Upgrade polymake to version 3.4

[mkoeppe]

​https://polymake.org/doku.php/download/start#get_latest_stable_release33

To build it for Sage do:

(cd upstream && wget https://polymake.org/lib/exe/fetch.php/download/polymake-3.4-minimal.tar.bz2)

pull this ticket and build sage

make build

Then Read (and follow) the installation instructions regarding Perl prereqs on your platform:

./sage -info polymake

Finally:

./sage -i polymake

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​ca75153

polymake: Add ninja_build as dependency

[jdemeyer]

ninja_build should be an order-only dependency (after the | symbol)

[jdemeyer]

All other packages have $(MP_LIBRARY) in their dependencies instead of $(INST)/$(SAGE_MP_LIBRARY). I guess this should be changed.

[jdemeyer]

Unfortunately, I cannot test this because perl_term_readline_gnu fails to install:

[perl_term_readline_gnu-1.34] Could not find neither libtermcap.a, libncurses.a, or libcurses.

Indeed, there is no libncurses.a installed (but libncurses.so is).

[mkoeppe]

Replying to jdemeyer:

Unfortunately, I cannot test this because perl_term_readline_gnu fails to install:

[perl_term_readline_gnu-1.34] Could not find neither libtermcap.a, libncurses.a, or libcurses.

Indeed, there is no libncurses.a installed (but libncurses.so is).

Could you create a separate ticket for this (and include more log detail)?

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​4fc26ff	ninja_build: Add python dependency
​3d6ae67	ninja_build: Make Python an order-only dependency
​acc3026	Merge remote-tracking branch 'trac/u/mkoeppe/add_optional_package__ninja_build___build_system_for_polymake_' into t/24905/upgrade_polymake_to_version_3_2r2
​196eb49	polymake dependencies: Use current format for MP_LIBRARY, make ninja_build order-only

[mkoeppe]

This upgrade seems to break the whole polymake interface. Next step: Compare what's happening on the wire (pexpect log) between the two polymake versions.

[mkoeppe]

Replying to mkoeppe:

Replying to jdemeyer:

Unfortunately, I cannot test this because perl_term_readline_gnu fails to install:

[perl_term_readline_gnu-1.34] Could not find neither libtermcap.a, libncurses.a, or libcurses.

Indeed, there is no libncurses.a installed (but libncurses.so is).

Could you create a separate ticket for this (and include more log detail)?

We have reproduced this problem on another linux box. Fix is in #25112.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​3ffafdf	Update perl_term_readline_gnu to 1.35
​672a3a2	perl_term_readline_gnu: Find ncurses
​0b818c3	Merge remote-tracking branch 'trac/u/mkoeppe/perl_term_readline_gnu__upgrade_to_1_35_and_patch_away_ncurses_problem' into t/24905/upgrade_polymake_to_version_3_2r2

[jipilab]

Compilation fails on Debian stretch. I copy the relevant section of the log file:

[706/940] LD /home/jplabbe/sage/local/var/tmp/sage/build/polymake-3.2r2/src/build/Opt/lib/polytope.so
FAILED: /home/jplabbe/sage/local/var/tmp/sage/build/polymake-3.2r2/src/build/Opt/lib/polytope.so 
g++ -shared -L/usr/local/lib -fstack-protector-strong -Wl,-z,lazy -Wl,--as-needed  -o 
LOOOOOOOOGGGGGGGGGGGGGGGGGGGGG LIST OF .o and .so files 
/home/jplabbe/sage/local/var/tmp/sage/build/polymake-3.2r2/src/build/Opt/staticlib/sympol/libsympol.a  -L/home/jplabbe/sage/local/lib -Wl,-rpath,/home/jplabbe/sage/local/lib -lsoplex -lz -lppl -llrsgmp -lnormaliz -lgmpxx -lcddgmp -L/home/jplabbe/sage/local/lib -Wl,-rpath,/home/jplabbe/sage/local/lib  -fopenmp -lmpfr -lgmp -lpthread  -ldl
/usr/bin/ld: /home/jplabbe/sage/local/lib/libsoplex.a(rational.cpp.o): relocation R_X86_64_TPOFF32 against symbol `_ZN6soplex8Rational10useListMemE' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/jplabbe/sage/local/lib/libsoplex.a(spxdefines.cpp.o): relocation R_X86_64_TPOFF32 against symbol `_ZN6soplex5Param9s_epsilonE' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​24aec38

polymake: disable SoPlex to avoid linking errors

[jipilab]

Now the compilation finishes without errors. Testing with --optional=polymake, I get:

----------------------------------------------------------------------
sage -t backend_polymake.py  # 53 doctests failed
sage -t base.py  # 13 doctests failed
----------------------------------------------------------------------

The first is:

sage: p = Polyhedron(vertices=[(0,0),(1,0),(0,1)], rays=[(1,1)],lines=[], backend='polymake')

for which I get:

Traceback (most recent call last):
...
TypeError: Can't locate File/Slurp.pm in @INC (you may need to install the File::Slurp module) (@INC contains: CODE(0x562008f51e88) /home/jplabbe/sage/local/share/polymake/perllib /home/jplabbe/sage/local/lib/polymake/perlx/5.24.1/x86_64-linux-gnu-thread-multi /home/jplabbe/sage/local/lib/polymake/perlx/5.24.1 /home/jplabbe/sage/local/lib/polymake/perlx /home/jplabbe/sage/local/lib/perl5/x86_64-linux-gnu-thread-multi /home/jplabbe/sage/local/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.24.1 /usr/local/share/perl/5.24.1 /usr/lib/x86_64-linux-gnu/perl5/5.24 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.24 /usr/share/perl/5.24 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base)
BEGIN failed--compilation aborted

Another type of error seems to be that not putting () at the end of a CAPITALIZEDPOLYMAKEMETHOD returns a function and not the result anymore.

[mkoeppe]

For the error with Slurp, merge #24152 (needs review) and then re-read the polymake SPKG.txt regarding the Perl libraries that need to be installed.

[mkoeppe]

Replying to jipilab:

Another type of error seems to be that not putting () at the end of a CAPITALIZEDPOLYMAKEMETHOD returns a function and not the result anymore.

Yes, that's exactly what I meant when I wrote "break[s] the whole polymake interface".

[jipilab]

Replying to mkoeppe:

Replying to jipilab:

Another type of error seems to be that not putting () at the end of a CAPITALIZEDPOLYMAKEMETHOD returns a function and not the result anymore.

Yes, that's exactly what I meant when I wrote "break[s] the whole polymake interface".

I wanted to emphaSIZE the problem! ;)

[jipilab]

Merged the dependency to #24152.

---

New commits:

​a924632	polymake SPKG.txt: Mention File::Slurp and CPAN
​30ea0b0	Merge branch 'u/mkoeppe/bug_when_converting_a_sage_polyhedron_into_polymake_pexpect' of trac.sagemath.org:sage into 24152
​2748391	Merge branch '24152' into 24905

[mkoeppe]

3.2r3 is out

[jipilab]

Ok, good to know. At the beginning of October, I have a week where I'll try this once more.

Further, I had a comment recently that one might want to add a link to the backend polymake in the documentation page for the interface (because the interface is not the only way to use polymake in sage...).

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​791f766

Merge branch 'develop' into public/upgrade_polymake_to_version_3_2r2

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​3ec32e8	Merge branch 'public/upgrade_polymake_to_version_3_2r2' of trac.sagemath.org:sage into new_24905
​f4dee94	Updated polymake to 3.2r4

[jipilab]

It seems that the commit 791f766 merged the develop branch into the upgrade polymake branch?

We then get all the diffs from the develop branch on this ticket... I would revert back to a previous commit if no changes were done at the same time as this merge... Let's see how it goes with this update on top of the last beta.

Now version 3.2.r4 is out as well and I updated the description of the ticket.

Polymake days are January 24-26 2019, I will ask them if a stable release is to be expected soon...

[jipilab]

I accidently erased the patch to compile with gcc7 form a previous ticket... I do not have gcc7 on my computer... But I guess it would be good to check it again anyways on this new release...

[jipilab]

I am looking at the broken polymake interface. I noticed a few things:

• Quotes do not work the same way as before:

    sage: polymake("'ok'")                              # optional - polymake
    'ok'

So we need to handle this differently when calling member functions.

• I get a compilation error directly while asking for the Type of a polytope:

polytope > $c = cube(3);
polytope > $t = typeof $c;
polymake:  ERROR: Compilation error

This breaks pretty much everything, as the object is not able to catch its type and get the proper names for functions, and lots of other things...

[jipilab]

New commits:

​d5b94d6	Fixed quotes and wiggled around
​b2e133c	Fixed the typeof
​d9af561	small fixes
​40c6098	pep8

[jipilab]

The previous commits fix the polymake interface, see ​https://forum.polymake.org/viewtopic.php?f=8&t=1675 for a discussion of the issue.

In short, the command

$t = typeof $c;

Stopped working (as in the tutorials mentionned in the discussion) and we should use:

$t = $c -> type;

This seems to have fixed the problems.

There is still a spurious failing test in the interface which is an appearing blankline. I ignore it for now...

Next, I'll check the polymake backend for polyhedron. There seems to be around 4 failing doctests. That's much better than the 100s... there was.

[jipilab]

Replying to jipilab:

I am looking at the broken polymake interface. I noticed a few things:

• Quotes do not work the same way as before:

    sage: polymake("'ok'")                              # optional - polymake
    'ok'

This was simply because of the failing evaluation when setting variables. It seems fine now.

