Bug #302649 “scipy.weave.inline compilation fails with gcc 4.3” : Bugs : python-scipy package : Ubuntu

Revision history for this message

Sameer Morar (smorar) wrote on 2008-11-27:

#1

Example python code which demonstrates the bug Edit (372 bytes, text/x-python)

Attached is some python code which demonstrates the bug. To reproduce, please follow the following steps:
1) Ensure that gcc-4.3 is installed:

root@spider:/usr/bin# ls -la g++
lrwxrwxrwx 1 root root 7 2008-11-27 02:37 g++ -> g++-4.3

2) Remove pre-compiled python snippets

smorar@spider:~$ rm -rf /home/smorar/.python25_compiled/

3) Run code

smorar@spider:~$ python weave_test.py
The compilation will fail with the above error.

To demonstrate that this is related to the latest gcc:
1) Ensure that gcc-4.2 is installed

root@spider:/usr/bin# rm g++
root@spider:/usr/bin# ln -s g++-4.2 g++

2) Remove pre-compiled python snippets

smorar@spider:~$ rm -rf /home/smorar/.python25_compiled/

3) Run code

smorar@spider:~$ python weave_test.py
The compilation will succeed (with many compiler warnings), and the python / c code produces the expected output.

Sameer Morar (smorar) on 2008-11-27

description:

updated

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Matthias Klose (doko) wrote on 2008-11-27:

#2

an include of cstdlib seems to be missing.

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Benjamin Horstman (yodenss) wrote on 2009-01-21:

#3

I can confirm the bug and workaround of linking g++-4.2.

For reference, here is the upstream ticket:
http://www.scipy.org/scipy/scipy/ticket/739

What Matthias has noted is present in the debian patch.

And the original (as far as I can tell) mention of this problem on the debian list, more than a year ago:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=455661

Bug Watch Updater (bug-watch-updater) on 2009-02-22

Changed in scipy:
status:	Unknown → Fix Released

Revision history for this message

Luca Falavigna (dktrkranz) wrote on 2009-03-02:

#4

Fixed upstream with new 0.7.0.

Changed in python-scipy:
importance:	Undecided → Medium
status:	New → Fix Committed

Revision history for this message

Launchpad Janitor (janitor) wrote on 2009-03-02:

#5

This bug was fixed in the package python-scipy - 0.7.0-0ubuntu1

---------------
python-scipy (0.7.0-0ubuntu1) jaunty; urgency=low

  * New upstream version (LP: #285936, #299375, #302649).
  * Apply changes from Debian's python-modules team, thanks!
  * debian/rules: make python-scipy ready for Python 2.6 (LP: #336239):
    - Include /usr/share/python/python.mk.
    - Pass $(py_setup_install_args) macro to setup.py install.
    - Remove some files present in new dist-packages directory too.

-- Luca Falavigna <email address hidden> Mon, 02 Mar 2009 17:28:08 +0100

Changed in python-scipy:
status:	Fix Committed → Fix Released

Bug Watch Updater (bug-watch-updater) on 2009-03-10

Changed in python-scipy:
status:	Unknown → Fix Released

Revision history for this message

Benjamin Horstman (yodenss) wrote on 2009-05-04:

#6

Note that according to the scipy bug tracker, this isn't going to be fixed until scipy 0.7.1, which means that this bug still exists in ubuntu 9.04.

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Sameer Morar (smorar) wrote on 2009-11-05:

#7

This bug also exists in ubuntu 9.10:

smorar@spud:~/$ dpkg -l|grep scipy
ii python-scipy 0.7.0-2

Changed in python-scipy (Ubuntu):
status:	Fix Released → Incomplete

Revision history for this message

Sameer Morar (smorar) wrote on 2009-11-05:

#8

I have changed the status in python-scipy (ubuntu) to incomplete, as it should only be tagged as fixed when scipy 0.7.1 is available in the ubuntu repository.

Revision history for this message

Jakob Runge (jakobrunge) wrote on 2010-01-05:

#9

Download full text (7.0 KiB)

The weave bug seems to be still present in scipy 0.7.1

I am running Ubuntu 9.10 (Karmic) and have scipy installed from source (since it is not in the repos) without problems, the required Atlas, ... libraries were installed using synaptic

ipython:
In [2]: scipy.__version__
Out[2]: '0.7.1'

Running a weave.blitz test routine:
"...
weave.inline(code, vars, type_converters = weave.converters.blitz)
..."

Output is:
starting weavefunc..
In file included from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/applics.h:394,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecexpr.h:26,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecpick.cc:16,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecpick.h:287,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vector.h:443,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/tinyvec.h:424,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array-impl.h:38,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array.h:26,
                 from /home/jakob/.python26_compiled/sc_6211de8cbbdd4538661eae1a48c2a9890.cpp:11:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/mathfunc.h: In static member function ‘static long int blitz::_bz_abs<long int>::apply(long int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/mathfunc.h:45: error: ‘labs’ is not a member of ‘std’
In file included from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/funcs.h:23,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/newet.h:23,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/et.h:21,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array-impl.h:2509,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array.h:26,
                 from /home/jakob/.python26_compiled/sc_6211de8cbbdd4538661eae1a48c2a9890.cpp:11:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h: In static member function ‘static int blitz::Fn_abs<int>::apply(int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h:503: error: call of overloaded ‘abs(int&)’ is ambiguous
/usr/include/c++/4.4/cmath:94: note: candidates are: double std::abs(double)
/usr/include/c++/4.4/cmath:98: note: float std::abs(float)
/usr/include/c++/4.4/cmath:102: note: long double std::abs(long double)
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h: In static member function ‘static long int blitz::Fn_abs<long int>::apply(long int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h:524: error: ‘labs’ is not a member of ‘std’
In file included from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/applics.h:394,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecexpr.h:26...

The weave bug seems to be still present in scipy 0.7.1

I am running Ubuntu 9.10 (Karmic)  and have scipy installed from source (since it is not in the repos) without problems, the required Atlas, ... libraries were installed using synaptic

ipython:
In [2]: scipy.__version__
Out[2]: '0.7.1'

Running a weave.blitz test routine:
"...
weave.inline(code, vars, type_converters = weave.converters.blitz)
..."

Output is:
starting weavefunc..
In file included from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/applics.h:394,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecexpr.h:26,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecpick.cc:16,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecpick.h:287,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vector.h:443,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/tinyvec.h:424,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array-impl.h:38,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array.h:26,
                 from /home/jakob/.python26_compiled/sc_6211de8cbbdd4538661eae1a48c2a9890.cpp:11:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/mathfunc.h: In static member function ‘static long int blitz::_bz_abs<long int>::apply(long int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/mathfunc.h:45: error: ‘labs’ is not a member of ‘std’
In file included from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/funcs.h:23,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/newet.h:23,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/et.h:21,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array-impl.h:2509,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array.h:26,
                 from /home/jakob/.python26_compiled/sc_6211de8cbbdd4538661eae1a48c2a9890.cpp:11:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h: In static member function ‘static int blitz::Fn_abs<int>::apply(int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h:503: error: call of overloaded ‘abs(int&)’ is ambiguous
/usr/include/c++/4.4/cmath:94: note: candidates are: double std::abs(double)
/usr/include/c++/4.4/cmath:98: note:                 float std::abs(float)
/usr/include/c++/4.4/cmath:102: note:                 long double std::abs(long double)
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h: In static member function ‘static long int blitz::Fn_abs<long int>::apply(long int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h:524: error: ‘labs’ is not a member of ‘std’
In file included from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/applics.h:394,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecexpr.h:26,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecpick.cc:16,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecpick.h:287,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vector.h:443,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/tinyvec.h:424,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array-impl.h:38,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array.h:26,
                 from /home/jakob/.python26_compiled/sc_6211de8cbbdd4538661eae1a48c2a9890.cpp:11:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/mathfunc.h: In static member function ‘static long int blitz::_bz_abs<long int>::apply(long int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/mathfunc.h:45: error: ‘labs’ is not a member of ‘std’
In file included from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/funcs.h:23,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/newet.h:23,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array/et.h:21,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array-impl.h:2509,
                 from /usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array.h:26,
                 from /home/jakob/.python26_compiled/sc_6211de8cbbdd4538661eae1a48c2a9890.cpp:11:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h: In static member function ‘static int blitz::Fn_abs<int>::apply(int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h:503: error: call of overloaded ‘abs(int&)’ is ambiguous
/usr/include/c++/4.4/cmath:94: note: candidates are: double std::abs(double)
/usr/include/c++/4.4/cmath:98: note:                 float std::abs(float)
/usr/include/c++/4.4/cmath:102: note:                 long double std::abs(long double)
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h: In static member function ‘static long int blitz::Fn_abs<long int>::apply(long int)’:
/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/funcs.h:524: error: ‘labs’ is not a member of ‘std’
Traceback (most recent call last):
  File "weavetestsingle.py", line 22, in <module>
    weave.inline(code, vars, type_converters = weave.converters.blitz, compiler = 'gcc', extra_compile_args = ["-O3"])
  File "/usr/local/lib/python2.6/dist-packages/scipy/weave/inline_tools.py", line 335, in inline
    **kw)
  File "/usr/local/lib/python2.6/dist-packages/scipy/weave/inline_tools.py", line 462, in compile_function
    verbose=verbose, **kw)
  File "/usr/local/lib/python2.6/dist-packages/scipy/weave/ext_tools.py", line 365, in compile
    verbose = verbose, **kw)
  File "/usr/local/lib/python2.6/dist-packages/scipy/weave/build_tools.py", line 272, in build_extension
    setup(name = module_name, ext_modules = [ext],verbose=verb)
  File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/core.py", line 186, in setup
    return old_setup(**new_attr)
  File "/usr/lib/python2.6/distutils/core.py", line 169, in setup
    raise SystemExit, "error: " + str(msg)
scipy.weave.build_tools.CompileError: error: Command "g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -fPIC -I/usr/local/lib/python2.6/dist-packages/scipy/weave -I/usr/local/lib/python2.6/dist-packages/scipy/weave/scxx -I/usr/local/lib/python2.6/dist-packages/scipy/weave/blitz -I/usr/local/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c /home/jakob/.python26_compiled/sc_6211de8cbbdd4538661eae1a48c2a9890.cpp -o /tmp/jakob/python26_intermediate/compiler_71e584768071aa3498d8ed2c780a199b/home/jakob/.python26_compiled/sc_6211de8cbbdd4538661eae1a48c2a9890.o -O3" failed with exit status 1

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Jakob Runge (jakobrunge) wrote on 2010-01-05:

#10

changing the compiler to g++-4.2 it works... Karmic comes with g++-4.4 though

Bug Watch Updater (bug-watch-updater) on 2010-04-28

Changed in scipy:
status:	Fix Released → New

Revision history for this message

Sameer Morar (smorar) wrote on 2010-09-29:

#11

This bug still exists in ubuntu 10.10:

smorar@spud:~/$ dpkg -l|grep scipy
ii python-scipy 0.7.2-2

Stefano Rivera (stefanor) on 2010-09-29

Changed in python-scipy (Ubuntu):
status:	Incomplete → Confirmed

Revision history for this message

Matthias Klose (doko) wrote on 2010-09-29:

#12

Sameer, Stefano, what is the problem in maverick?

Changed in python-scipy (Ubuntu):
status:	Confirmed → Incomplete

Revision history for this message

Stefano Rivera (stefanor) wrote on 2010-09-29:

#13

weave_test.log Edit (6.1 KiB, text/plain)

Matthias: Haven't had a proper look at these headers, but the test case attached to this bug seems to show up some bugs in them.

Full output attached

In file included from /usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/applics.h:394,
                 from /usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecexpr.h:26,
                 from /usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecpick.cc:16,
                 from /usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vecpick.h:287,
                 from /usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/vector.h:443,
                 from /usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/tinyvec.h:424,
                 from /usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array-impl.h:38,
                 from /usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/array.h:26,
                 from /home/stefanor/.python26_compiled/sc_3ec397f0c53c3b3e50e2375deba7b7ed1.cpp:11:
/usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/mathfunc.h: In static member function ‘static long int blitz::_bz_abs<long int>::apply(long int)’:
/usr/lib/python2.6/dist-packages/scipy/weave/blitz/blitz/mathfunc.h:45: error: ‘labs’ is not a member of ‘std’

Changed in python-scipy (Ubuntu):
status:	Incomplete → Confirmed

Revision history for this message

Stefano Rivera (stefanor) wrote on 2010-09-29:

#14

Err, meant to add, obviously this is now an issue with 4.4

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Sameer Morar (smorar) wrote on 2010-09-29:

#15

The fix for this bug is simple. As per the debian patch linked to below, one needs to add an include for cstdlib above the BZ_NAMESPACE(blitz) call in the following files:
/usr/share/pyshared/scipy/weave/blitz/blitz/blitz.h
/usr/share/pyshared/scipy/weave/blitz/blitz/mathfunc.h

http://bugs.debian.org/cgi-bin/bugreport.cgi?msg=10;filename=blitz%2B%2B.patch;att=1;bug=455661

This fix works for me by manually editing those files.

Revision history for this message

Sameer Morar (smorar) wrote on 2010-09-29:

#16

Patch to fix this bug Edit (2.3 KiB, text/plain)

Patch to fix this bug

Stefano Rivera (stefanor) on 2010-09-29

Changed in python-scipy (Ubuntu):
assignee:	nobody → Stefano Rivera (stefanor)

Revision history for this message

Sameer Morar (smorar) wrote on 2010-09-29:

#17

Patch v2 Edit (2.7 KiB, text/plain)

Updated patch - added an cstdlib include to prettyprint.h
Change reference to launchpad bug number.
Updated the Patch Tags to only use a description and bug-ubuntu fields.

Revision history for this message

Stefano Rivera (stefanor) wrote on 2010-09-29:

#18

Thanks for the patch, I'll forward this to Debian

Changed in python-scipy (Ubuntu):
assignee:	Stefano Rivera (stefanor) → Sameer Morar (smorar)
status:	Confirmed → Fix Committed

Sameer Morar (smorar) on 2010-09-29

Changed in python-scipy (Ubuntu Lucid):
assignee:	nobody → Sameer Morar (smorar)

Revision history for this message

Sameer Morar (smorar) wrote on 2010-09-29:

#19

Patch for lucid Edit (1.3 KiB, text/plain)

Here is a patch for lucid

Revision history for this message

Sameer Morar (smorar) wrote on 2010-09-29:

#20

Patch for lucid Edit (1.3 KiB, text/plain)

Here is a patch for lucid

Stefano Rivera (stefanor) on 2010-09-29

affects:

python-scipy (Debian) → blitz++ (Debian)

Brian Murray (brian-murray) on 2010-09-29

tags:

added: patch

Revision history for this message

Launchpad Janitor (janitor) wrote on 2010-09-30:

#21

This bug was fixed in the package python-scipy - 0.7.2-2ubuntu1

---------------
python-scipy (0.7.2-2ubuntu1) maverick; urgency=low

* debian/patches/blitz++.patch:
- Fix scipy.weave.inline compilations (LP: #302649)
-- Sameer Morar <email address hidden> Wed, 29 Sep 2010 13:42:10 +0200

Changed in python-scipy (Ubuntu):
status:	Fix Committed → Fix Released

Revision history for this message

Stefano Rivera (stefanor) wrote on 2010-09-30:

#22

Uploaded to lucid-proposed, pending SRU team verification.

Changed in python-scipy (Ubuntu Lucid):
importance:	Undecided → Low
status:	New → Fix Committed

Revision history for this message

Martin Pitt (pitti) wrote on 2010-10-05: Please test proposed package

#23

Accepted python-scipy into lucid-proposed, the package will build now and be available in a few hours. Please test and give feedback here. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation how to enable and use -proposed. Thank you in advance!

tags:

added: verification-needed

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Sameer Morar (smorar) wrote on 2010-10-05:

#24

The new package works for me.

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Sameer Morar (smorar) wrote on 2010-10-05:

#25

Addendum to comment 24:

To verify the fix, python-dev needs to be installed. Will open this as a separate bug, as python-scipy does not recommend or suggest python-dev to be installed.

tags:

added: verification-done
removed: verification-needed

Bug Watch Updater (bug-watch-updater) on 2010-10-11

Changed in python-scipy (Debian):
status:	Unknown → Fix Committed

Revision history for this message

Launchpad Janitor (janitor) wrote on 2010-10-12:

#26

This bug was fixed in the package python-scipy - 0.7.0-2ubuntu0.1

---------------
python-scipy (0.7.0-2ubuntu0.1) lucid-proposed; urgency=low

* Fix scipy.weave.inline compilations (LP: #302649)
-- Sameer Morar <email address hidden> Thu, 30 Sep 2010 15:32:13 +0200

Changed in python-scipy (Ubuntu Lucid):
status:	Fix Committed → Fix Released

Bug Watch Updater (bug-watch-updater) on 2011-01-10

Changed in python-scipy (Debian):
status:	Fix Committed → Fix Released

Ubuntu
python-scipy package

scipy.weave.inline compilation fails with gcc 4.3

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	Status	Importance	Assigned to
SciPy	New	Unknown	scipy-bugs #739
blitz++ (Debian)	Fix Released	Unknown	debbugs #455661
python-scipy (Debian)	Fix Released	Unknown	debbugs #598520
python-scipy (Ubuntu)	Fix Released	Medium	Sameer Morar
Lucid	Fix Released	Low	Sameer Morar

Ubuntupython-scipy package

scipy.weave.inline compilation fails with gcc 4.3

Bug Description

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Other bug subscribers

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Ubuntu
python-scipy package