sage fails to build on (fresh install of) debian linux 8.4 (64 bit)...

[Eric Larson]

Any suggestions? From /home/eric/sage/logs/pkgs/sagelib-7.2.log (full log file attached):

make[3]: Entering directory '/home/eric/sage/src'

python -u setup.py install

************************************************************************

Traceback (most recent call last):

  File "setup.py", line 67, in <module>

    include_dirs = sage_include_directories(use_sources=True)

  File "/home/eric/sage/src/sage/env.py", line 172, in sage_include_directories

    import os, numpy

  File "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/__init__.py", line 180, in <module>

    from . import add_newdocs

  File "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/add_newdocs.py", line 13, in <module>

    from numpy.lib import add_newdoc

  File "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/lib/__init__.py", line 8, in <module>

    from .type_check import *

  File "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/lib/type_check.py", line 11, in <module>

    import numpy.core.numeric as _nx

  File "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/core/__init__.py", line 14, in <module>

    from . import multiarray

ImportError: libatlas.so.3: cannot open shared object file: No such file or directory

************************************************************************

Error building the Sage library

************************************************************************

[Dima Pasechnik]

On Friday, May 27, 2016 at 11:31:59 PM UTC+1, Eric Larson wrote:

Any suggestions? From /home/eric/sage/logs/pkgs/sagelib-7.2.log (full log file attached):

nothing seems to be attached; 

anyway, it looks like there was a failure to build Sage's atlas package.

Please check by looking at the log at logs/pkgs/

[Eric Larson]

Hi Dima,

Hm... I think most of the issue was that my fresh install of debian 8 was from the initial release CD, which included a buggy compiler? Because when I ran system updates, I noticed that one of the things updated was gcc, and figured I should try recompilation. This time I get a different error --- sage itself builds fine, and appears to run fine, unlike last time, but it was unable to build the documentation:

[plot3d   ] RuntimeError: Jmol failed to create file '/home/eric/.sage/temp/serre/31647/dir_gUwtRI/preview.png', see '/home/eric/.sage/temp/serre/31647/tmp_xSBzt6.txt' for details

Error building the documentation.

Traceback (most recent call last):

  File "/home/eric/sage-src/local/lib/python/runpy.py", line 162, in _run_module_as_main

    "__main__", fname, loader, pkg_name)

  File "/home/eric/sage-src/local/lib/python/runpy.py", line 72, in _run_code

    exec code in run_globals

  File "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>

    main()

  File "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 1629, in main

    builder()

  File "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 284, in _wrapper

    getattr(get_builder(document), 'inventory')(*args, **kwds)

  File "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 495, in _wrapper

    x.get(99999)

  File "/home/eric/sage-src/local/lib/python/multiprocessing/pool.py", line 567, in get

    raise self._value

OSError: [plot3d   ] /home/eric/sage-src/local/lib/python2.7/site-packages/sage/plot/plot3d/platonic.py:docstring of sage.plot.plot3d.platonic:10: WARNING: Exception occurred in plotting platonic-1

Makefile:1003: recipe for target 'doc-html' failed

make[2]: *** [doc-html] Error 1

make[2]: Leaving directory '/home/eric/sage-src/build/make'

Makefile:826: recipe for target 'all' failed

make[1]: *** [all] Error 2

make[1]: Leaving directory '/home/eric/sage-src/build/make'

real  314m1.704s

user  286m3.212s

sys   12m12.704s

***************************************************************

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make all'):

* documentation: dochtml

  log file: /home/eric/sage-src/logs/pkgs/../dochtml.log

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.

I can't find either file mentioned (/home/eric/sage-src/logs/pkgs/../dochtml.log OR /home/eric/.sage/temp/serre/31647/tmp_xSBzt6.txt) --- I'm not sure how to expand the former file into a full path (what's the /../?); and the later file doesn't exist on my system.

Also when I try to upload a file here I get an "upload error"...

Best,
-Eric

[Eric Larson]

...But I can attach a google drive link to the file:

​

 install.log

​

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[Vincent Delecroix]

The error occurred during the documentation build. You should be able to
start Sage without any problem.

If it works, try to create some 3d plots and see them (via jmol).

