the pseudo-packages whose type is "pip" 
> (since there is the "sage -pip install" command), that is: 
>
> beautifulsoup 
> biopython 
> brian 
> guppy 
> mercurial 
> mpi4py 
> nibabel 
> pybtex 
> pyflakes 
> sqlalchemy 
> trac 
>

As long as we can test that this works properly with "our" Python and make 
sure to update any documentation, that would be okay.  brian for instance 
probably doesn't need too much doc change.  beautifulsoup was (is?) used 
for sagenb -> rst conversion, if I recall correctly, and if it isn't used 
elsewhere would probably be reasonable to deprecate, much as one might 
mourn the loss of sagenb in the near future.  (Though there may still be 
some places in some tutorials where this is mentioned, beautifulsoup I 
mean.) 

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Re: [sage-devel] Re: OSX Catalina works

[Andrew]

Thanks Dima

On Tuesday, 29 October 2019 17:51:02 UTC+11, Dima Pasechnik wrote:
>
> Did you  run 
>
> xcode-select --install 
>
> after Xcode upgrade? 
>

Yes, the command line tools are correctly installed but, as far as I can 
see, xcode-select --install  is no longer the correct way to check this 
because it results in the error:

xcode-select: error: command line tools are already installed, use 
"Software Update" to install updates
 

> By the way, why don't you use NTL from brew? 
> https://formulae.brew.sh/formula/ntl#default 
>
> you can also make things easier by installing Flint and Arb into 
> homebrew, by using formulas from 
> https://github.com/dimpase/homebrew-science 
>
> Run 
>
> brew install dimpase/science/flint 
> brew install dimpase/science/arb 
>

Thanks. I didn't know that there were homebrew formulas for any of these. 
Unfortunately, neither of these work either, giving similar (but shorter) 
messages to the compilation errors with sage. Installing flint results in:

==> Downloading http://flintlib.org/flint-2.5.2.tar.gz
 
100.0%
==> ./configure --prefix=/usr/local/Cellar/flint/2.5.2_1 
--with-gmp=/usr/local/opt/gmp --with-mpfr=/u
==> make
Last 15 lines from /Users/andrew/Library/Logs/Homebrew/flint/02.make:
  ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:324:9:
 
error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
  ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:325:9:
 
error: no member named 'isunordered' in the global namespace
using ::isunordered;
  ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:326:9:
 
error: no member named 'isunordered' in the global namespace
using ::isunordered;
  ~~^
13 errors generated.
make[2]: *** [build/interfaces/NTL-interface.lo] Error 1
clang: error: no such file or directory: 'build/interfaces/NTL-interface.lo'
make[1]: *** [libflint-13.5.2.dylib] Error 1
make: *** [library] Error 2


and arb fails in the same way because it first tries to install flint.

Andrew



> (these are source-only, so this will build packages from source) 
>
>
> On Tue, Oct 29, 2019 at 2:01 AM Andrew > 
> wrote: 
> > 
> > I (stupidly) upgraded to XCode 11.1 on catalina. I have succeeded in 
> compiling sage with python2, not python 3, on an imac but can't get it to 
> compile on a macbook pro with fairly similar specs.I am using homebrew and 
> have: 
> > 
> > ProductName:Mac OS X 
> > ProductVersion:10.15 
> > BuildVersion:19A603 
> > Xcode 11.1 
> > Build version 11A1027 
> > 
> > with gcc --version returning 
> > 
> > Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
>  
>
> > Apple clang version 11.0.0 (clang-1100.0.33.8) 
> > Target: x86_64-apple-darwin19.0.0 
> > Thread model: posix 
> > InstalledDir: 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>  
>
> > 
> > When I try to compile sage is breaks with: 
> > 
> > * package: givaro-4.1.1 
> >   log file: /usr/local/src/sage/logs/pkgs/givaro-4.1.1.log 
> >   build directory: 
> /usr/local/src/sage/local/var/tmp/sage/build/givaro-4.1.1 
> > * package: ntl-11.3.2 
> >   log file: /usr/local/src/sage/logs/pkgs/ntl-11.3.2.log 
> >   build directory: 
> /usr/local/src/sage/local/var/tmp/sage/build/ntl-11.3.2 
> > 
> > Sometimes I also get ntl failing to compile. I have compared the log 
> files one the two machines but can't identify the problem. I attach the log 
> files for givaro and ntl and the install.log from the machine that has the 
> problem. Does anyone have any ideas how to fix this? 
> > 
> > Andrew 
> > 
> > -- 
> > 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-...@googlegroups.com . 
> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/695c9caa-6efe-49ad-a05f-100c49be7a93%40googlegroups.com.
>  
>
>

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Re: [sage-devel] Optional and experimental packages

[Nico Van Cleemput]

OK, the answer is below:

The file splay.c is actually taken from Nauty, so that issue should be
resolved there. The most obvious solution is to not compile this as C99,
but as C89 since that is what buckygen was written in.

So, I can mail this to Brendan McKay to ask to solve this, but since Nauty
is already in Sage the issue should already be resolved in that code, so we
could also just take splay.c from there.

Nico

Op di 29 okt. 2019 om 09:31 schreef Nico Van Cleemput <
nico.vancleem...@gmail.com>:

> Well, upstream sits at another desk in my office, so I will ask when he
> gets in.
>
> Nico
>
> Op di 29 okt. 2019 09:29 schreef Dima Pasechnik :
>
>> clang is unhappy about C standards violations. E.g. this is what I get
>> with clang 7:
>>
>> cc -O4 buckygen.c -o buckygen
>> cc: warning: -O4 is equivalent to -O3 [-Wdeprecated]
>> In file included from buckygen.c:272:
>> ./splay.c:139:6: warning: implicit declaration of function
>> 'outputnode' is invalid in C99 [-Wimplicit-function-declaration]
>> ACTION(p);
>> ^
>> buckygen.c:254:19: note: expanded from macro 'ACTION'
>> #define ACTION(p) outputnode(p)
>>   ^
>> In file included from buckygen.c:272:
>> ./splay.c:263:15: warning: implicit declaration of function
>> 'comparenodes' is invalid in C99 [-Wimplicit-function-declaration]
>> cmp = COMPARE(p);
>>   ^
>> buckygen.c:260:20: note: expanded from macro 'COMPARE'
>> #define COMPARE(p) comparenodes(canong, codelength, type, p)
>>^
>> In file included from buckygen.c:272:
>> ./splay.c:328:15: warning: implicit declaration of function
>> 'comparenodes' is invalid in C99 [-Wimplicit-function-declaration]
>> cmp = COMPARE(p);
>>   ^
>> buckygen.c:260:20: note: expanded from macro 'COMPARE'
>> #define COMPARE(p) comparenodes(canong, codelength, type, p)
>>^
>> In file included from buckygen.c:272:
>> ./splay.c:352:20: error: non-void function 'splay_delete' should
>> return a value [-Wreturn-type]
>> if (p == NULL) return;
>>^
>> ./splay.c:366:2: error: non-void function 'splay_delete' should return
>> a value [-Wreturn-type]
>> return;
>> ^
>> ./splay.c:376:9: error: non-void function 'splay_delete' should return
>> a value [-Wreturn-type]
>> return;
>> ^
>> buckygen.c:943:1: warning: type specifier missing, defaults to 'int'
>> [-Wimplicit-int]
>> outputnode(SPLAYNODE *liste)
>> ^
>> 4 warnings and 3 errors generated.
>> make: *** [makefile:12: buckygen] Error 1
>>
>> Easy to fix, I'd say - can this be done upstream?
>>
>> On Tue, Oct 29, 2019 at 8:31 AM Nico Van Cleemput
>>  wrote:
>> >
>> > buckygen is a pure C package, so I doubt that this has anything to do
>> with the switch to Python 3. Do you have any more information about the
>> fail build, because here it built fine.
>> >
>> > Nico
>> >
>> > Op ma 28 okt. 2019 om 23:02 schreef John H Palmieri <
>> jhpalmier...@gmail.com>:
>> >>
>> >> With a Python 3 build of Sage on OS X 10.14.6, I decided to install as
>> many optional and experimental packages as I could. The results:
>> >>
>> >> Optional:
>> >>
>> >> - the following packages failed to build, and the reason wasn't
>> completely obvious:
>> >>
>> >> awali
>> >> buckygen
>> >> cbc
>> >> gambit
>> >> gdb
>> >> mpi4py
>> >>
>> >> - the following packages failed because they (or their installation
>> scripts) are not compatible with Python 3:
>> >>
>> >> beautifulsoup
>> >> brian
>> >> guppy
>> >> mercurial
>> >> p_group_cohomology (but work is in progress)
>> >> pyx
>> >> scons
>> >> trac
>> >>
>> >> - the following packages failed at first, but built after installing
>> some prerequisities:
>> >>
>> >> deformation — requires installation of mpir
>> >> dot2tex — requires Graphviz
>> >> rst2ipynb — requires pandoc
>> >>
>> >> - I skipped the following packages:
>> >>
>> >> atlas (installation is skipped on OS X)
>> >> python2 (I wanted to use a pure Python 3 build)
>> >>
>> >> - Every other optional package built.
>> >>
>> >> Question/Proposal: do we demote the failed packages to experimental?
>> (Not deformation, dot2tex, or rst2ipynb, also not p_group_cohomology
>> because it is just about ready for py3, but the others.) I plan to do this
>> unless there are objections.
>> >>
>> >>
>> >> Experimental:
>> >>
>> >> - the following failed to build:
>> >>
>> >> autotools
>> >> cocoalib
>> >> libtheora
>> >> polymake
>> >> qepcad
>> >> scipoptsuite
>> >> surf
>> >> valgrind
>> >>
>> >> - the following succeeded:
>> >>
>> >> gap3
>> >> lie
>> >> modular_decomposition
>> >> perl_term_readline_gnu
>> >>
>> >> polymake succeeded but only after installing the perl JSON package.
>> (Why is jupymake optional and polymake experimental? jupymake has polymake
>> as a dependency, and optional packages should not depend on experimental
>> packages.)
>> >>
>> >> - I skipped the following:
>> >>
>> >> compilerwrapper — when I install this, 

Re: [sage-devel] Optional and experimental packages

[Nico Van Cleemput]

Well, upstream sits at another desk in my office, so I will ask when he
gets in.

Nico

Op di 29 okt. 2019 09:29 schreef Dima Pasechnik :

> clang is unhappy about C standards violations. E.g. this is what I get
> with clang 7:
>
> cc -O4 buckygen.c -o buckygen
> cc: warning: -O4 is equivalent to -O3 [-Wdeprecated]
> In file included from buckygen.c:272:
> ./splay.c:139:6: warning: implicit declaration of function
> 'outputnode' is invalid in C99 [-Wimplicit-function-declaration]
> ACTION(p);
> ^
> buckygen.c:254:19: note: expanded from macro 'ACTION'
> #define ACTION(p) outputnode(p)
>   ^
> In file included from buckygen.c:272:
> ./splay.c:263:15: warning: implicit declaration of function
> 'comparenodes' is invalid in C99 [-Wimplicit-function-declaration]
> cmp = COMPARE(p);
>   ^
> buckygen.c:260:20: note: expanded from macro 'COMPARE'
> #define COMPARE(p) comparenodes(canong, codelength, type, p)
>^
> In file included from buckygen.c:272:
> ./splay.c:328:15: warning: implicit declaration of function
> 'comparenodes' is invalid in C99 [-Wimplicit-function-declaration]
> cmp = COMPARE(p);
>   ^
> buckygen.c:260:20: note: expanded from macro 'COMPARE'
> #define COMPARE(p) comparenodes(canong, codelength, type, p)
>^
> In file included from buckygen.c:272:
> ./splay.c:352:20: error: non-void function 'splay_delete' should
> return a value [-Wreturn-type]
> if (p == NULL) return;
>^
> ./splay.c:366:2: error: non-void function 'splay_delete' should return
> a value [-Wreturn-type]
> return;
> ^
> ./splay.c:376:9: error: non-void function 'splay_delete' should return
> a value [-Wreturn-type]
> return;
> ^
> buckygen.c:943:1: warning: type specifier missing, defaults to 'int'
> [-Wimplicit-int]
> outputnode(SPLAYNODE *liste)
> ^
> 4 warnings and 3 errors generated.
> make: *** [makefile:12: buckygen] Error 1
>
> Easy to fix, I'd say - can this be done upstream?
>
> On Tue, Oct 29, 2019 at 8:31 AM Nico Van Cleemput
>  wrote:
> >
> > buckygen is a pure C package, so I doubt that this has anything to do
> with the switch to Python 3. Do you have any more information about the
> fail build, because here it built fine.
> >
> > Nico
> >
> > Op ma 28 okt. 2019 om 23:02 schreef John H Palmieri <
> jhpalmier...@gmail.com>:
> >>
> >> With a Python 3 build of Sage on OS X 10.14.6, I decided to install as
> many optional and experimental packages as I could. The results:
> >>
> >> Optional:
> >>
> >> - the following packages failed to build, and the reason wasn't
> completely obvious:
> >>
> >> awali
> >> buckygen
> >> cbc
> >> gambit
> >> gdb
> >> mpi4py
> >>
> >> - the following packages failed because they (or their installation
> scripts) are not compatible with Python 3:
> >>
> >> beautifulsoup
> >> brian
> >> guppy
> >> mercurial
> >> p_group_cohomology (but work is in progress)
> >> pyx
> >> scons
> >> trac
> >>
> >> - the following packages failed at first, but built after installing
> some prerequisities:
> >>
> >> deformation — requires installation of mpir
> >> dot2tex — requires Graphviz
> >> rst2ipynb — requires pandoc
> >>
> >> - I skipped the following packages:
> >>
> >> atlas (installation is skipped on OS X)
> >> python2 (I wanted to use a pure Python 3 build)