[jipilab]

On the release page of polymake 3.2 ​https://polymake.org/doku.php/news/release_3_2

one can read under "polytope":

• zero vectors in input properties throw an exception

This breaks a few of our tests.

[jipilab]

Replying to jipilab:

On the release page of polymake 3.2 ​https://polymake.org/doku.php/news/release_3_2

one can read under "polytope":

• zero vectors in input properties throw an exception

This breaks a few of our tests.

The question is now: how to get the full space as a polyhedron is polymake?

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​a5bf869

Fixed backend polymake

[jipilab]

It seems that the tests now pass.

Ready for review!

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​7a5de5a

Merge branch 'public/upgrade_polymake_to_version_3_2r4' of trac.sagemath.org:sage into polymake32r4

[gh-kliem]

I'm getting the following error:

Running doctests with ID 2019-03-11-14-11-33-0ac43552.
Git branch: public/upgrade_polymake_to_version_3_2r4
Using --optional=4ti2,bliss,cmake,dochtml,gmpy2,latte_int,lidia,lrslib,memlimit,mpir,ninja_build,normaliz,polymake,pynormaliz,python2,qhull,sage,topcom
Doctesting 1 file.
sage -t --long --warn-long 41.5 src/sage/interfaces/polymake.py
**********************************************************************
File "src/sage/interfaces/polymake.py", line 1735, in sage.interfaces.polymake.PolymakeElement.get_member_function
Failed example:
    c.get_member_function("foo")()                        # optional - polymake
Expected:
    Traceback (most recent call last):
    ...
    TypeError: Can't locate object method "foo" via package "Polymake::polytope::Polytope__Rational" at input line 1.
Got:
    <BLANKLINE>
    Traceback (most recent call last):
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.polymake.PolymakeElement.get_member_function[6]>", line 1, in <module>
        c.get_member_function("foo")()                        # optional - polymake
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py", line 2114, in __call__
        return self._obj._check_valid().function_call(self._name, list(args), kwds)
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py", line 284, in function_call
        return self(s)
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/interface.py", line 288, in __call__
        return cls(self, x, name=name)
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 1442, in __init__
        raise_(TypeError, TypeError(*x.args), sys.exc_info()[2])
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 1437, in __init__
        self._name = parent._create(value, name=name)
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py", line 628, in _create
        self.set(name, value)
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py", line 717, in set
        self.eval(cmd)
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 1351, in eval
        for L in code.split('\n') if L != ''])
      File "/srv/public/kliem/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py", line 1068, in _eval_line
        raise PolymakeError(e)
    TypeError: Can't locate object method "foo" via package "Polymake::polytope::Polytope__Rational"

Also, I had to install perl yet with

cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp

yet. With polymake 3.1 in sage, there was not need of that.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​7ca4434

Fixed a failing doctest

[jipilab]

Replying to gh-kliem:

The failing doctest should be fixed now.

Also, I had to install perl yet with

cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp

yet. With polymake 3.1 in sage, there was not need of that.

Could you be more specific about this? Could you say in which order you did this and if we have to add this to the installation instruction?

[gh-kliem]

I had polymake installed via ./sage -i polymake before. This didn't require any extra installations.

I went through the instructions of this ticket and ignored ./sage -info polymake. This failed. Following the instructions and executing

cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp

beforehand worked fine.

To me it looks like ./sage -i polymake worked somehow out of the box before and now it doesn't anymore.

Replying to jipilab:

Replying to gh-kliem:

The failing doctest should be fixed now.

Also, I had to install perl yet with

cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp

yet. With polymake 3.1 in sage, there was not need of that.

Could you be more specific about this? Could you say in which order you did this and if we have to add this to the installation instruction?

[gh-kliem]

Btw, also polymake is not auto-detected when running doctests.

So ./sage -t --all --long will not use polymake unless specified.

I don't know, if this is a problem specific to my installation or not.

[gh-kliem]

Almost everything passed now. This is the only thing remaining on my machine:

File "src/sage/interfaces/polymake.py", line 823, in sage.interfaces.polymake.Polymake._eval_line
Failed example:
    p.N_LATTICE_POINTS                # optional - polymake
Expected:
    used package latte
      LattE (Lattice point Enumeration) is a computer software dedicated to the
      problems of counting lattice points and integration inside convex polytopes.
      Copyright by Matthias Koeppe, Jesus A. De Loera and others.
      http://www.math.ucdavis.edu/~latte/
    27
Got:
    27

[jipilab]

Replying to gh-kliem:

I had polymake installed via ./sage -i polymake before. This didn't require any extra installations.

I went through the instructions of this ticket and ignored ./sage -info polymake. This failed. Following the instructions and executing

cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp

beforehand worked fine.

To me it looks like ./sage -i polymake worked somehow out of the box before and now it doesn't anymore.

Have a look at the commit to see what changed. When we update a package, we change the source and the place to download the package. Since the package is not yet on the sage mirror, this is why you download it and put it in the appropriate folder by hand.

After doing so, as long as you are on this branch, installing polymake will install the newest version (the one written with this new ticket). If you go back to a different ticket, you have to (re-)install polymake the usual way. And it should work. But well, polymake installation used to not work before, so there's no discussion to have on this aspect. We should focus on the present installation.

Again, can you state clearly what you did step-by-step and say if each step worked or not. It is difficult to follow from what you write about what worked and what did not work.

[jipilab]

Replying to gh-kliem:

Btw, also polymake is not auto-detected when running doctests.

So ./sage -t --all --long will not use polymake unless specified.

I don't know, if this is a problem specific to my installation or not.

Polymake is an experimental package, so it is not included in the default testing. Perhaps there is a way to include all experimental package. But this is a recipe for disaster anyway. So just add it by hand each time you test. That's the cheapest solution.

[jipilab]

Replying to gh-kliem:

Almost everything passed now. This is the only thing remaining on my machine:

File "src/sage/interfaces/polymake.py", line 823, in sage.interfaces.polymake.Polymake._eval_line
Failed example:
    p.N_LATTICE_POINTS                # optional - polymake
Expected:
    used package latte
      LattE (Lattice point Enumeration) is a computer software dedicated to the
      problems of counting lattice points and integration inside convex polytopes.
      Copyright by Matthias Koeppe, Jesus A. De Loera and others.
      http://www.math.ucdavis.edu/~latte/
    27
Got:
    27

Okay, this is annoying, as I do not get this error in my case. It seems that they randomly throw out such transparency statements about libraries it uses. Okay. Thanks for pointing this out.

[gh-kliem]

Ok, let's try again.

In my current Sage installation I had polymake 3.1 installed. When installing it, this worked out of the box. So a simply run of ./sage -i polymake and I had polymake 3.3. No prereqs.

When testing this ticket, I checked out this branch and pulled and did everything as instructed, but ignored ./sage -info polymake. This did not work (yes I didn't follow the instructions completely).

When I paid attention to ./sage -info polymake and installed the perl thing, it worked fine.

If somehow possible, it would be nice to have ./sage -i polymake work without any prereqs again. But I have no idea whats going on and whether this depends on my specific computer or not.

I just wanted to point out, that the update to polymake 3.2 has a prequirement that wasn't there before. You are probably aware of this, I just wanted to mention it.

Replying to jipilab:

Replying to gh-kliem:

I had polymake installed via ./sage -i polymake before. This didn't require any extra installations.

I went through the instructions of this ticket and ignored ./sage -info polymake. This failed. Following the instructions and executing

cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp

beforehand worked fine.

To me it looks like ./sage -i polymake worked somehow out of the box before and now it doesn't anymore.

Have a look at the commit to see what changed. When we update a package, we change the source and the place to download the package. Since the package is not yet on the sage mirror, this is why you download it and put it in the appropriate folder by hand.

After doing so, as long as you are on this branch, installing polymake will install the newest version (the one written with this new ticket). If you go back to a different ticket, you have to (re-)install polymake the usual way. And it should work. But well, polymake installation used to not work before, so there's no discussion to have on this aspect. We should focus on the present installation.

Again, can you state clearly what you did step-by-step and say if each step worked or not. It is difficult to follow from what you write about what worked and what did not work.

[slabbe]

On Ubuntu 16.04 with sage 8.7.beta7, after installing the dependencies, the command

sage -t --optional=sage,optional,experimental,external,polymake src/sage/interfaces/polymake.py

gives:

Using --optional=4ti2,bliss,cbc,ccache,cmake,cryptominisat,dot2tex,experimental,external,glucose,latte_int,lidia,lrslib,memlimit,mpir,ninja_build,normaliz,notedown,pandoc_attributes,polymake,pycosat,pynormaliz,python2,qhull,rst2ipynb,sage,topcom
External software to be detected: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,scilab
Doctesting 1 file.
sage -t src/sage/interfaces/polymake.py
    [245 tests, 8.19 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 11.7 seconds
    cpu time: 1.8 seconds
    cumulative wall time: 8.2 seconds
External software detected for doctesting: 

[gh-kliem]

Just to mention this.

I am using cofio: ​https://patchbot.sagemath.org/ticket/?machine=debian&machine=9.6&machine=x86_64&machine=4.9.0-8-amd64&machine=cofio&status=open

Not with the Sage same install, but I don't think it matters.

Replying to jipilab:

Replying to gh-kliem:

Almost everything passed now. This is the only thing remaining on my machine:

File "src/sage/interfaces/polymake.py", line 823, in sage.interfaces.polymake.Polymake._eval_line
Failed example:
    p.N_LATTICE_POINTS                # optional - polymake
Expected:
    used package latte
      LattE (Lattice point Enumeration) is a computer software dedicated to the
      problems of counting lattice points and integration inside convex polytopes.
      Copyright by Matthias Koeppe, Jesus A. De Loera and others.
      http://www.math.ucdavis.edu/~latte/
    27
Got:
    27

Okay, this is annoying, as I do not get this error in my case. It seems that they randomly throw out such transparency statements about libraries it uses. Okay. Thanks for pointing this out.

