7.3.beta6

[Volker Braun]

As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

d091c43 Updated SageMath version to 7.3.beta6

0ca345f Trac #20906: rank is missing in Combinatorial free modules

44c700c Trac #20705: Classes for Reed Muller Codes

d7ab9c6 Trac #20693: Sage crashes when inverting/dividing large number field elements

c3269eb Trac #20891: public method for _mul_trunc_

44820b6 Trac #20840: Automatically add generic encoders/decoders to any linear code class

6c27608 Trac #20848: Degree and arithmetic genus for projective curves

ccc94a0 Trac #20890: plethysm of certain symmetric functions raises an error

1d74066 Trac #20883: py3 imports in combinat folder

173f395 Trac #20882: py3 divisions

7435287 Trac #16697: implement symbolic lower incomplete gamma function

b19b6ae Trac #10034: Make evaluation possible for 'hold' objects

1dddfaa Trac #20880: Update git-trac package

2b3688a Trac #20878: PointConfiguration: Add plot method

d43b98e Trac #20869: better check for correct pprof

45ec27e Trac #20832: Add a doctest for GLPK error handling and verbose output

5097e5f Trac #20760: Mirror image of links

8012bce Trac #20424: More tests for common MIP TestSuite: add_col, solve; some fixes for backends

54f5c21 Trac #20837: Cleanup patching of some spkgs

c8d9311 Trac #20855: py3 print : not tested cases, step 6

66989ab Trac #15152: Sage interpreter blocks Tkinter GUI

b189d4c Trac #20845: Backport ecl long pathname fix

f602851 Trac #20839: Basic intersection analysis for algebraic curves

dfebda3 Trac #20874: LPAbstractDictionary: Add objective_name method

bd9a9fb Trac #20873: py3 print : not tested cases in pyx files, step1

e5b30c3 Trac #20862: unicode art for partitions, compositions and skew partitions

8c4bd50 Trac #20854: adding the descent algebra to the algebras catalog

1a43c41 Trac #20844: py3 division in ell_rational_field

e0bf148 Trac #20629: some absolute imports in the rings folder

2cf5e41 Trac #20868: Homfly doctest errors

671c3d1 Updated SageMath version to 7.3.beta5

[William Stein]

Hi,

On sagemathcloud (Ubuntu 16.04+lots) I've built all the betas up to
7.3.beta4 fine. 7.3.beta5 (via upgrade) won't build, nor will
7.3.beta6. The complete failed at pynac build log for 7.3.beta6 is
attached.

"I am unable to get 7.3.beta5 to compile on this project. I tried
updating from the developer version rsynced from
/projects/sage/sage-dev/ and then building with ./sage -b, but it
fails when compiling gen.pyx. Alternatively, when I run 'make', it
fails on building pynac. I've also tried wgetting the 7.3.beta5
tarball and making from scratch, but still get the same failure on
pynac. I feel like I must be missing something obvious. Thanks in
advance for any help! [...] FYI, 7.3.beta6 still fails to build on
pynac. For now, I'm just sticking with 7.3.beta4. Thank you both for
your help!"

Build ends with:

---

pynac-0.6.7] CXX libpynac_la-infoflagbase.lo

[pynac-0.6.7] CXX libpynac_la-order.lo

sage-logger -p 'sage-spkg speaklater-1.3'
'/projects/74fa0622-89a5-45b8-9451-eaaacd2ad12b/sage-git/logs/pkgs/speaklater-1.3.log'

[speaklater-1.3] Found local metadata for speaklater-1.3

[speaklater-1.3] Attempting to download package speaklater-1.3.tar.gz
from mirrors

[speaklater-1.3]
http://mirrors.mit.edu/sage/spkg/upstream/speaklater/speaklater-1.3.tar.gz

[pynac-0.6.7] CXXLD libpynac.la

[speaklater-1.3]
[......................................................................]

[speaklater-1.3] speaklater-1.3

[speaklater-1.3] ====================================================

[speaklater-1.3] Setting up build directory for speaklater-1.3

[speaklater-1.3] Finished extraction

[speaklater-1.3] ****************************************************

[speaklater-1.3] Host system:

[speaklater-1.3] Linux compute6-us 4.2.0-30-generic #36-Ubuntu SMP Fri
Feb 26 00:58:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

[speaklater-1.3] ****************************************************

[speaklater-1.3] C compiler: gcc

[speaklater-1.3] C compiler version:

[speaklater-1.3] Using built-in specs.

