Building Sage from source fails on OS X with NFS-mounted home directory

[Bill Janssen]

I just tried building Sage from source on a PARC machine. On this
machine, my home directory is an NFS-mounted share. The build fails
with a shower of messages of this form:

Build finished. The built documents can be found in /local/sage-4.7.2/
devel/sage/doc/output/html/en/numerical_sage
Traceback (most recent call last):
File "/local/sage-4.7.2/devel/sage/doc/common/builder.py", line
1059, in <module>
getattr(get_builder(name), type)()
File "/local/sage-4.7.2/devel/sage/doc/common/builder.py", line 243,
in _wrapper
getattr(get_builder(document), name)(*args, **kwds)
File "/local/sage-4.7.2/devel/sage/doc/common/builder.py", line 354,
in _wrapper
self.write_auto_rest_file(module_name)
File "/local/sage-4.7.2/devel/sage/doc/common/builder.py", line 593,
in write_auto_rest_file
title = self.get_module_docstring_title(module_name)
File "/local/sage-4.7.2/devel/sage/doc/common/builder.py", line 563,
in get_module_docstring_title
import sage.all
File "/local/sage-4.7.2/local/lib/python2.6/site-packages/sage/
all.py", line 321, in <module>
sage.misc.lazy_import.save_cache_file()
File "lazy_import.pyx", line 817, in
sage.misc.lazy_import.save_cache_file (sage/misc/lazy_import.c:4503)
File "/local/sage-4.7.2/local/lib/python/shutil.py", line 264, in
move
copy2(src, real_dst)
File "/local/sage-4.7.2/local/lib/python/shutil.py", line 100, in
copy2
copystat(src, dst)
File "/local/sage-4.7.2/local/lib/python/shutil.py", line 77, in
copystat
os.chflags(dst, st.st_flags)
OSError: [Errno 45] Operation not supported: '/tilde/janssen/.sage/
_Volumes_data_local_sage-4.7.2_devel_sage-main-
lazy_import_cache.pickle'
make: *** [doc-html] Error 1
%

Can this safely be ignored?

[Bill Janssen]

"make test" fails as well. This is Sage 4.7.2 on OS X 10.5.

Bill

[Bill Janssen]

This is a Python bug. Fixed in late March 2010.

http://bugs.python.org/issue7512

[Maarten Derickx]

Ah, then this issue will hopefully be fixed with changing the python in sage to 2.7. There is already work being done on that issue at http://trac.sagemath.org/sage_trac/ticket/9958 . You can also find a new spkg there, so with that spkg you might be able to build from source. But the doctest will give probably still a lot of failures.

[Bill Janssen]

Could I really be the first user in this vast assemblage to have an
NFS-mounted home directory?

I tried building and installing sage with a local account, then just
using it from my network account (which is the account I generally
use). Here's the error from *that*:

/tilde/janssen 34 % /local/sage-4.7.2/sage
----------------------------------------------------------------------
| Sage Version 4.7.2, Release Date: 2011-10-29 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
---------------------------------------------------------------------------
OSError Traceback (most recent call
last)

/local/sage-4.7.2/local/lib/python2.6/site-packages/IPython/
ipmaker.pyc in force_import(modname, force_reload)
61 reload(sys.modules[modname])
62 else:
---> 63 __import__(modname)
64
65

/Volumes/data/local/sage-4.7.2/local/bin/ipy_profile_sage.py in
<module>()
5 preparser(True)
6
----> 7 import sage.all_cmdline
8 sage.all_cmdline._init_cmdline(globals())
9

/local/sage-4.7.2/local/lib/python2.6/site-packages/sage/
all_cmdline.py in <module>()
12 try:
13
---> 14 from sage.all import *
15 from sage.calculus.predefined import x
16 preparser(on=True)

/local/sage-4.7.2/local/lib/python2.6/site-packages/sage/all.py in
<module>()
319 # Cache the contents of star imports.
320 import sage.misc.lazy_import
--> 321 sage.misc.lazy_import.save_cache_file()
322
323