[jipilab]

Replying to gh-kliem:

Ok, let's try again.

In my current Sage installation I had polymake 3.1 installed. When installing it, this worked out of the box. So a simply run of ./sage -i polymake and I had polymake 3.3. No prereqs.

When testing this ticket, I checked out this branch and pulled and did everything as instructed, but ignored ./sage -info polymake. This did not work (yes I didn't follow the instructions completely).

When I paid attention to ./sage -info polymake and installed the perl thing, it worked fine.

If somehow possible, it would be nice to have ./sage -i polymake work without any prereqs again. But I have no idea whats going on and whether this depends on my specific computer or not.

I just wanted to point out, that the update to polymake 3.2 has a prequirement that wasn't there before. You are probably aware of this, I just wanted to mention it.

Okay, thanks for the clarification. I do not know if there is a way to fix this through the installation of polymake. Since there is no section Debian in the installation instruction coming from sage -info polymake which one did you execute? The ubuntu ones? None?

[jipilab]

File "src/sage/interfaces/polymake.py", line 823, in sage.interfaces.polymake.Polymake._eval_line
Failed example:
    p.N_LATTICE_POINTS                # optional - polymake
Expected:
    used package latte
      LattE (Lattice point Enumeration) is a computer software dedicated to the
      problems of counting lattice points and integration inside convex polytopes.
      Copyright by Matthias Koeppe, Jesus A. De Loera and others.
      http://www.math.ucdavis.edu/~latte/
    27
Got:
    27

Typing in the terminal I get:

$ sage -experimental
[package]...............................[latest version] ([version])
perl_term_readline_gnu..................1.35 (1.35)
polymake................................3.2r4 (3.2r4)

I do get the verbose out from using polymake3.2r4. And all tests passed on an fresh install on a Ubuntu machine. Could you make sure that you used the latest polymake? Somehow it seems really odd to me and I can't figure out why it does not show the verbose in your case.

[gh-kliem]

./sage -info polymake

...

A distribution-independent way to install Perl modules (into a user's
home directory) is using CPAN.

 cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp

This did the job. I also did sage -i 4ti2 latte_int topcom qhull then, but this has most likely nothing to do with the issue.

Replying to jipilab:

Replying to gh-kliem:

Ok, let's try again.

In my current Sage installation I had polymake 3.1 installed. When installing it, this worked out of the box. So a simply run of ./sage -i polymake and I had polymake 3.3. No prereqs.

When testing this ticket, I checked out this branch and pulled and did everything as instructed, but ignored ./sage -info polymake. This did not work (yes I didn't follow the instructions completely).

When I paid attention to ./sage -info polymake and installed the perl thing, it worked fine.

If somehow possible, it would be nice to have ./sage -i polymake work without any prereqs again. But I have no idea whats going on and whether this depends on my specific computer or not.

I just wanted to point out, that the update to polymake 3.2 has a prequirement that wasn't there before. You are probably aware of this, I just wanted to mention it.

Okay, thanks for the clarification. I do not know if there is a way to fix this through the installation of polymake. Since there is no section Debian in the installation instruction coming from sage -info polymake which one did you execute? The ubuntu ones? None?

[gh-kliem]

kliem@cofio:~/localhome/sage$ sage -experimental
[package]...............................[latest version] ([version])

autotools...............................20141105.p0 (not_installed)
cocoalib................................0.99564 (not_installed)
compilerwrapper.........................1.2 (not_installed)
gap3....................................04jul17 (not_installed)
libtheora...............................1.1.1 (not_installed)
lie.....................................2.2.2 (not_installed)
modular_decomposition...................20100607 (not_installed)
perl_term_readline_gnu..................1.35 (1.35)
polymake................................3.2r4 (3.2r4)
qepcad..................................B.1.71 (not_installed)
scipoptsuite............................5.0.1 (not_installed)
surf....................................1.0.6-gcc6 (not_installed)
valgrind................................3.10.0 (not_installed)

Replying to jipilab:

File "src/sage/interfaces/polymake.py", line 823, in sage.interfaces.polymake.Polymake._eval_line
Failed example:
    p.N_LATTICE_POINTS                # optional - polymake
Expected:
    used package latte
      LattE (Lattice point Enumeration) is a computer software dedicated to the
      problems of counting lattice points and integration inside convex polytopes.
      Copyright by Matthias Koeppe, Jesus A. De Loera and others.
      http://www.math.ucdavis.edu/~latte/
    27
Got:
    27

Typing in the terminal I get:

$ sage -experimental
[package]...............................[latest version] ([version])
perl_term_readline_gnu..................1.35 (1.35)
polymake................................3.2r4 (3.2r4)

I do get the verbose out from using polymake3.2r4. And all tests passed on an fresh install on a Ubuntu machine. Could you make sure that you used the latest polymake? Somehow it seems really odd to me and I can't figure out why it does not show the verbose in your case.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​38319e2

Update polymake to version 3.3

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​2879106

Added a required package for polymake install

[jipilab]

Achhhh...

libjson-perl is now a requirement since version 3.3:

​https://polymake.org/doku.php/news/release_3_3

I added it to the Ubuntu requirements, I will check how to install this on other platforms...

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​6755b5b

Added readkey dependency

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

[jipilab]

It seems that polymake 3.3 does not compile out of the box on my stable Debian distribution...

I feel like version 3.3 should be a separate ticket and have a compiling, and working version of polymake as an experimental package. It is better than having the very latest release which fails to compile. Once this ticket is merged, I might invest time again to figure out what goes wrong in the compilation.

[jipilab]

@MKoeppe: could you eventually check that the above works on OSX machine?

Best,

[vklein]

This ticket with polymake 3.3 (before last push) compile on ubuntu 16.04.

[embray]

Ticket retargeted after milestone closed (if you don't believe this ticket is appropriate for the Sage 8.8 release please retarget manually)

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​b674466

Merge branch 'public/upgrade_polymake_to_version_3_2r4' of trac.sagemath.org:sage into 24905

[selia]

log of a failed compilation.

[selia]

I tried to compile on macOS Mojave and it failed. I attached my log file.

[jipilab]

Replying to selia:

I tried to compile on macOS Mojave and it failed. I attached my log file.

The failure was reported on the polymake forum here:

​https://forum.polymake.org/viewtopic.php?f=8&t=1702

[slelievre]

Replying to jipilab:

Replying to selia:

I tried to compile on macOS Mojave and it failed. I attached my log file.

The failure was reported on the polymake forum here:

​https://forum.polymake.org/viewtopic.php?f=8&t=1702

Upstream say this is fixed in Polymake 3.4, released 2019-04-15.

Should we upgrade to Polymake 3.4 instead of 3.2 in this ticket?

[vdelecroix]

Replying to slelievre:

Replying to jipilab:

Replying to selia:

I tried to compile on macOS Mojave and it failed. I attached my log file.

The failure was reported on the polymake forum here:

​https://forum.polymake.org/viewtopic.php?f=8&t=1702

Upstream say this is fixed in Polymake 3.4, released 2019-04-15.

Should we upgrade to Polymake 3.4 instead of 3.2 in this ticket?

+1. It makes no sense to upgrade to 3.2 before 3.4.

[jipilab]

Replying to vdelecroix:

Replying to slelievre:

Replying to jipilab:

Replying to selia:

I tried to compile on macOS Mojave and it failed. I attached my log file.

The failure was reported on the polymake forum here:

​https://forum.polymake.org/viewtopic.php?f=8&t=1702

Upstream say this is fixed in Polymake 3.4, released 2019-04-15.

Should we upgrade to Polymake 3.4 instead of 3.2 in this ticket?

+1. It makes no sense to upgrade to 3.2 before 3.4.

Agreed. Although the version 3.3 did not compile on debian stretch and this is why I thought that having 3.2rc4 working could have fixed the backend quickly. Since I do not know how long it will take to make the version 3.4 work, I thought it is better to do things one step at a time.

The whole interface was broken and at least now it works on debian and they proposed a fix.

Anyhow, yes, we can just skip to 3.4, let's just hope it is not a quantum leap...

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​3c968c3

Merge tag '8.8.beta3' into t/24905/public/upgrade_polymake_to_version_3_2r4

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​4fa202d

Add to macOS install instructions for polymake

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​aa058a3	Upgrade polymake to 3.4
​c6f05d8	Update polymake prereq instructions

[mkoeppe]

Upgrading to 3.4 now. Builds OK on Mac OS Mojave (see updated instructions for prerequisites!)

Many test failures from ./sage -t --optional=sage,polymake src/sage/interfaces/polymake.py

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​7339ef6	polymake doc test fixes: list of properties, output
​7018013	polymake doctest: Mark a doctest random that depends on installed packages
​78c10fb	Polymake._tab_completion: Fix for new apropos format in Polymake 3.4
​1699019	Doctest fix for polymake 3.4: false/true instead of 0/1
​f595909	Doctest fix for polymake 3.4: Use different function from the tropical application
​76701f6	Doctest fix for polymake 3.4: Differences in available properties
​83b51de	Polymake 3.4: Fix for typeof small objects
​8510124	Polymake: Remove copy/paste error handling for code that cannot raise

[mkoeppe]

Works now (on macOS Mojave). Please test on other platforms.