[speaklater-1.3] COLLECT_GCC=gcc

[speaklater-1.3] COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper

[speaklater-1.3] Target: x86_64-linux-gnu

[speaklater-1.3] Configured with: ../src/configure -v
--with-pkgversion='Ubuntu 5.2.1-22ubuntu2'
--with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs
--enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++
--prefix=/usr --program-suffix=-5 --enable-shared
--enable-linker-build-id --libexecdir=/usr/lib
--without-included-gettext --enable-threads=posix --libdir=/usr/lib
--enable-nls --with-sysroot=/ --enable-clocale=gnu
--enable-libstdcxx-debug --enable-libstdcxx-time=yes
--with-default-libstdcxx-abi=new --enable-gnu-unique-object
--disable-vtable-verify --enable-libmpx --enable-plugin
--with-system-zlib --disable-browser-plugin --enable-java-awt=gtk
--enable-gtk-cairo
--with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre
--enable-java-home
--with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64
--with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64
--with-arch-directory=amd64
--with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc
--enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64
--with-multilib-list=m32,m64,mx32 --enable-multilib
--with-tune=generic --enable-checking=release --build=x86_64-linux-gnu
--host=x86_64-linux-gnu --target=x86_64-linux-gnu

[speaklater-1.3] Thread model: posix

[speaklater-1.3] gcc version 5.2.1 20151010 (Ubuntu 5.2.1-22ubuntu2)

[speaklater-1.3] ****************************************************

[speaklater-1.3] running install

[pynac-0.6.7] /usr/bin/ld: cannot find -lao

[pynac-0.6.7] collect2: error: ld returned 1 exit status

[pynac-0.6.7] Makefile:493: recipe for target 'libpynac.la' failed

[pynac-0.6.7] make[5]: *** [libpynac.la] Error 1

[pynac-0.6.7] make[5]: Leaving directory
'/projects/74fa0622-89a5-45b8-9451-eaaacd2ad12b/sage-git/local/var/tmp/sage/build/pynac-0.6.7/src/ginac'

[pynac-0.6.7] Makefile:480: recipe for target 'all-recursive' failed

[pynac-0.6.7] make[4]: *** [all-recursive] Error 1

[pynac-0.6.7] make[4]: Leaving directory
'/projects/74fa0622-89a5-45b8-9451-eaaacd2ad12b/sage-git/local/var/tmp/sage/build/pynac-0.6.7/src'

[pynac-0.6.7] Makefile:386: recipe for target 'all' failed

[pynac-0.6.7] make[3]: *** [all] Error 2

[pynac-0.6.7] make[3]: Leaving directory
'/projects/74fa0622-89a5-45b8-9451-eaaacd2ad12b/sage-git/local/var/tmp/sage/build/pynac-0.6.7/src'

[pynac-0.6.7] Error building pynac.

[pynac-0.6.7]

[pynac-0.6.7] real 2m34.853s

[pynac-0.6.7] user 2m59.392s

[pynac-0.6.7] sys 0m14.004s

[pynac-0.6.7] ************************************************************************

[pynac-0.6.7] Error installing package pynac-0.6.7

[pynac-0.6.7] ************************************************************************
---

> --
> You received this message because you are subscribed to the Google Groups
> "sage-release" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to sage-release...@googlegroups.com.
> To post to this group, send email to sage-r...@googlegroups.com.
> Visit this group at https://groups.google.com/group/sage-release.
> For more options, visit https://groups.google.com/d/optout.



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

[William Stein]

Hi,

Since the build failed with "> [pynac-0.6.7] /usr/bin/ld: cannot find
-lao", I installed libao-dev, which is an Ubuntu package:

libao-dev - Cross Platform Audio Output Library Development

and after doing that the build got past pynac. Also, a correction,
SMC is running Ubuntu 15.10 and I said 16.04 before.