On 28/05/16 17:35, Eric Larson wrote:
> ...But I can attach a google drive link to the file:
> ​

> install.log
> <https://drive.google.com/file/d/0BzxearNxPfAuTGZ3YVFvS0dHN1U/view?usp=drive_web>

> ​
>
> On Sat, May 28, 2016 at 6:29 PM, Eric Larson <elar...@gmail.com> wrote:
>
>> Hi Dima,
>>
>> Hm... I think most of the issue was that my fresh install of debian 8 was
>> from the initial release CD, which included a buggy compiler? Because when
>> I ran system updates, I noticed that one of the things updated was gcc, and

>> figured I should try recompilation. This time I get a *different* error

[Eric Larson]

Hi all,

Yes, sage mostly works --- except I cannot create a 3D graphics object:

sage: point3d((0, 0, 0))

/home/eric/sage-src/local/lib/python2.7/site-packages/sage/repl/rich_output/display_manager.py:590: RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol failed to create file '/home/eric/.sage/temp/serre/4032/dir_Kn6nvZ/preview.png', see '/home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt' for details

  RichReprWarning,

Graphics3d Object

sage:

The file /home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt disappears after exiting sage; but while sage is still running, I can view it, and it contains the following text:

Error: Unable to access jarfile /home/eric/sage-src/local/share/jmol/JmolData.jar

The directory /home/eric/sage-src/local/share/jmol/ does not exist:

eric@serre:~$ cd /home/eric/sage-src/local/share/jmol/

bash: cd: /home/eric/sage-src/local/share/jmol/: No such file or directory

eric@serre:~$ cd /home/eric/sage-src/local/share/

eric@serre:~/sage-src/local/share$ ls

aclocal             doc        iml      lrcalc   maxima  singular

cliquer             gc         info     man      pari    tabset

conway_polynomials  gcc-4.9.3  jupyter  mathjax  sage    terminfo

eric@serre:~/sage-src/local/share$ 

Best,

-Eric

[Dima Pasechnik]

probably Jmol problem is Java-related, i.e. it perhaps needs a different version of Java, or at least some working Java version.

[Joseph Hundley]

Was this ever resolved? 

I seem to be having the same problem trying to build on both a Mac and a recent install of elementary OS.  

Certainly there is recent Java on this machine. Other Java programs run fine. 

The error message appears to say that sage (or Jmol called by sage?) is looking for JmolData.jar in 

local/share/jmol/. I decided to try downloading Jmol from https://sourceforge.net/projects/jmol/?source=typ_redirect

One of the files is indeed JmolData.jar. Instead of moving just that file into a directory called /local/share/jmol

what I did is move/rename the whole folder it is in into local/share/jmol. This had an interesting effect. 

The first time I tried point3d((0,0,0)) in sage after making these changes I got a new, pretty long error message 

which I regrettably neglected to save. The second time (different Sage session) I got "Launched jmol viewer 

for Graphics3d Object."

Best, 

JH

[Dima Pasechnik]

On Sunday, June 26, 2016 at 2:48:26 AM UTC+1, Joseph Hundley wrote:

Was this ever resolved? 

I seem to be having the same problem trying to build on both a Mac and a recent install of elementary OS.  

Certainly there is recent Java on this machine. Other Java programs run fine. 

The error message appears to say that sage (or Jmol called by sage?) is looking for JmolData.jar in 

local/share/jmol/.

local/share/jmol/ is meant to be $SAGE_ROOT/local/share/jmol/

and these files are meant to be installed there during Sage installation.

What do you see in $SAGE_ROOT/logs/pkgs/jmol-14.2.11_2015.01.20.log ?

(or perhaps in $SAGE_ROOT/logs/pkgs/jmol-<someoterversion>.log)

[Dima Pasechnik]

On Sunday, June 26, 2016 at 8:21:16 AM UTC+1, Dima Pasechnik wrote:

On Sunday, June 26, 2016 at 2:48:26 AM UTC+1, Joseph Hundley wrote:

Was this ever resolved? 

I seem to be having the same problem trying to build on both a Mac and a recent install of elementary OS.  

Certainly there is recent Java on this machine. Other Java programs run fine. 

The error message appears to say that sage (or Jmol called by sage?) is looking for JmolData.jar in 

local/share/jmol/.

local/share/jmol/ is meant to be $SAGE_ROOT/local/share/jmol/

and these files are meant to be installed there during Sage installation.

What do you see in $SAGE_ROOT/logs/pkgs/jmol-14.2.11_2015.01.20.log ?

(or perhaps in $SAGE_ROOT/logs/pkgs/jmol-<someoterversion>.log)

 

I decided to try downloading Jmol from https://sourceforge.net/projects/jmol/?source=typ_redirect

One of the files is indeed JmolData.jar. Instead of moving just that file into a directory called /local/share/jmol

what I did is move/rename the whole folder it is in into local/share/jmol. This had an interesting effect. 