The following gives sporadic errors (can happen during doctest too):

sage: polymake.eval('help "TRIANGULATION";')
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-14-18a26ee8f157> in <module>()
----> 1 polymake.eval('help "TRIANGULATION";')

/Users/mkoeppe/s/sage/sage-rebasing/local/lib/python2.7/site-packages/sage/interfaces/expect.pyc in eval(self, code, strip, synchronize, locals, allow_use_file, split_lines, **kwds)
   1349                 elif split_lines:
   1350                     return '\n'.join([self._eval_line(L, allow_use_file=allow_use_file, **kwds)
-> 1351                                         for L in code.split('\n') if L != ''])
   1352                 else:
   1353                     return self._eval_line(code, allow_use_file=allow_use_file, **kwds)

/Users/mkoeppe/s/sage/sage-rebasing/local/lib/python2.7/site-packages/sage/interfaces/polymake.pyc in _eval_line(self, line, allow_use_file, wait_for_prompt, restart_if_needed, **kwds)
   1020                         i = pat
   1021                         while i:
-> 1022                             self._expect.send(chr(3))
   1023                             sleep(0.1)
   1024                             i = self._expect.expect(self._prompt, timeout=0.1)

/Users/mkoeppe/s/sage/sage-rebasing/local/lib/python2.7/site-packages/pexpect/pty_spawn.pyc in send(self, s)
    566 
    567         b = self._encoder.encode(s, final=False)
--> 568         return os.write(self.child_fd, b)
    569 
    570     def sendline(self, s=''):

OSError: [Errno 5] Input/output error

[jipilab]

Replying to mkoeppe:

Works now (on macOS Mojave). Please test on other platforms.

The following gives sporadic errors (can happen during doctest too):

sage: polymake.eval('help "TRIANGULATION";')
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-14-18a26ee8f157> in <module>()
----> 1 polymake.eval('help "TRIANGULATION";')

/Users/mkoeppe/s/sage/sage-rebasing/local/lib/python2.7/site-packages/sage/interfaces/expect.pyc in eval(self, code, strip, synchronize, locals, allow_use_file, split_lines, **kwds)
   1349                 elif split_lines:
   1350                     return '\n'.join([self._eval_line(L, allow_use_file=allow_use_file, **kwds)
-> 1351                                         for L in code.split('\n') if L != ''])
   1352                 else:
   1353                     return self._eval_line(code, allow_use_file=allow_use_file, **kwds)

/Users/mkoeppe/s/sage/sage-rebasing/local/lib/python2.7/site-packages/sage/interfaces/polymake.pyc in _eval_line(self, line, allow_use_file, wait_for_prompt, restart_if_needed, **kwds)
   1020                         i = pat
   1021                         while i:
-> 1022                             self._expect.send(chr(3))
   1023                             sleep(0.1)
   1024                             i = self._expect.expect(self._prompt, timeout=0.1)

/Users/mkoeppe/s/sage/sage-rebasing/local/lib/python2.7/site-packages/pexpect/pty_spawn.pyc in send(self, s)
    566 
    567         b = self._encoder.encode(s, final=False)
--> 568         return os.write(self.child_fd, b)
    569 
    570     def sendline(self, s=''):

OSError: [Errno 5] Input/output error

Is there a way to control/predict this kind of behavior? It would be annoying to have such errors in the doctests.

Since it is an experimental package, this could be tolerable, but it would be good to grasp how this occurs...

I will this new branch.

[jipilab]

Compilation works on debian.

I get the following errors in the interface:

sage -t polymake.py
**********************************************************************
File "polymake.py", line 884, in sage.interfaces.polymake.Polymake._eval_line
Failed example:
    c                                 # optional - polymake
Expected:
    cube of dimension 15
Got:
    <repr(<sage.interfaces.polymake.PolymakeElement at 0x7fe892d55cd0>) failed: PolymakeError: Can't locate object method "description" via package "1" (perhaps you forgot to load "1"?)>
**********************************************************************
File "polymake.py", line 886, in sage.interfaces.polymake.Polymake._eval_line
Failed example:
    c.N_VERTICES                      # optional - polymake
Expected:
    32768
Got:
    Member function 'N_VERTICES' of print ref(@SAGE590);
    1 object
**********************************************************************
File "polymake.py", line 1133, in sage.interfaces.polymake.Polymake.application
Failed example:
    q.VERY_AMPLE                  # optional - polymake
Exception raised:
    Traceback (most recent call last):
      File "/home/jplabbe/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/jplabbe/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.polymake.Polymake.application[3]>", line 1, in <module>
        q.VERY_AMPLE                  # optional - polymake
      File "/home/jplabbe/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py", line 1680, in __getattr__
        raise AttributeError
    AttributeError
**********************************************************************

All tests pass on the backend_polymake.py.

Will investigate.

[jipilab]

I lauched the test with:

sage -t src/sage/interfaces/polymake.py --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,pynormaliz,python2,sage,topcom,polymake

Here is a longer trace about the last doctest failure:

sage: q = polymake.new_object("Polytope", INEQUALITIES=[[5,-4,0,1],[-3,0,-4,1],[-2,1,0,0],[-4,4,4,-1],[0,0,1,0],[8,0,0,-1],[1,0,-1,0],[3,-1,0,0]])
sage: q.H_VECTOR
1 5 5 1
sage: q.F_VECTOR
8 14 8
sage: q.VERY_AMPLE
/home/jplabbe/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py:1064: RuntimeWarning: could not compute 'HILBERT_BASIS_GENERATORS' probably because of unsatisfied preconditions:
precondition : POINTED ( HILBERT_BASIS_GENERATORS , N_HILBERT_BASIS : )
  warnings.warn(w, RuntimeWarning)
/home/jplabbe/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py:1064: RuntimeWarning: rule VERY_AMPLE : GRAPH.ADJACENCY, GRAPH.EDGE_DIRECTIONS, N_VERTICES, VERTICES, FACETS | INEQUALITIES failed: Can't use an undefined value as an ARRAY reference at /home/jplabbe/sage/local/share/polymake/apps/polytope/rules/lattice.rules line 603.
  warnings.warn(w, RuntimeWarning)
/home/jplabbe/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.py:1064: RuntimeWarning: rule HILBERT_BASIS_GENERATORS , N_HILBERT_BASIS : failed: 
*** Missing external software:
*** To compute Hilbert bases you need to have one of the following:
***    - bundled:libnormaliz enabled (requires boost, rerun configure)
***    - 4ti2 installed and configured (check 'show_unconfigured;')
  warnings.warn(w, RuntimeWarning)
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-7-1f21cb7f3e00> in <module>()
----> 1 q.VERY_AMPLE

/home/jplabbe/sage/local/lib/python2.7/site-packages/sage/interfaces/polymake.pyc in __getattr__(self, attrname)
   1678                     return P('{}->{}'.format(self._name, attrname))
   1679                 except (TypeError, PolymakeError):
-> 1680                     raise AttributeError
   1681             else:
   1682                 return P._function_element_class()(self, '{}->{}'.format(self._name, attrname), memberfunction=True)

AttributeError: 

[jipilab]

Here's the log of the configuration of polymake:

gcc version 6.3.0 20170516 (Debian 6.3.0-18+deb9u1) 
[polymake-3.4] ****************************************************
[polymake-3.4] Package 'polymake' is currently not installed
[polymake-3.4] No legacy uninstaller found for 'polymake'; nothing to do
[polymake-3.4] checking C++ compiler ... ok (g++ -std=gnu++11 is GCC 6.3.0)
[polymake-3.4] checking C++ library ... ok (GNU libstdc++ 20170516, C++ 201402)
[polymake-3.4] determining architecture ... ok (x86_64)
[polymake-3.4] determining compiler flags ... ok
[polymake-3.4]    CFLAGS= -march=native
[polymake-3.4]    CXXFLAGS= -std=c++14 -march=native -ftemplate-depth-200 -fno-strict-aliasing -Wno-parentheses -Wshadow -fopenmp -Wno-error=unused-function -Wno-maybe-uninitialized
[polymake-3.4]    LDFLAGS=-L/home/jplabbe/sage/local/lib -Wl,-rpath,/home/jplabbe/sage/local/lib  -fuse-ld=gold -fopenmp
[polymake-3.4] checking gmp installation ... ok
[polymake-3.4] checking mpfr installation ... ok
[polymake-3.4] checking boost installation ... ok
[polymake-3.4] checking libxml2 installation ... ok
[polymake-3.4] checking perl module XML::Writer ... ok
[polymake-3.4] checking perl module XML::LibXML ... ok
[polymake-3.4] checking perl module XML::LibXSLT ... ok
[polymake-3.4] checking perl module Term::ReadKey ... ok
[polymake-3.4] checking perl module Term::ReadLine ... ok
[polymake-3.4] checking perl module JSON ... ok
[polymake-3.4] checking shared perl library ... ok
[polymake-3.4] 
[polymake-3.4] Configuring bundled extensions:
[polymake-3.4] bundled extension java ... disabled by command-line
[polymake-3.4] bundled extension javaview ... disabled by command-line
[polymake-3.4] bundled extension soplex ... disabled by command-line
[polymake-3.4] bundled extension atint ... ok
[polymake-3.4] bundled extension bliss ... ok
[polymake-3.4] bundled extension cdd ... ok (0.94g @ system)
[polymake-3.4] bundled extension libnormaliz ... failed
[polymake-3.4] bundled extension lrs ... ok (6.2 @ system)
[polymake-3.4] bundled extension nauty ... disabled because of conflict with other extension: bliss
[polymake-3.4] bundled extension ppl ... ok (1.2.0 @ /home/jplabbe/sage/local)
[polymake-3.4] bundled extension scip ... failed
[polymake-3.4] bundled extension singular ... ok (4.1.1 @ system)
[polymake-3.4] bundled extension sympol ... ok (bundled)
[polymake-3.4] * If you want to change the configuration of bundled extensions please see build/bundled.log and try configure --help.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​3c6ae95	polymake: Make normaliz a dependency
​b6eeaa1	polymake: Add a patch to polymake's libnormaliz configure

[jipilab]

Compiled fine on debian stretch and all relevant tests pass:

$ sage -t /sage/src/sage/interfaces/polymake.py --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,normaliz,pynormaliz,python2,sage,topcom,polymake
Using --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,normaliz,polymake,pynormaliz,python2,sage,topcom
Doctesting 1 file.
sage -t polymake.py
    [245 tests, 14.65 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------

and

$ sage -t sage/src/sage/geometry/polyhedron/*.py --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,normaliz,pynormaliz,python2,sage,topcom,polymake
too few successful tests, not using stored timings
Using --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,normaliz,polymake,pynormaliz,python2,sage,topcom
Doctesting 25 files.
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------

[mkoeppe]

polymake patch sent upstream.

[gh-LaisRast]

It compiled on Debian GNU/Linux 9.8 (stretch) x86_64. All relevant tests pass:

$ ./sage -t src/sage/interfaces/polymake.py --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,normaliz,pynormaliz,python2,sage,topcom,polymake

too few successful tests, not using stored timings
Running doctests with ID 2019-04-26-23-04-17-71ea1904.
Git branch: polymake
Using --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,normaliz,polymake,pynormaliz,python2,sage,topcom
Doctesting 1 file.
sage -t src/sage/interfaces/polymake.py
    [245 tests, 6.94 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 11.6 seconds
    cpu time: 1.4 seconds
    cumulative wall time: 6.9 seconds

$ ./sage -t src/sage/geometry/polyhedron/*.py --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,python2,sage,topcom,polymake

too few successful tests, not using stored timings
Running doctests with ID 2019-04-26-23-12-47-322d8126.
Git branch: polymake
Using --optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,polymake,python2,sage,topcom
Doctesting 25 files.
...
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 65.0 seconds
    cpu time: 43.6 seconds
    cumulative wall time: 64.1 seconds

[gh-sophiasage]

log of failed compilation. mac os mojave

[mkoeppe]

See the updated Perl module prerequisites by typing "sage -info polymake".

[gh-LaisRast]

sage -t src/sage/interfaces/polymake.py

[gh-LaisRast]

It compiled on Arch Linux x86_64 (5.0.9-arch1-1-ARCH). All relevant tests pass except for three. ​https://trac.sagemath.org/attachment/ticket/24905/polymake.log

[gh-kliem]

[polymake-3.4] FAILED: /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/bundled/singular/apps/ideal/cpperl/auto-contains_monomial.o                                                                                                    
[polymake-3.4]   g++ -std=gnu++11 -c -o /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/bundled/singular/apps/ideal/cpperl/auto-contains_monomial.o -MMD -MT /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.
4/src/build/Opt/bundled/singular/apps/ideal/cpperl/auto-contains_monomial.o -MF /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/bundled/singular/apps/ideal/cpperl/auto-contains_monomial.o.d -fPIC -pipe -std=c++14 -march=native -ft
emplate-depth-200 -fno-strict-aliasing -Wno-parentheses -Wshadow -fopenmp -Wno-error=unused-function -Wno-maybe-uninitialized  -DPOLYMAKE_DEBUG=0 -DNDEBUG -O3 -DPOLYMAKE_APPNAME=ideal -DPOLYMAKE_BUNDLED_EXT=singular -DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG -DS
ING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG -I/srv/public/kliem/patchbot-sage/sage/local/include -I/srv/public/kliem/patchbot-sage/sage/local/include/singular -I/srv/public/kliem/patchbot-sage/sage/local/include -I/srv/public/kliem/patchbot-sage/sage/local/include/s
ingular -I/srv/public/kliem/patchbot-sage/sage/local/include/ -I/srv/public/kliem/patchbot-sage/sage/local/include -I/srv/public/kliem/patchbot-sage/sage/local/include/ -I/srv/public/kliem/patchbot-sage/sage/local/include -Wno-unused-value -I/srv/public/kliem/patchbot-sa
ge/sage/local/var/tmp/sage/build/polymake-3.4/src/bundled/singular/include/app-wrappers -I/srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/bundled/singular/include/apps -I/srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake
-3.4/src/include/app-wrappers -I/srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/include/apps -I/srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/include/external/permlib -I/srv/public/kliem/patchbot-sage/sage/lo
cal/var/tmp/sage/build/polymake-3.4/src/include/external/TOSimplex -I/srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/include/core-wrappers -I/srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/include/core /srv/pu
blic/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/bundled/singular/apps/ideal/cpperl/generated/auto-contains_monomial.cc && : 'COMPILER_USED=6.3.0'
[polymake-3.4] In file included from ../../../../../../../../include/polymake/client.h:25:0,
[polymake-3.4]                  from ../../bundled/singular/apps/ideal/cpperl/generated/auto-contains_monomial.cc:6:
[polymake-3.4] ../../../../../../../../include/polymake/perl/calls.h: In constructor 'pm::perl::PropertyValue::PropertyValue(sv*, TOptions ...)':
[polymake-3.4] ../../../../../../../../include/polymake/perl/calls.h:48:7: warning: declaration of 'options' shadows a member of 'pm::perl::PropertyValue' [-Wshadow]
[polymake-3.4]        : Value(sv_arg)
[polymake-3.4]        ^
[polymake-3.4] In file included from ../../../../../../../../include/polymake/client.h:21:0,
[polymake-3.4]                  from ../../bundled/singular/apps/ideal/cpperl/generated/auto-contains_monomial.cc:6:
[polymake-3.4] ../../../../../../../../include/polymake/perl/Value.h:633:16: note: shadowed declaration is here
[polymake-3.4]     value_flags options;
[polymake-3.4]                 ^~~~~~~
[polymake-3.4] In file included from ../../../../../../../../include/polymake/next/SparseMatrix.h:24:0,
[polymake-3.4]                  from ../../../../../../../../include/polymake/SparseMatrix.h:20,
[polymake-3.4]                  from ../../../../../../../../include/polymake/PolynomialImpl.h:24,
[polymake-3.4]                  from ../../../../../../../../include/polymake/next/Polynomial.h:21,
[polymake-3.4]                  from ../../../../../../../../include/polymake/Polynomial.h:20,
[polymake-3.4]                  from ../../../../../../../../include/polymake/ideal/next/singularIdeal.h:24,
[polymake-3.4]                  from ../../../../../../../../include/polymake/ideal/singularIdeal.h:20,
[polymake-3.4]                  from ../../bundled/singular/apps/ideal/cpperl/generated/auto-contains_monomial.cc:7:
[polymake-3.4] ../../../../../../../../include/polymake/internal/sparse2d.h: In member function 'void pm::sparse2d::sym_permute_entries<Traits>::copy(const typename Traits::ruler*, typename Traits::ruler*, const Perm&, const InvPerm&)':
[polymake-3.4] ../../../../../../../../include/polymake/internal/sparse2d.h:881:4: warning: declaration of 'inv_perm' shadows a member of 'pm::sparse2d::sym_permute_entries<Traits>' [-Wshadow]
[polymake-3.4]     {
[polymake-3.4]     ^
[polymake-3.4] ../../../../../../../../include/polymake/internal/sparse2d.h:906:21: note: shadowed declaration is here
[polymake-3.4]     std::vector<int> inv_perm;
[polymake-3.4]                      ^~~~~~~~
[polymake-3.4] ../../bundled/singular/apps/ideal/cpperl/generated/auto-contains_monomial.cc: At global scope:
[polymake-3.4] ../../bundled/singular/apps/ideal/cpperl/generated/auto-contains_monomial.cc:10:1: error: 'FunctionCallerStart4perl' does not name a type
[polymake-3.4]  FunctionCallerStart4perl {
[polymake-3.4]  ^~~~~~~~~~~~~~~~~~~~~~~~
[polymake-3.4] ../../bundled/singular/apps/ideal/cpperl/generated/auto-contains_monomial.cc:13:20: error: expected constructor, destructor, or type conversion before '(' token
[polymake-3.4]  FunctionCaller4perl(contains_monomial, meth);
[polymake-3.4]                     ^
[polymake-3.4] ../../bundled/singular/apps/ideal/cpperl/generated/auto-contains_monomial.cc:14:30: error: expected constructor, destructor, or type conversion before '(' token
[polymake-3.4]  FunctionTemplateInstance4perl(0, contains_monomial, meth, contains_monomial:M, perl::Returns::normal, 0, (perl::Canned<const SingularIdeal&>));
[polymake-3.4]                               ^
[polymake-3.4] [359/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/lex_min_representative.o
[polymake-3.4] [360/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/orbit_permlib.o
[polymake-3.4] [361/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/permlib_group_tools.o
[polymake-3.4] [362/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/induced_action.o
[polymake-3.4] [363/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/conjugacy_classes.o
[polymake-3.4] [364/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/permlib.o
[polymake-3.4] [365/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/orbit.o
[polymake-3.4] [366/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/sparse_isotypic_components.o
[polymake-3.4] [367/902] COMPILE /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/apps/group/representations.o
[polymake-3.4] ninja: build stopped: subcommand failed.
[polymake-3.4] Makefile:34: recipe for target 'all' failed
[polymake-3.4] make[2]: *** [all] Error 1
[polymake-3.4] make[2]: Leaving directory '/srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src'
[polymake-3.4] Error building polymake
[polymake-3.4]
[polymake-3.4] real     7m41.235s
[polymake-3.4] user     57m24.108s
[polymake-3.4] sys      1m28.580s
[polymake-3.4] ************************************************************************
[polymake-3.4] Error installing package polymake-3.4
[polymake-3.4] ************************************************************************
[polymake-3.4] Please email sage-devel (http://groups.google.com/group/sage-devel)
[polymake-3.4] explaining the problem and including the log file
[polymake-3.4]   /srv/public/kliem/patchbot-sage/sage/logs/pkgs/polymake-3.4.log
[polymake-3.4] Describe your computer, operating system, etc.
[polymake-3.4] If you want to try to fix the problem yourself, *don't* just cd to
[polymake-3.4] /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4 and type 'make' or whatever is appropriate.
[polymake-3.4] Instead, the following commands setup all environment variables
[polymake-3.4] correctly and load a subshell for you to debug the error:
[polymake-3.4]   (cd '/srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4' && '/srv/public/kliem/patchbot-sage/sage/sage' --sh)
[polymake-3.4] When you are done debugging, you can type "exit" to leave the subshell.
[polymake-3.4] ************************************************************************
Makefile:2162: recipe for target '/srv/public/kliem/patchbot-sage/sage/local/var/lib/sage/installed/polymake-3.4' failed
make[1]: *** [/srv/public/kliem/patchbot-sage/sage/local/var/lib/sage/installed/polymake-3.4] Error 1
make[1]: Leaving directory '/srv/public/kliem/patchbot-sage/sage/build/make'

real    7m44,443s
user    57m25,204s
sys     1m28,764s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make polymake'):

* package: ecl-16.1.3.p0
  log file: /srv/public/kliem/patchbot-sage/sage/logs/pkgs/ecl-16.1.3.p0.log
  build directory: /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/ecl-16.1.3.p0

* package: numpy-1.16.0
  log file: /srv/public/kliem/patchbot-sage/sage/logs/pkgs/numpy-1.16.0.log
  build directory: /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/numpy-1.16.0

* package: polymake-3.4
  log file: /srv/public/kliem/patchbot-sage/sage/logs/pkgs/polymake-3.4.log
  build directory: /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4

* package: python
  log file: /srv/public/kliem/patchbot-sage/sage/logs/pkgs/python.log
  build directory: /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/python

* package: r-3.4.4.p1
  log file: /srv/public/kliem/patchbot-sage/sage/logs/pkgs/r-3.4.4.p1.log
  build directory: /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/r-3.4.4.p1

The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

Makefile:31: recipe for target 'polymake' failed
make: *** [polymake] Error 1

[mkoeppe]

Replying to gh-kliem:

[polymake-3.4] FAILED: /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/bundled/singular/apps/ideal/cpperl/auto-contains_monomial.o    

Which compiler is that? Did Sage install its own gcc?

[gh-kliem]

I don't know. I suppose its the systems gcc (Debian 6.3.0-18+deb9u1).

(This is the default gcc in the sage subshell as well.)

Now I did ./sage -i gcc and will see if that makes any difference.

It does Replying to mkoeppe:

Replying to gh-kliem:

[polymake-3.4] FAILED: /srv/public/kliem/patchbot-sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/Opt/bundled/singular/apps/ideal/cpperl/auto-contains_monomial.o    

Which compiler is that? Did Sage install its own gcc?

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​624ac01

polymake: Also provide core functions

[mkoeppe]

Replying to gh-kliem:

I don't know. I suppose its the systems gcc (Debian 6.3.0-18+deb9u1).

(This is the default gcc in the sage subshell as well.)

Now I did ./sage -i gcc and will see if that makes any difference.

It does

It may also be worth checking whether polymake builds OK from its source package with your system's gcc.

[mkoeppe]

(outside of sage.)

[gh-kliem]

polymake 3.3 worked fine. I didn't check with polymake 3.4.

[gh-kliem]

Now my sage is messed up.

Those are some of the error that occure

File "src/sage/groups/generic.py", line 1104, in sage.groups.generic.?
Failed example:                                               
    F=GF(2^1279,'a')
Exception raised:                
    Traceback (most recent call last):
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)       
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)       
      File "<doctest sage.groups.generic.?[14]>", line 1, in <module>
        F=GF(Integer(2)**Integer(1279),'a')
      File "sage/structure/factory.pyx", line 367, in sage.structure.factory.UniqueFactory.__call__ (build/cythonized/sage/structure/factory.c:2059)
        key, kwds = self.create_key_and_extra_args(*args, **kwds)
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/rings/finite_rings/finite_field_constructor.py", line 566, in create_key_and_extra_args
        raise ValueError("the order of a finite field must be a prime power")
    ValueError: the order of a finite field must be a prime power
**********************************************************************
File "src/sage/groups/generic.py", line 1105, in sage.groups.generic.?
Failed example:           
    n=F.cardinality()-1 # Mersenne prime
Exception raised:                                                           
    Traceback (most recent call last):             
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.groups.generic.?[15]>", line 1, in <module>
        n=F.cardinality()-Integer(1) # Mersenne prime
    AttributeError: 'IntegerFactorization' object has no attribute 'cardinality'
**********************************************************************
File "src/sage/groups/generic.py", line 1106, in sage.groups.generic.?
Failed example:
    order_from_multiple(F.random_element(),n,factorization=[(n,1)],operation='*')==n
Exception raised:
    Traceback (most recent call last):
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.groups.generic.?[16]>", line 1, in <module>
        order_from_multiple(F.random_element(),n,factorization=[(n,Integer(1))],operation='*')==n
    AttributeError: 'IntegerFactorization' object has no attribute 'random_element'

It seems that almost nothing works anymore. I have no idea what I can do about it besides deleting everything and reinstalling sage.

Those errors are happening in the develop branch as well.

By the way, nothing works in src/sage/interfaces/polymake.py. This is the start of a very long list.

kliem@zancara:~/localhome/patchbot-sage/sage$  sage -t --long  src/sage/interfaces/polymake.py --optional=bliss,ccache,dochtml,lrslib,memlimit,mpir,ninja_build,normaliz,openssl,pynormaliz,python2,sage,polymake 
too many failed tests, not using stored timings
Running doctests with ID 2019-04-27-22-43-17-aca10dd8.
Git branch: develop
Using --optional=bliss,ccache,dochtml,lrslib,memlimit,mpir,ninja_build,normaliz,openssl,polymake,pynormaliz,python2,sage
Doctesting 1 file.
sage -t --long src/sage/interfaces/polymake.py
**********************************************************************
File "src/sage/interfaces/polymake.py", line 71, in sage.interfaces.polymake.PolymakeError
Failed example:
    polymake.eval('print foo;')    # optional polymake
Expected:
    Traceback (most recent call last):
    ...
    PolymakeError: Unquoted string "foo" may clash with future reserved word...
Got:
    <BLANKLINE>
    Traceback (most recent call last):
      File "/import/sage-7.4/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 498, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/import/sage-7.4/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 861, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.polymake.PolymakeError[0]>", line 1, in <module>
        polymake.eval('print foo;')    # optional polymake
    AttributeError: Polymake instance has no attribute 'eval'
**********************************************************************
File "src/sage/interfaces/polymake.py", line 86, in sage.interfaces.polymake.polymake_console
Failed example:
    from sage.interfaces.polymake import polymake_console
Exception raised:
    Traceback (most recent call last):
      File "/import/sage-7.4/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 498, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/import/sage-7.4/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 861, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.polymake.polymake_console[0]>", line 1, in <module>
        from sage.interfaces.polymake import polymake_console
    ImportError: No module named polymake
**********************************************************************
File "src/sage/interfaces/polymake.py", line 127, in sage.interfaces.polymake.Polymake
Failed example:
    p = polymake.rand_sphere(4, 20, seed=5)       # optional - polymake
Exception raised:
    Traceback (most recent call last):
      File "/import/sage-7.4/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 498, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/import/sage-7.4/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 861, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.polymake.Polymake[0]>", line 1, in <module>
        p = polymake.rand_sphere(Integer(4), Integer(20), seed=Integer(5))       # optional - polymake
    AttributeError: Polymake instance has no attribute 'rand_sphere'
**********************************************************************

[gh-kliem]

When I run polymake in the sage subshell I get a compilation error upon running $p = rand_sphere<4,20>;.

[jipilab]

Run a sage distclean and reinstall sage from scratch. Installing polymake also broke my sage somehow a some point. Reinstalling worked for me.

[gh-kliem]

I already did it. Now openssl isn't working again. It will take a while until I have a working version of sage on this machine again.

Replying to jipilab:

Run a sage distclean and reinstall sage from scratch. Installing polymake also broke my sage somehow a some point. Reinstalling worked for me.

[mkoeppe]

Replying to gh-LaisRast:

It compiled on Arch Linux x86_64 (5.0.9-arch1-1-ARCH). All relevant tests pass except for three. ​https://trac.sagemath.org/attachment/ticket/24905/polymake.log

Thanks for checking. In these three doctests it looks like polymake is emitting some extra newlines. This is probably some nondeterministic pty interaction.

[mkoeppe]

polymake 3.4 on macOS Mojave (built within sage, but also the official DMG from the polymake website) dies if one presses ^C in quick succession during a computation such as the following:

  $p = cube(20);
  $p->VOLUME;

[jipilab]

Replying to mkoeppe:

polymake 3.4 on macOS Mojave (built within sage, but also the official DMG from the polymake website) dies if one presses ^C in quick succession during a computation such as the following:

  $p = cube(20);
  $p->VOLUME;

Similar on debian using ./sage -polymake.

[mkoeppe]

Replying to mkoeppe:

polymake 3.4 on macOS Mojave (built within sage, but also the official DMG from the polymake website) dies if one presses ^C in quick succession during a computation such as the following:

  $p = cube(20);
  $p->VOLUME;

polymake 3.2 (from the official DMG) has the same problem.

[mkoeppe]

Replying to mkoeppe:

Replying to mkoeppe:

polymake 3.4 on macOS Mojave (built within sage, but also the official DMG from the polymake website) dies if one presses ^C in quick succession during a computation such as the following:

  $p = cube(20);
  $p->VOLUME;

polymake 3.2 (from the official DMG) has the same problem.

Likewise, polymake 3.1

[gh-kliem]

I set up my sage again and everything worked (all tests passed).

After installing polymake (and normaliz pynormaliz 4ti2 latte_int topcom qhull) I am getting the following failure:

kliem@zancara:~/localhome/patchbot-sage/sage$ ./sage -t --long src/sage/rings/integer.pyx --exitfirst
too many failed tests, not using stored timings
Running doctests with ID 2019-04-28-22-27-17-978fe65b.
Git branch: polymake
Using --optional=4ti2,bliss,cmake,dochtml,latte_int,lidia,lrslib,memlimit,ninja_build,normaliz,openssl,pynormaliz,python2,qhull,sage,topcom
Doctesting 1 file.
sage -t --long src/sage/rings/integer.pyx
**********************************************************************
File "src/sage/rings/integer.pyx", line 3009, in sage.rings.integer.Integer.divisors
Failed example:
    for i in range(20):  # long time
        try:
            alarm(RDF.random_element(1e-3, 0.5))
            _ = n.divisors()
            cancel_alarm()  # we never get here
        except AlarmInterrupt:
            pass
Exception raised:
    Traceback (most recent call last):
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.rings.integer.Integer.divisors[20]>", line 4, in <module>
        _ = n.divisors()
      File "sage/rings/integer.pyx", line 3079, in sage.rings.integer.Integer.divisors (build/cythonized/sage/rings/integer.c:19767)
        ptr = <unsigned long*>check_allocarray(divisor_count, 3 * sizeof(unsigned long))
      File "memory.pxd", line 87, in cysignals.memory.check_allocarray (build/cythonized/sage/rings/integer.c:47077)
    MemoryError: failed to allocate 33554432 * 24 bytes
**********************************************************************
1 item had failures:
   1 of  21 in sage.rings.integer.Integer.divisors
    [1127 tests, 1 failure, 19.40 s]
----------------------------------------------------------------------
sage -t --long src/sage/rings/integer.pyx  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 19.6 seconds
    cpu time: 19.4 seconds
    cumulative wall time: 19.4 seconds

This looks familiar and indeed I have had this issue before:

​https://groups.google.com/forum/#!topic/sage-devel/wqnilUCLsT4

The last time I had this issue this also happened in connection with this ticket on a different machine.

There are several more failures in this file, but I believe they are all due to the same issue.

[jipilab]

Replying to gh-kliem:

[snip]

I do not think that this error is related to this ticket as we are not touching the file src/sage/rings/integer.pyx directly, nor does the installation (as far as I can see) is related to this module. This looks like a local error on this machine.

Considering that:

• This error was not so far reproduced on other machines,
• that the package is experimental,
• it compiles on macOS Mojave, debian, and ArchLinux?,

I would set this ticket to positive review. Further issues can be reported here: #22710.

[gh-kliem]

Replying to jipilab:

Replying to gh-kliem:

[snip]

I do not think that this error is related to this ticket as we are not touching the file src/sage/rings/integer.pyx directly, nor does the installation (as far as I can see) is related to this module. This looks like a local error on this machine.

I have this error occuring on two different machines and it's installation dependent (on one machine it only shows up in one installation). As it hasn't been there in this installation before installing normaliz pynormaliz 4ti2 latte_int topcom qhull polymake, I suppose that one of them for some strange reason causes alarm to not work correctly anymore (this causes the memory overflow as the list of divisors is too long for ./sage -t default).

It is possible that a patchbot cannot have polymake installed. But I'm not certain of this yet.

Considering that:

• This error was not so far reproduced on other machines,
• that the package is experimental,
• it compiles on macOS Mojave, debian, and ArchLinux?,

I would set this ticket to positive review. Further issues can be reported here: #22710.

[mkoeppe]

I can't seem to reproduce a failure in the tests for src/sage/rings/integer.pyx.

[gh-kliem]

The failure has nothing to do with this ticket.

I updated my post on sage-devel.

It seems that many patchbots fail that test in the sense that alarm interrupt takes way too long (they all take about a minute for this file and this seems to be the reason why). In my case the machine allocates the list for the divisors already, which exceeds the default allowance for .sage -t.

[fbissey]

These two doctests need to be marked optional

sage -t --long /usr/lib64/python2.7/site-packages/sage/interfaces/polymake.py
**********************************************************************
File "/usr/lib64/python2.7/site-packages/sage/interfaces/polymake.py", line 1097, in sage.interfaces.polymake.Polymake._tab_completion
Failed example:
    'show_credits' in dir(polymake)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib64/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.polymake.Polymake._tab_completion[0]>", line 1, in <module>
        'show_credits' in dir(polymake)
      File "/usr/lib64/python2.7/site-packages/sage/interfaces/tab_completion.py", line 52, in __dir__
        return dir(self.__class__) + list(self.__dict__) + tab_fn()
      File "/usr/lib64/python2.7/site-packages/sage/interfaces/polymake.py", line 1107, in _tab_completion
        self._start()
      File "/usr/lib64/python2.7/site-packages/sage/interfaces/polymake.py", line 362, in _start
        Expect._start(self, alt_message=None)
      File "/usr/lib64/python2.7/site-packages/sage/interfaces/expect.py", line 523, in _start
        raise RuntimeError("unable to start %s: %s" % (self.name(), msg))
    RuntimeError: unable to start polymake: End Of File (EOF). Exception style platform.
    Polymake finished running /usr/bin/env TERM=dumb polymake
    command: /usr/bin/env
    args: ['/usr/bin/env', 'TERM=dumb', 'polymake']
    buffer (last 100 chars): ''
    before (last 100 chars): '/usr/bin/env: \xe2\x80\x98polymake\xe2\x80\x99: No such file or directory\r\n'
    after: <class 'pexpect.exceptions.EOF'>
    match: None
    match_index: None
    exitstatus: 127
    flag_eof: True
    pid: 26727
    child_fd: 15
    closed: False
    timeout: None
    delimiter: <class 'pexpect.exceptions.EOF'>
    logfile: None
    logfile_read: None
    logfile_send: None
    maxread: 4194304
    ignorecase: False
    searchwindowsize: None
    delaybeforesend: None
    delayafterclose: 0.1
    delayafterterminate: 0.1
    searcher: searcher_re:
        0: re.compile('polytope > ')
**********************************************************************
File "/usr/lib64/python2.7/site-packages/sage/interfaces/polymake.py", line 1102, in sage.interfaces.polymake.Polymake._tab_completion
Failed example:
    'lex_ordered' in dir(polymake)
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib64/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.polymake.Polymake._tab_completion[1]>", line 1, in <module>
        'lex_ordered' in dir(polymake)
      File "/usr/lib64/python2.7/site-packages/sage/interfaces/tab_completion.py", line 52, in __dir__
        return dir(self.__class__) + list(self.__dict__) + tab_fn()
      File "/usr/lib64/python2.7/site-packages/sage/interfaces/polymake.py", line 1107, in _tab_completion
        self._start()
      File "/usr/lib64/python2.7/site-packages/sage/interfaces/polymake.py", line 362, in _start
        Expect._start(self, alt_message=None)
      File "/usr/lib64/python2.7/site-packages/sage/interfaces/expect.py", line 523, in _start
        raise RuntimeError("unable to start %s: %s" % (self.name(), msg))
    RuntimeError: unable to start polymake: End Of File (EOF). Exception style platform.
    Polymake finished running /usr/bin/env TERM=dumb polymake
    command: /usr/bin/env
    args: ['/usr/bin/env', 'TERM=dumb', 'polymake']
    buffer (last 100 chars): ''
    before (last 100 chars): '/usr/bin/env: \xe2\x80\x98polymake\xe2\x80\x99: No such file or directory\r\n'
    after: <class 'pexpect.exceptions.EOF'>
    match: None
    match_index: None
    exitstatus: 127
    flag_eof: True
    pid: 26731
    child_fd: 15
    closed: False
    timeout: None
    delimiter: <class 'pexpect.exceptions.EOF'>
    logfile: None
    logfile_read: None
    logfile_send: None
    maxread: 4194304
    ignorecase: False
    searchwindowsize: None
    delaybeforesend: None
    delayafterclose: 0.1
    delayafterterminate: 0.1
    searcher: searcher_re:
        0: re.compile('polytope > ')
**********************************************************************
1 item had failures:
   2 of   3 in sage.interfaces.polymake.Polymake._tab_completion
    [24 tests, 2 failures, 0.09 s]

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​666db96

Added two missing optional tags

[dimpase]

please provide a precise link to the tarball. The link in the description leads to source tarball, minimal tarball, etc...

[mkoeppe]

The wget command line has the URL.

[dimpase]

I see - but the instructions like this are flaky. By right, one has to get the branch and the tarball first, and only then go about building things. Otherwise chances are that building chokes up on an unavailable tarball.

And you should run make build to get all the deps right (sage -b is really a quick and dirty plug that should go away)

[dimpase]

why does one need libncurses-dev? Sage provides ncurses, and as soon as #27277 is in, it should be able to use system's (n)curses.

[mkoeppe]

Replying to dimpase:

why does one need libncurses-dev? Sage provides ncurses, and as soon as #27277 is in, it should be able to use system's (n)curses.

This might be copy-paste from polymake install instructions. Certainly the ncurses spkg is pulled in via perl_term_readline_gnu and readline. It would be good to test if the install works without this system package (it should).

[dimpase]

OK - the previous instruction didn't work if polymake was already installed. (Surely, the fact that it's an experimental package only makes it more complicated).

[dimpase]

some errors, please have a look at mis-posted ​https://trac.sagemath.org/ticket/27763#comment:9 and ​https://trac.sagemath.org/ticket/27763#comment:11

[dimpase]

Please apply this

src/sage/interfaces/polymake.py

@@ -874 +874 @@
         sometimes it hangs, and therefore we remove it from the tests, for now::
 
             sage: c = polymake.cube(15)             # optional - polymake
-            sage: polymake.eval('print {}->F_VECTOR;'.format(c.name()), timeout=1) # optional - polymake # not tested
+            sage: polymake.eval('print {}->F_VECTOR;'.format(c.name()), timeout=1) # not tested # optional - polymake
             Traceback (most recent call last):
             ...
             RuntimeError: Polymake fails to respond timely

this order indeed suppresses running this line, otherwise it does not work for me.

[mkoeppe]

Very strange. I don't think the order of these annotations makes a difference

[dimpase]

The doctesting framework is a pile of .... - so I'm not surprised that on different platforms it behaves differently. E.g. we see doctests passing with --serial options and mysteriously crashing without it.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​4e91dcc

Change format of a 'not tested' doc test annotation

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​a3a8247

update docs, as discussed on #24905

[dimpase]

looks good now.

[git]

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. This was a forced push. New commits:

​575c2e1	Add support for unconditional pre- and post-check actions in spkg-configure.m4
​46ae057	Refactor the mpir/spkg-configure.m4 (and to a lesser extent the one for gmp) to use the new pre and post arguments to SAGE_SPKG_CONFIGURE
​a79e020	Refactor the mpir/spkg-configure.m4 (and to a lesser extent the one for gmp) to use the new pre and post arguments to SAGE_SPKG_CONFIGURE
​d6024f3	Trac #27642: Initial attempt at fix: re-run `configure` and `make all-build` after
​56bf67a	leave GMP's spkg-configure.m4 as it was

[dimpase]

oops, sorry, I keep pushing into wrong branches these days! Please save your old branch...

[dimpase]

specifically, Matthias, could you force-push your last ​https://trac.sagemath.org/ticket/24905#comment:133 ?

[dimpase]

On ​https://github.com/sagemath/sagetrac-mirror/tree/public/upgrade_polymake_to_version_3_2r4

we have everything till comment:101 - so I can recreate the thing from history here... <facepalm>

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

​f595909	Doctest fix for polymake 3.4: Use different function from the tropical application
​76701f6	Doctest fix for polymake 3.4: Differences in available properties
​83b51de	Polymake 3.4: Fix for typeof small objects
​8510124	Polymake: Remove copy/paste error handling for code that cannot raise
​3c6ae95	polymake: Make normaliz a dependency
​b6eeaa1	polymake: Add a patch to polymake's libnormaliz configure
​624ac01	polymake: Also provide core functions
​9440e3d	Added two missing optional tags
​5c598b0	Change format of a 'not tested' doc test annotation
​1fd7112	update docs, as discussed on #24905

[dimpase]

OK, this looks like a correctly recovered branch to me.

[dimpase]

On Debian I also had to install libterm-readkey-perl

[git]

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. This was a forced push. New commits:

​666db96	Added two missing optional tags
​4e91dcc	Change format of a 'not tested' doc test annotation
​05f3e61	update docs, as discussed on #24905

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​53c8ee6

Mention libterm-readkey-perl

[mkoeppe]

I restored the old branch and cherry-picked your "update docs" commit

[dimpase]

could you also mention libterm-readline-gnu-perl as a package to install on Debian/Ubuntu?

[mkoeppe]

Perhaps it's time to change this package from "experimental" to "optional"?

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​b613e57

Mention libterm-readline-gnu-perl

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​e5c3249	polymake: Mention MOngoDB for polydb
​b89376a	polymake: Update info on macOS

[dimpase]

Let's get this done and open another ticket for promotion to optional. IMHO it is not quite ready, e.g. it does not run on all supported platforms. And the installation procedure isn't nice. I don't think we have a optional package where to install it one needs to install many things by hand in an ad hoc way.

---

New commits:

​e5c3249	polymake: Mention MOngoDB for polydb
​b89376a	polymake: Update info on macOS

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​0c1b044

polymake: update MongoDB information for linux distros

[mkoeppe]

Replying to dimpase:

Let's get this done and open another ticket for promotion to optional. IMHO it is not quite ready, e.g. it does not run on all supported platforms. And the installation procedure isn't nice. I don't think we have a optional package where to install it one needs to install many things by hand in an ad hoc way.

OK, I agree, good point.

[mkoeppe]

I added one more perl package. Could you check this on Linux? After adding it, the following should work:

polytope > $A = db_query( { "_id"=>"F.4D.0047" }, db=>"LatticePolytopes", collection=>"SmoothReflexive" );
polymake: used package polyDB
   Access to the polymake polytope database.
   (c) 2013-2018 Silke Horn, Andreas Paffenholz
   http://solros.de
   http://www.mathematik.tu-darmstadt.de/~paffenholz


polymake:  ERROR: #
# *** DEPRECATION WARNING ***
# ...

(The deprecation warning is normal.}

[dimpase]

Building 72 more Perl packages now :-) Why is polymake itself not on CPAN?

[dimpase]

this is what I got (after installing moar perl and rebuilding polymake)

 $ ./sage --polymake
Welcome to polymake version 3.4
Copyright (c) 1997-2019
Ewgenij Gawrilow, Michael Joswig (TU Berlin)
https://polymake.org

This is free software licensed under GPL; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Press F1 or enter 'help;' for basic instructions.

Application polytope currently uses following contributed and third-party software packages:
SVG, bliss, cdd, graphviz, latte, libnormaliz, lrs, permlib, polyDB, povray, ppl, qhull, singular, sketch, sympol, threejs, tikz, tosimplex
For more details:  show_credits;
polytope > $A = db_query( { "_id"=>"F.4D.0047" }, db=>"LatticePolytopes", collection=>"SmoothReflexive" );
polymake: used package polyDB
   Access to the polymake polytope database.
   (c) 2013-2018 Silke Horn, Andreas Paffenholz
   http://solros.de
   http://www.mathematik.tu-darmstadt.de/~paffenholz


polytope > 

perhaps you could add a meaningful doctest, tagged internet, for this?

[mkoeppe]

When MongoDB is not available, the function db_query is not even present. Not sure if/why we want to doctest that.

Let's postpone doctesting the db_query function in Sage to #27802, which adds support for the dictionary that appears in the argument list.

[dimpase]

OK then.

[dimpase]

one last nitpick yum install perl-Term-ReadLine-Gnu should be added to Fedora instructions

[mkoeppe]

Thank you!

[git]

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:

​2eda6e1

polymake: add to fedora instructions

[dimpase]

Fedora's 26 perl is however not good.

[polymake-3.4] FAILED: /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/perlx/5.24.4/x86_64-linux-thread-multi/Customize.cc
[polymake-3.4] /usr/bin/perl /usr/share/perl5/ExtUtils/xsubpp -typemap /usr/share/perl5/ExtUtils/typemap  --output /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/perlx/5.24.4/x86_64-linux-thread-multi/Customize.cc /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/lib/core/src/perl/Customize.xxs
[polymake-3.4] Can't open perl script "/usr/share/perl5/ExtUtils/xsubpp": No such file or directory

This seems to be a known problem - not sure it's worthwhile to try to fix it though.

And, by the way, on stable Debian I get a problem building with (the standard) gcc 6.3.

[mkoeppe]

Replying to dimpase:

Fedora's 26 perl is however not good.

[polymake-3.4] FAILED: /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/perlx/5.24.4/x86_64-linux-thread-multi/Customize.cc
[polymake-3.4] /usr/bin/perl /usr/share/perl5/ExtUtils/xsubpp -typemap /usr/share/perl5/ExtUtils/typemap  --output /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/perlx/5.24.4/x86_64-linux-thread-multi/Customize.cc /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/lib/core/src/perl/Customize.xxs
[polymake-3.4] Can't open perl script "/usr/share/perl5/ExtUtils/xsubpp": No such file or directory

This seems to be a known problem - not sure it's worthwhile to try to fix it though.

Known to who?

[mkoeppe]

Follow-up ticket: Fix polymake 3.4 lrslib detection (#27803).

[dimpase]

It's known to the internet that Fedora/Centos perform a surgery on its Perl installation resulting in breakages like in comment:163 (missing /usr/share/perl5/ExtUtils/xsubpp; of course xsubpp is present, it's only not in this locaton, hardcoded somewhere...)

[vbraun]

Too late, a previous version was released in 8.8.beta5. Move any new code to a separate ticket

[mkoeppe]

Replying to vbraun:

Too late, a previous version was released in 8.8.beta5. Move any new code to a separate ticket

No problem, the missing commit is on the branch of #27803