William

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

[Ralf Stephan]

> [pynac-0.6.7] /usr/bin/ld: cannot find -lao
> [pynac-0.6.7] collect2: error: ld returned 1 exit status

No idea where you get that library dependence from. What changed

with beta5 was that if giac was installed that would be linked, so an

experiment would be to uninstall giac and sage -p pynac after that. 

[Ralf Stephan]

Or even add --with-giac=no in the Pynac spkg-install script.

[William Stein]

On Thu, Jun 30, 2016 at 11:56 PM, Ralf Stephan <gtr...@gmail.com> wrote:
>> [pynac-0.6.7] /usr/bin/ld: cannot find -lao
>> [pynac-0.6.7] collect2: error: ld returned 1 exit status
>
> No idea where you get that library dependence from. What changed
> with beta5 was that if giac was installed that would be linked, so an
> experiment would be to uninstall giac and sage -p pynac after that.

giac is definitely installed. Maybe giac or something related now
has some new support for libao -- audio output? It makes sense...

For me, I'm fine: I just now consider libao-dev something I have to
install before Sage, given that I have also installed giac. I'm
sure this will cause great confusion to other people who like to
install lots of math software on the same system in the future though.

William

[Ralf Stephan]

I don't get it. Why would the ao-devel pkg resolve the issue. Why don't

I get libao if I do 

ralf@ark:~/sage> ldd local/lib/libgiac.so
on OpenSuSE?

[Ralf Stephan]

I confirm this is a dependency IF you have giac installed on a Debian system.

giac/src/debian/README.debian:Build-Depends: debhelper, libgmp-dev, libreadline-dev, libgsl0-dev, libpng12-dev, libjpeg-dev, libpari-dev, libntl-dev, libmpfr-dev, liblapack-dev, libfltk1.3-dev, libgl1-mesa-dev, libxft-dev, libx11-dev, libxt-dev, libao-dev, libmpfi-dev, texlive, texlive-math-extra, texlive-pstricks

Why it was not picked up when you installed giac, and why it is needed

only later when Pynac is installed is still unclear. I will set --with-giac=no

as default in a Sage ticket (and you can do this too if it bothers you).

[Ralf Stephan]

https://trac.sagemath.org/ticket/20916

[leif]

William Stein wrote:
> On Thu, Jun 30, 2016 at 11:56 PM, Ralf Stephan <gtr...@gmail.com> wrote:
>>> [pynac-0.6.7] /usr/bin/ld: cannot find -lao
>>> [pynac-0.6.7] collect2: error: ld returned 1 exit status
>>
>> No idea where you get that library dependence from. What changed
>> with beta5 was that if giac was installed that would be linked, so an
>> experiment would be to uninstall giac and sage -p pynac after that.
>
> giac is definitely installed. Maybe giac or something related now
> has some new support for libao -- audio output? It makes sense...
>
> For me, I'm fine: I just now consider libao-dev something I have to
> install before Sage, given that I have also installed giac. I'm
> sure this will cause great confusion to other people who like to
> install lots of math software on the same system in the future though.

For 7.3.beta5 and beta6,

./sage -i giac && make

should get you past that error as well.


-leif

[Eric Gourgoulhon]

Build OK + make ptestlong passed on Ubuntu 15.10 x86_64 Xeon E5-2623 + 16 GB RAM.

[William Stein]

On Thu, Jun 30, 2016 at 11:53 PM, William Stein <wst...@gmail.com> wrote:
> Hi,
>

> Since the build failed with "> [pynac-0.6.7] /usr/bin/ld: cannot find
> -lao", I installed libao-dev, which is an Ubuntu package:
>
> libao-dev - Cross Platform Audio Output Library Development
>
> and after doing that the build got past pynac. Also, a correction,
> SMC is running Ubuntu 15.10 and I said 16.04 before.

The build still failed due to libpynac issues
"/projects/sage/dev/sage-7.3.beta6/local/lib/libpynac.so.2: undefined
symbol: _ZN4giac3genC1ERKNSt7__cxx1112basic_stringIcSt11char_t
"raitsIcESaIcEEEPKNS_7contextE; 'sage_setup.docbuild' is a package and
cannot be directly executed. See below.

I said:
> For me, I'm fine: I just now consider libao-dev something I have to
install before Sage, given that I have also installed giac.