/local/sage-4.7.2/local/lib/python2.6/site-packages/sage/misc/
lazy_import.so in sage.misc.lazy_import.save_cache_file (sage/misc/
lazy_import.c:4503)()
815
816
--> 817
818
819

/local/sage-4.7.2/local/lib/python/shutil.pyc in move(src, dst)
262 rmtree(src)
263 else:
--> 264 copy2(src, real_dst)
265 os.unlink(src)
266

/local/sage-4.7.2/local/lib/python/shutil.pyc in copy2(src, dst)
98 dst = os.path.join(dst, os.path.basename(src))
99 copyfile(src, dst)
--> 100 copystat(src, dst)
101
102 def ignore_patterns(*patterns):

/local/sage-4.7.2/local/lib/python/shutil.pyc in copystat(src, dst)
75 os.chmod(dst, mode)
76 if hasattr(os, 'chflags') and hasattr(st, 'st_flags'):
---> 77 os.chflags(dst, st.st_flags)
78
79

OSError: [Errno 45] Operation not supported: '/tilde/janssen/.sage/
_Volumes_data_local_sage-4.7.2_devel_sage-main-
lazy_import_cache.pickle'

Error importing ipy_profile_sage - perhaps you should run %upgrade?
WARNING: Loading of ipy_profile_sage failed.

sage:

[Bill Janssen]

On Nov 15, 2:34 pm, Maarten Derickx <m.derickx.stud...@gmail.com>
wrote:

> Ah, then this issue will hopefully be fixed with changing the python in
> sage to 2.7.

What's the ETA on that? Is there a patch I could apply in the
meantime?

[William Stein]

On Wednesday, November 16, 2011, Bill Janssen <bill.j...@gmail.com> wrote:
> Could I really be the first user in this vast assemblage to have an
> NFS-mounted home directory?
>

No, many people do, eg all users of the sage.math devel cluster, our remote build farm, etc.   Maybe your issues are Mac + NSF specific - that is a less common combo.

> --
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>

--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

[Maarten Derickx]

What's the ETA on that?  Is there a patch I could apply in the 
meantime? 

Sage does not really work with ETA's, everything depends if there is someone willing to work on a specific issue voluntarily. The patches you could apply are all mentioned on that ticket, you will also need the spkg from there. Let me know if you have problems installing these.

 

No, many people do, eg all users of the sage.math devel cluster, our remote build farm, etc.   Maybe your issues are Mac + NSF specific - that is a less common combo.

Or even specific to the settings you use to export and mount your NFS (things such as lock vs nolock etc. might have a huge inpact on how programs behave on your NFS mount).

[Bill Janssen]

On Nov 16, 8:14 am, William Stein <wst...@gmail.com> wrote:
> On Wednesday, November 16, 2011, Bill Janssen <bill.jans...@gmail.com>

> wrote:
>
> > Could I really be the first user in this vast assemblage to have an
> > NFS-mounted home directory?
>
> No, many people do, eg all users of the sage.math devel cluster, our remote
> build farm, etc.   Maybe your issues are Mac + NSF specific - that is a
> less common combo.

Yes, that's probably it. I'm guessing this doesn't happen with Python
2.5, which is what comes installed on my machine. And one reason I'm
not running Snow Leopard is that it doesn't do well with Sun-style NIS
maps, whereas Leopard can still tolerate them.

Bill

[Bill Janssen]

On Nov 16, 8:35 am, Maarten Derickx <m.derickx.stud...@gmail.com>
wrote:

> > What's the ETA on that?  Is there a patch I could apply in the
> > meantime?
>
> Sage does not really work with ETA's, everything depends if there is
> someone willing to work on a specific issue voluntarily. The patches you
> could apply are all mentioned on that ticket, you will also need the spkg
> from there. Let me know if you have problems installing these.

I was thinking of just patching the Python source used with Sage
4.7.2, instead of upgrading it. Basically applying the patch attached
to the Python bug-tracker issue.

Maybe I'll just try that and report back.

Bill