> >>
> >> - Every other optional package built.
> >>
> >> Question/Proposal: do we demote the failed packages to experimental?
> (Not deformation, dot2tex, or rst2ipynb, also not p_group_cohomology
> because it is just about ready for py3, but the others.) I plan to do this
> unless there are objections.
> >>
> >>
> >> Experimental:
> >>
> >> - the following failed to build:
> >>
> >> autotools
> >> cocoalib
> >> libtheora
> >> polymake
> >> qepcad
> >> scipoptsuite
> >> surf
> >> valgrind
> >>
> >> - the following succeeded:
> >>
> >> gap3
> >> lie
> >> modular_decomposition
> >> perl_term_readline_gnu
> >>
> >> polymake succeeded but only after installing the perl JSON package.
> (Why is jupymake optional and polymake experimental? jupymake has polymake
> as a dependency, and optional packages should not depend on experimental
> packages.)
> >>
> >> - I skipped the following:
> >>
> >> compilerwrapper — when I install this, it breaks the Sage library:
> after touching any .pyx file, "sage -b" or "make" fails with an error about
> ld.
> >>
> >>
> >> Doctesting:
> >>
> >> Then I ran `make ptestalllong`. There were lots of "internet" failures.
> Otherwise:
> >>
> >> - failures in one file because of rst2ipynb
> >> - failures in two files because of dot2tex
> >> - failures in one file because of latex
> >> - failures in one file because of gap_packages (reported by Emmanuel
> Charpentier on sage-release many times)
> >>
> >> Other than the internet problems, not too bad.
> >>
> >> --
> >> John
> >>
> >> --
> >> You received this message because you are subscribed to the 

Re: [sage-devel] Optional and experimental packages

[Dima Pasechnik]

clang is unhappy about C standards violations. E.g. this is what I get
with clang 7:

cc -O4 buckygen.c -o buckygen
cc: warning: -O4 is equivalent to -O3 [-Wdeprecated]
In file included from buckygen.c:272:
./splay.c:139:6: warning: implicit declaration of function
'outputnode' is invalid in C99 [-Wimplicit-function-declaration]
ACTION(p);
^
buckygen.c:254:19: note: expanded from macro 'ACTION'
#define ACTION(p) outputnode(p)
  ^
In file included from buckygen.c:272:
./splay.c:263:15: warning: implicit declaration of function
'comparenodes' is invalid in C99 [-Wimplicit-function-declaration]
cmp = COMPARE(p);
  ^
buckygen.c:260:20: note: expanded from macro 'COMPARE'
#define COMPARE(p) comparenodes(canong, codelength, type, p)
   ^
In file included from buckygen.c:272:
./splay.c:328:15: warning: implicit declaration of function
'comparenodes' is invalid in C99 [-Wimplicit-function-declaration]
cmp = COMPARE(p);
  ^
buckygen.c:260:20: note: expanded from macro 'COMPARE'
#define COMPARE(p) comparenodes(canong, codelength, type, p)
   ^
In file included from buckygen.c:272:
./splay.c:352:20: error: non-void function 'splay_delete' should
return a value [-Wreturn-type]
if (p == NULL) return;
   ^
./splay.c:366:2: error: non-void function 'splay_delete' should return
a value [-Wreturn-type]
return;
^
./splay.c:376:9: error: non-void function 'splay_delete' should return
a value [-Wreturn-type]
return;
^
buckygen.c:943:1: warning: type specifier missing, defaults to 'int'
[-Wimplicit-int]
outputnode(SPLAYNODE *liste)
^
4 warnings and 3 errors generated.
make: *** [makefile:12: buckygen] Error 1

Easy to fix, I'd say - can this be done upstream?

On Tue, Oct 29, 2019 at 8:31 AM Nico Van Cleemput
 wrote:
>
> buckygen is a pure C package, so I doubt that this has anything to do with 
> the switch to Python 3. Do you have any more information about the fail 
> build, because here it built fine.
>
> Nico
>
> Op ma 28 okt. 2019 om 23:02 schreef John H Palmieri :
>>
>> With a Python 3 build of Sage on OS X 10.14.6, I decided to install as many 
>> optional and experimental packages as I could. The results:
>>
>> Optional:
>>
>> - the following packages failed to build, and the reason wasn't completely 
>> obvious:
>>
>> awali
>> buckygen
>> cbc
>> gambit
>> gdb
>> mpi4py
>>
>> - the following packages failed because they (or their installation scripts) 
>> are not compatible with Python 3:
>>
>> beautifulsoup
>> brian
>> guppy
>> mercurial
>> p_group_cohomology (but work is in progress)
>> pyx
>> scons
>> trac
>>
>> - the following packages failed at first, but built after installing some 
>> prerequisities:
>>
>> deformation — requires installation of mpir
>> dot2tex — requires Graphviz
>> rst2ipynb — requires pandoc
>>
>> - I skipped the following packages:
>>
>> atlas (installation is skipped on OS X)
>> python2 (I wanted to use a pure Python 3 build)
>>
>> - Every other optional package built.
>>
>> Question/Proposal: do we demote the failed packages to experimental? (Not 
>> deformation, dot2tex, or rst2ipynb, also not p_group_cohomology because it 
>> is just about ready for py3, but the others.) I plan to do this unless there 
>> are objections.
>>
>>
>> Experimental:
>>
>> - the following failed to build:
>>
>> autotools
>> cocoalib
>> libtheora
>> polymake
>> qepcad
>> scipoptsuite
>> surf
>> valgrind
>>
>> - the following succeeded:
>>
>> gap3
>> lie
>> modular_decomposition
>> perl_term_readline_gnu
>>
>> polymake succeeded but only after installing the perl JSON package. (Why is 
>> jupymake optional and polymake experimental? jupymake has polymake as a 
>> dependency, and optional packages should not depend on experimental 
>> packages.)
>>
>> - I skipped the following:
>>
>> compilerwrapper — when I install this, it breaks the Sage library: after 
>> touching any .pyx file, "sage -b" or "make" fails with an error about ld.
>>
>>
>> Doctesting:
>>
>> Then I ran `make ptestalllong`. There were lots of "internet" failures. 
>> Otherwise:
>>
>> - failures in one file because of rst2ipynb
>> - failures in two files because of dot2tex
>> - failures in one file because of latex
>> - failures in one file because of gap_packages (reported by Emmanuel 
>> Charpentier on sage-release many times)
>>
>> Other than the internet problems, not too bad.
>>
>> --
>> John
>>
>> --
>> 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+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/sage-devel/150bd508-b9b2-4953-aa50-cb27cc840b78%40googlegroups.com.
>
> --
> You received this message because you are subscribed to the Google Groups 
> "sage-devel" group.
> 

Re: [sage-devel] Re: OSX Catalina works

[Dima Pasechnik]

Did you  run

xcode-select --install

after Xcode upgrade?
By the way, why don't you use NTL from brew?
https://formulae.brew.sh/formula/ntl#default

you can also make things easier by installing Flint and Arb into
homebrew, by using formulas from
https://github.com/dimpase/homebrew-science

Run

brew install dimpase/science/flint
brew install dimpase/science/arb

(these are source-only, so this will build packages from source)


On Tue, Oct 29, 2019 at 2:01 AM Andrew  wrote:
>
> I (stupidly) upgraded to XCode 11.1 on catalina. I have succeeded in 
> compiling sage with python2, not python 3, on an imac but can't get it to 
> compile on a macbook pro with fairly similar specs.I am using homebrew and 
> have:
>
> ProductName:Mac OS X
> ProductVersion:10.15
> BuildVersion:19A603
> Xcode 11.1
> Build version 11A1027
>
> with gcc --version returning
>
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
> Apple clang version 11.0.0 (clang-1100.0.33.8)
> Target: x86_64-apple-darwin19.0.0
> Thread model: posix
> InstalledDir: 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>
> When I try to compile sage is breaks with:
>
> * package: givaro-4.1.1
>   log file: /usr/local/src/sage/logs/pkgs/givaro-4.1.1.log
>   build directory: /usr/local/src/sage/local/var/tmp/sage/build/givaro-4.1.1
> * package: ntl-11.3.2
>   log file: /usr/local/src/sage/logs/pkgs/ntl-11.3.2.log
>   build directory: /usr/local/src/sage/local/var/tmp/sage/build/ntl-11.3.2
>
> Sometimes I also get ntl failing to compile. I have compared the log files 
> one the two machines but can't identify the problem. I attach the log files 
> for givaro and ntl and the install.log from the machine that has the problem. 
> Does anyone have any ideas how to fix this?
>
> Andrew
>
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Re: [sage-devel] Optional and experimental packages

[Nico Van Cleemput]

buckygen is a pure C package, so I doubt that this has anything to do with
the switch to Python 3. Do you have any more information about the fail
build, because here it built fine.

Nico

Op ma 28 okt. 2019 om 23:02 schreef John H Palmieri :

> With a Python 3 build of Sage on OS X 10.14.6, I decided to install as
> many optional and experimental packages as I could. The results:
>
> *Optional:*
>
> - the following packages failed to build, and the reason wasn't completely
> obvious:
>
> awali
> buckygen
> cbc
> gambit
> gdb
> mpi4py
>
> - the following packages failed because they (or their installation
> scripts) are not compatible with Python 3:
>
> beautifulsoup
> brian
> guppy
> mercurial
> p_group_cohomology (but work is in progress)
> pyx
> scons
> trac
>
> - the following packages failed at first, but built after installing some
> prerequisities:
>
> deformation — requires installation of mpir
> dot2tex — requires Graphviz
> rst2ipynb — requires pandoc
>
> - I skipped the following packages:
>
> atlas (installation is skipped on OS X)
> python2 (I wanted to use a pure Python 3 build)
>
> - Every other optional package built.
>
> *Question/Proposal:* do we demote the failed packages to experimental?
> (Not deformation, dot2tex, or rst2ipynb, also not p_group_cohomology
> because it is just about ready for py3, but the others.) I plan to do this
> unless there are objections.
>
>
> *Experimental:*
>
> - the following failed to build:
>
> autotools
> cocoalib
> libtheora
> polymake
> qepcad
> scipoptsuite
> surf
> valgrind
>
> - the following succeeded:
>
> gap3
> lie
> modular_decomposition
> perl_term_readline_gnu
>
> polymake succeeded but only after installing the perl JSON package. (Why
> is jupymake optional and polymake experimental? jupymake has polymake as a
> dependency, and optional packages should not depend on experimental
> packages.)
>
> - I skipped the following:
>
> compilerwrapper — when I install this, it breaks the Sage library: after
> touching any .pyx file, "sage -b" or "make" fails with an error about ld.
>
>
> *Doctesting:*
>
> Then I ran `make ptestalllong`. There were lots of "internet" failures.
> Otherwise:
>
> - failures in one file because of rst2ipynb
> - failures in two files because of dot2tex
> - failures in one file because of latex
> - failures in one file because of gap_packages (reported by Emmanuel
> Charpentier on sage-release many times)
>
> Other than the internet problems, not too bad.
>
> --
> John
>
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> 
> .
>

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