Which I now retract... and Ralf+Volker, many thanks for (presumably)
fixing this in https://trac.sagemath.org/ticket/20916. I'm testing
installing giac into Sage in order to finish my build, as Lief
suggested. And, as an aside, I'm really happy to see people
working on better Sage/giac integration! I tried looking at source
code and google searching "giac ginac" and all results are from 2008,
so I don't really know what's going on yet. But clearly a lot of
great work has gone into giac during the last few years. I found in
the sources for pynac "use giac for polynomial manipulations", so
there is that, which sounds exciting.


Build log:
....
[tachyon-0.98.9.p5] real 0m6.015s
[tachyon-0.98.9.p5] user 0m5.204s
[tachyon-0.98.9.p5] sys 0m0.508s
[tachyon-0.98.9.p5] Successfully installed tachyon-0.98.9.p5
[tachyon-0.98.9.p5] Deleting temporary build directory
[tachyon-0.98.9.p5]
/projects/sage/dev/sage-7.3.beta6/local/var/tmp/sage/build/tachyon-0.98.9.p5
[tachyon-0.98.9.p5] Finished installing tachyon-0.98.9.p5.spkg
cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html
' logs/dochtml.log
[dochtml] /projects/sage/dev/sage-7.3.beta6/local/bin/python:
/projects/sage/dev/sage-7.3.beta6/local/lib/libpynac.so.2: undefined
symbol: _ZN4giac3genC1ERKNSt7__cxx1112basic_stringIcSt11char_t
raitsIcESaIcEEEPKNS_7contextE; 'sage_setup.docbuild' is a package and
cannot be directly executed
Makefile:1012: recipe for target 'doc-html' failed
make[2]: *** [doc-html] Error 1
make[2]: Leaving directory '/projects/sage/dev/sage-7.3.beta6/build/make'
Makefile:835: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/projects/sage/dev/sage-7.3.beta6/build/make'

real 91m26.763s
user 87m28.916s
sys 3m28.656s
***************************************************************
Error building Sage.

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

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:16: recipe for target 'all' failed
make: *** [all] Error 1
You have new mail in /var/mail/salvus
salvus@compute7-us:/projects/sage/dev/sage-7.3.beta6$

[Volker Braun]

On Friday, July 1, 2016 at 6:36:49 PM UTC+2, William Stein wrote:

The build still failed due to libpynac issues
"/projects/sage/dev/sage-7.3.beta6/local/lib/libpynac.so.2: undefined
symbol: _ZN4giac3genC1ERKNSt7__cxx1112basic_stringIcSt11char_t
"raitsIcESaIcEEEPKNS_7contextE; 'sage_setup.docbuild' is a package and
cannot be directly executed.

Thats the C++11 ABI change: https://trac.sagemath.org/ticket/20350

The easiest workaround is to just not build Sage's own gcc but rely on the system one.

[William Stein]

On Fri, Jul 1, 2016 at 9:52 AM, Volker Braun <vbrau...@gmail.com> wrote:
> On Friday, July 1, 2016 at 6:36:49 PM UTC+2, William Stein wrote:
>>
>> The build still failed due to libpynac issues
>> "/projects/sage/dev/sage-7.3.beta6/local/lib/libpynac.so.2: undefined
>> symbol: _ZN4giac3genC1ERKNSt7__cxx1112basic_stringIcSt11char_t
>> "raitsIcESaIcEEEPKNS_7contextE; 'sage_setup.docbuild' is a package and
>> cannot be directly executed.
>

As a follow up -- after doing "./sage -i giac" the build completed
enough that I could run sage (docs still building).

[William Stein]

The docs fail to build with some issue with jmol producing images
(again, Ubuntu 15.10 + many things installed systemwide):

eometry ] reading sources... [ 92%] sage/geometry/toric_plotter
[dochtml] [geometry ] reading sources... [ 94%] sage/geometry/triangulation/base
[dochtml] [geometry ] reading sources... [ 96%]
sage/geometry/triangulation/element
[dochtml] [geometry ] reading sources... [ 98%]
sage/geometry/triangulation/point_configuration
[dochtml] [geometry ] reading sources... [100%]
sage/rings/polynomial/groebner_fan
[dochtml] [geometry ]
/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py:docstring
of sage.geometry.hyperbolic_space.hyperbolic_geodesic.HyperbolicGeodesic.is_complete:42:
WARNING: Exception occurred in plotting hyperbolic_geodesic-9
[dochtml] [geometry ] from
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/hyperbolic_space/hyperbolic_geodesic.rst:
[dochtml] [geometry ] Traceback (most recent call last):
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/sphinxext/plot_directive.py",
line 517, in run_code
[dochtml] [geometry ] six.exec_(code, ns)
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/externals/six.py",
line 672, in exec_
[dochtml] [geometry ] exec("""exec _code_ in _globs_, _locs_""")
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 3, in <module>
[dochtml] [geometry ] File "<string>", line 8, in sphinx_plot
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1515, in
sage.plot.plot3d.base.Graphics3d.save
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17559)
[dochtml] [geometry ] self.save_image(filename)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1444, in
sage.plot.plot3d.base.Graphics3d.save_image
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17101)
[dochtml] [geometry ] self._save_image_png(filename, **kwds)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1408, in
sage.plot.plot3d.base.Graphics3d._save_image_png
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:16685)
[dochtml] [geometry ] scene = self._rich_repr_jmol(**opts)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 269, in
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:6520)
[dochtml] [geometry ] jdata.export_image(targetfile=preview_png,
datafile=script,
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py",
line 181, in export_image
[dochtml] [geometry ] raise RuntimeError("Jmol failed to create file
%s, see %s for details"%(repr(targetfile), repr(scratchout)))
[dochtml] [geometry ] RuntimeError: Jmol failed to create file
'/home/salvus/.sage/temp/compute7-us/17023/dir__P5ust/preview.png',
see '/home/salvus/.sage/temp/compute7-us/17023/tmp_8M_fV1.txt' for
details
[dochtml] [geometry ]
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/hyperbolic_space/hyperbolic_geodesic.rst:1383:
WARNING: Exception occurred in plotting hyperbolic_geodesic-19
[dochtml] [geometry ] from
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/hyperbolic_space/hyperbolic_geodesic.rst:
[dochtml] [geometry ] Traceback (most recent call last):
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/sphinxext/plot_directive.py",
line 517, in run_code
[dochtml] [geometry ] six.exec_(code, ns)
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/externals/six.py",
line 672, in exec_
[dochtml] [geometry ] exec("""exec _code_ in _globs_, _locs_""")
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 5, in <module>
[dochtml] [geometry ] File "<string>", line 8, in sphinx_plot
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1515, in
sage.plot.plot3d.base.Graphics3d.save
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17559)
[dochtml] [geometry ] self.save_image(filename)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1444, in
sage.plot.plot3d.base.Graphics3d.save_image
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17101)
[dochtml] [geometry ] self._save_image_png(filename, **kwds)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1408, in
sage.plot.plot3d.base.Graphics3d._save_image_png
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:16685)
[dochtml] [geometry ] scene = self._rich_repr_jmol(**opts)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 269, in
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:6520)
[dochtml] [geometry ] jdata.export_image(targetfile=preview_png,
datafile=script,
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py",
line 181, in export_image
[dochtml] [geometry ] raise RuntimeError("Jmol failed to create file
%s, see %s for details"%(repr(targetfile), repr(scratchout)))
[dochtml] [geometry ] RuntimeError: Jmol failed to create file
'/home/salvus/.sage/temp/compute7-us/17023/dir_y08pt5/preview.png',
see '/home/salvus/.sage/temp/compute7-us/17023/tmp_3sDTqa.txt' for
details
[dochtml] [geometry ]
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/hyperbolic_space/hyperbolic_geodesic.rst:1426:
WARNING: Exception occurred in plotting hyperbolic_geodesic-20
[dochtml][...] 2:ssh 3:bash 4:ssh 5:ssh- 6:[tmux]*






"admin0"
17:04 01-Jul-16
[dochtml] [geometry ] Traceback (most recent call last):
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/sphinxext/plot_directive.py",
line 517, in run_code
[dochtml] [geometry ] six.exec_(code, ns)
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/externals/six.py",
line 672, in exec_
[dochtml] [geometry ] exec("""exec _code_ in _globs_, _locs_""")
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 8, in sphinx_plot
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1515, in
sage.plot.plot3d.base.Graphics3d.save
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17559)
[dochtml] [geometry ] self.save_image(filename)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1444, in
sage.plot.plot3d.base.Graphics3d.save_image
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17101)
[dochtml] [geometry ] self._save_image_png(filename, **kwds)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1408, in
sage.plot.plot3d.base.Graphics3d._save_image_png
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:16685)
[dochtml] [geometry ] scene = self._rich_repr_jmol(**opts)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 269, in
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:6520)
[dochtml] [geometry ] jdata.export_image(targetfile=preview_png,
datafile=script,
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py",
line 181, in export_image
[dochtml] [geometry ] raise RuntimeError("Jmol failed to create file
%s, see %s for details"%(repr(targetfile), repr(scratchout)))
[dochtml] [geometry ] RuntimeError: Jmol failed to create file
'/home/salvus/.sage/temp/compute7-us/17023/dir_fw3KJ0/preview.png',
see '/home/salvus/.sage/temp/compute7-us/17023/tmp_R0KgFC.txt' for
details
[dochtml] [geometry ]
/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/geometry/triangulation/point_configuration.py:docstring
of sage.geometry.triangulation.point_configuration:167: WARNING:
Exception occurred in plotting point_configuration-3
[dochtml] [geometry ] from
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/triangulation/point_configuration.rst:
[dochtml] [geometry ] Traceback (most recent call last):
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/sphinxext/plot_directive.py",
line 517, in run_code
[dochtml] [geometry ] six.exec_(code, ns)
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/externals/six.py",
line 672, in exec_
[dochtml] [geometry ] exec("""exec _code_ in _globs_, _locs_""")
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 4, in <module>
[dochtml] [geometry ] File "<string>", line 8, in sphinx_plot
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1515, in
sage.plot.plot3d.base.Graphics3d.save
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17559)
[dochtml] [geometry ] self.save_image(filename)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1444, in
sage.plot.plot3d.base.Graphics3d.save_image
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17101)
[dochtml] [geometry ] self._save_image_png(filename, **kwds)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1408, in
sage.plot.plot3d.base.Graphics3d._save_image_png
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:16685)
[dochtml] [geometry ] scene = self._rich_repr_jmol(**opts)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 269, in
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:6520)
[dochtml] [geometry ] jdata.export_image(targetfile=preview_png,
datafile=script,
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py",
line 181, in export_image
[dochtml] [geometry ] raise RuntimeError("Jmol failed to create file
%s, see %s for details"%(repr(targetfile), repr(scratchout)))
[dochtml] [geometry ] RuntimeError: Jmol failed to create file
'/home/salvus/.sage/temp/compute7-us/17023/dir_rLuY6t/preview.png',
see '/home/salvus/.sage/temp/compute7-us/17023/tmp_rtflAt.txt' for
details
[dochtml] Error building the documentation.
[dochtml] Traceback (most recent call last):
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python/runpy.py", line
162, in _run_module_as_main
[dochtml] "__main__", fname, loader, pkg_name)
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python/runpy.py", line
72, in _run_code
[dochtml] exec code in run_globals
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py",
line 2, in <module>
[dochtml] main()
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py",
line 1629, in main
[dochtml] builder()
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py",
line 284, in _wrapper
[dochtml] getattr(get_builder(document), 'inventory')(*args, **kwds)
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py",
line 495, in _wrapper
[dochtml] x.get(99999)
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python/multiprocessing/pool.py",
line 567, in get
[dochtml] raise self._value
[dochtml] OSError: [geometry ]
/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py:docstring
of sage.geometry.hyperbolic_space.hyperbolic_geodesic.HyperbolicGeodesic.is_complete:42:
WARNING: Exception occurred in plotting hyperbolic_geodesic-9
[dochtml]

Makefile:1012: recipe for target 'doc-html' failed
make[2]: *** [doc-html] Error 1
make[2]: Leaving directory '/projects/sage/dev/sage-7.3.beta6/build/make'
Makefile:835: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/projects/sage/dev/sage-7.3.beta6/build/make'

real 9m38.602s
user 9m14.940s
sys 1m10.148s
***************************************************************

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

[leif]

Volker Braun wrote:
> On Friday, July 1, 2016 at 6:36:49 PM UTC+2, William Stein wrote:
>
> The build still failed due to libpynac issues
> "/projects/sage/dev/sage-7.3.beta6/local/lib/libpynac.so.2: undefined
> symbol: _ZN4giac3genC1ERKNSt7__cxx1112basic_stringIcSt11char_t
> "raitsIcESaIcEEEPKNS_7contextE; 'sage_setup.docbuild' is a package and
> cannot be directly executed.
>
>
> Thats the C++11 ABI change: https://trac.sagemath.org/ticket/20350

Not exactly. The missing function is

$ c++filt
_ZN4giac3genC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKNS_7contextE
giac::gen::gen(std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&, giac::context const*)

so presumably contained in libgiac.so...

> The easiest workaround is to just not build Sage's own gcc but rely on
> the system one.

At least the original reporter did use the system's GCC (5.2.1 from
Ubuntu), don't know what William afterwards used.


I would have checked the offending pynac library with

$ readelf -d local/lib/libpynac.so.2

to see if it is underlinked and

$ ./sage --sh -c 'ldd local/lib/libpynac.so.2'

to see how the needed libraries are resolved in the Sage environment.


But now it's too late, unless someone wants to retry (without having
Sage's giac already installed)...

(The current solution on #20916 is a temporary work-around, namely to
simply disable the use of giac in Sage's pynac.)


-leif

> I said:
> > For me, I'm fine: I just now consider libao-dev something I have to
> install before Sage, given that I have also installed giac.
>
> Which I now retract... and Ralf+Volker, many thanks for (presumably)
> fixing this in https://trac.sagemath.org/ticket/20916

> <https://trac.sagemath.org/ticket/20916>. I'm testing

[leif]

Volker Braun wrote:
> As always, you can get the latest beta version from the "develop" git
> branch. Alternatively, the self-contained source tarball is at
> http://www.sagemath.org/download-latest.html
>
> d091c43 Updated SageMath version to 7.3.beta6

With FSF GCC 5.4 on Linux x86_64 (Haswell) just the usual noise:

**********************************************************************
File "src/sage/matrix/matrix_double_dense.pyx", line 3761, in
sage.matrix.matrix_double_dense.Matrix_double_dense.exp
Failed example:
A.exp() # tol 1e-14
Expected:
[-19.614602953804912 + 12.517743846762578*I 3.7949636449582176 +
28.88379930658099*I]
[ -32.383580980922254 + 21.88423595789845*I 2.269633004093535 +
44.901324827684824*I]
Got:
[-19.614602953804923 + 12.517743846762574*I 3.7949636449582007 +
28.883799306580993*I]
[-32.383580980922275 + 21.884235957898447*I 2.2696330040935115 +
44.901324827684846*I]
Tolerance exceeded in 1 of 8:
2.269633004093535 vs 2.2696330040935115, tolerance 1e-14 > 1e-14
**********************************************************************


In ptestlong, two other tests also failed, but passed when rerun:

----------------------------------------------------------------------
sage -t --long src/sage/libs/gap/element.pyx # Bad exit: 2
sage -t --long src/sage/matrix/matrix_double_dense.pyx # 1 doctest failed
sage -t --long src/sage/libs/gap/assigned_names.py # 1 doctest failed
----------------------------------------------------------------------


-leif

[Eric Gourgoulhon]

Hi,

Le vendredi 1 juillet 2016 19:07:16 UTC+2, William Stein a écrit :

The docs fail to build with some issue with jmol producing images
(again, Ubuntu 15.10 + many things installed systemwide):

I had exactly the same issue with sage 7.3.beta5 and Ubuntu 14.04:
https://groups.google.com/d/msg/sage-release/dwD5Lm82q5M/FuAST_9hBQAJ
On the opposite, no issue with my Ubuntu 15.10 computer. I could not figure out the difference between the two systems that could explain this...

Best wishes,

Eric.

[Eric Gourgoulhon]

The issue seems to be the lack of explicit dependency of docbuilding on jmol in the makefile system, as discussed at
https://groups.google.com/d/msg/sage-devel/SlpXXtK_Cy0/XM39BelTAAAJ