The first time I tried point3d((0,0,0)) in sage after making these changes I got a new, pretty long error message 

which I regrettably neglected to save. The second time (different Sage session) I got "Launched jmol viewer 

for Graphics3d Object."

anyhow, you should reinstall jmol package, by doing

./sage -i jmol

(or ./sage -f jmol)

[Joseph Hundley]

Running ./sage -i jmol fixes the problem of "point3d((0,0,0))" producing a message about a Jmol viewer being launched but no actual Jmol 

viewer.  And fixing jmol fixes the problem with building dochtml. 

Thanks!

I went to check $SAGE_ROOT/logs/pkgs/jmol-*.log  after issuing the ./sage -i jmol command, unfortunately. So, all I found there was the log file being written 

at that time. 

Interestingly enough, my first run of "make" on my other machine (running elementary OS) produced a nearly identical dochtml problem. I presumed I'd have to fix jmol on that one too. But A second run of "make" just now failed to replicated the problem and Jmol works over there. 

Sorry for not better documenting the bug.

Best, 

JH

[leif]

Joseph Hundley wrote:
> Running ./sage -i jmol fixes the problem of "point3d((0,0,0))" producing
> a message about a Jmol viewer being launched but no actual Jmol
> viewer. And fixing jmol fixes the problem with building dochtml.
>
> Thanks!
>
> I went to check $SAGE_ROOT/logs/pkgs/jmol-*.log after issuing the
> ./sage -i jmol command, unfortunately. So, all I found there was the log
> file being written
> at that time.

Sage doesn't overwrite existing logs, so the log should contain the
output from both attempts.


-leif

> '/home/eric/.sage/temp/serre/31647/dir_gUwtRI/preview..png',

[Joseph Hundley]

Ah. Then I think we can say with reasonable certainty that there was nothing in  

$SAGE_ROOT/logs/pkgs/jmol-*.log  
before today, because when I looked the first time today, there was only 

Found local metadata for jmol-14.2.11_2015.01.20

Attempting to download package jmol-14.2.11_2015.01.20.tar.bz2 from mirrors

Downloading the Sage mirror list

Searching fastest mirror

  227ms: http://echidna.maths.usyd.edu.au/sage/

<snip... list of mirrors> 

  178ms: http://www.mirrorservice.org/sites/www.sagemath.org/

Fastest mirror: http://ftp.ntua.gr/pub/sagemath/

http://ftp.ntua.gr/pub/sagemath/spkg/upstream/jmol/jmol-14.2.11_2015.01.20.tar.$

[................

[Joseph Hundley]

Installing on yet another computer today.  Same basic deal: everything builds except dochtml. This time I did check the logs before running ./sage -i jmol, and can confirm that no file with a name of the form 

$SAGE_ROOT/logs/pkgs/jmol-*.log  
was written on the initial build.

[Johan S. H. Rosenkilde]

Are you having the same problem as me:

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

For instance, do you have sympy installed? (if you don't, "./sage -t
src/sage/arith.py" will fail immediately due to uninstalled sympy).

Do you have Cremona's mini-database installed? Test by running

sage: db = CremonaDatabase()
<BOOM>
ValueError: Desired database (='cremona mini') does not exist

I'm missing many other vital packages on a fresh install, for some
reason, including Jmol.

Best,
Johan

--

[Joseph Hundley]

"./sage -t src/sage/arith.py" gets this.

hundleymac:sage jahundle$ ./sage -t src/sage/arith.py

init.sage does not exist ... creating

no stored timings available

Running doctests with ID 2016-07-07-13-47-14-67aaeb78.

Git branch: develop

Using --optional=mpir,python2,sage

Doctesting 1 file.

sage -t src/sage/arith.py

    IOError in doctesting framework

**********************************************************************

Traceback (most recent call last):

  File "/Users/jahundle/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 2127, in __call__

    doctests, extras = self.source.create_doctests(sage_namespace)

  File "/Users/jahundle/sage/local/lib/python2.7/site-packages/sage/doctest/sources.py", line 661, in create_doctests

    raise IOError(errno.ENOENT, "File does not exist", self.path)

IOError: [Errno 2] File does not exist: 'src/sage/arith.py'

----------------------------------------------------------------------

sage -t src/sage/arith.py  # IOError in doctesting framework

----------------------------------------------------------------------

Total time for all tests: 0.0 seconds

    cpu time: 0.0 seconds

    cumulative wall time: 0.0 seconds

[Joseph Hundley]

I would guess that this means I *do* have the Cremona database (?).

JH

sage: db = CremonaDatabase()

sage: 

On Friday, July 1, 2016 at 9:30:24 AM UTC-4, Johan S. R. Nielsen wrote: