Marc Colosimo | 3 May 18:04 2004
Picon

setup.py bug

There is a bug in setup.py. I don't know how people got it to work, but 
on my system I get this  (python 2.2.2, Linux):

  python setup.py build
Traceback (most recent call last):
   File "setup.py", line 392, in ?
     language="c++"
TypeError: __init__() got an unexpected keyword argument 'language'

Removing this from:

     Extension('Bio.KDTree._CKDTree',
               ["Bio/KDTree/KDTree.C",
                "Bio/KDTree/KDTree.swig.C"],
               libraries=["stdc++"]
               language=["c++"]
               ),

I get the second error at:

   File "setup.py", line 163, in build_extension
     if ext.language == "c++":
AttributeError: Extension instance has no attribute 'language'

If these files are c++, then they should be named correctly (many 
choices, none with C).

Marc
Pieter Laeremans | 3 May 19:59 2004

Re: How many people on biopython lists?

Iddo Friedberg <idoerg <at> burnham.org> writes:

> Hi,
>
> Can someone tell me how many subscribers are there on the biopython and 
> biopython-dev lists? It's for a book chapter.. good PR.
>

Hello, 

I think this is extremly difficult to estimate.  As there are probably
other people like me, who read the mailinglist to a news interface
(gmane.org)

kind regards,

Pieter
bugzilla-daemon | 4 May 12:44 2004

[Bug 1630] New: Install errors on debian

http://bugzilla.bioperl.org/show_bug.cgi?id=1630

           Summary: Install errors on debian
           Product: Biopython
           Version: 1.24
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: david <at> compbio.dundee.ac.uk

I get the following error when trying to install on a debian system. I have tried to find the distutils 
package to install it but without success. Any hints?

% python setup.py build
Traceback (most recent call last):
  File "setup.py", line 31, in ?
    from distutils.core import setup
ImportError: No module named distutils.core

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bugzilla-daemon | 4 May 13:03 2004

[Bug 1630] Install errors on debian

http://bugzilla.bioperl.org/show_bug.cgi?id=1630

hoffman <at> ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |INVALID

------- Additional Comments From hoffman <at> ebi.ac.uk  2004-05-04 07:03 -------
Biopython requires Python 2.2 or later. Please install the latest version of
Python and try again.

Hint: in some distributions there might be a newer version of Python called
python2, python2.3, or something similar.

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bugzilla-daemon | 4 May 14:30 2004

[Bug 1630] Install errors on debian

http://bugzilla.bioperl.org/show_bug.cgi?id=1630

------- Additional Comments From david <at> compbio.dundee.ac.uk  2004-05-04 08:30 -------
I am using 2.3.3
% python
Python 2.3.3 (#2, Feb 24 2004, 09:29:20) 
[GCC 3.3.3 (Debian)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>

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bugzilla-daemon | 4 May 14:50 2004

[Bug 1630] Install errors on debian

http://bugzilla.bioperl.org/show_bug.cgi?id=1630

------- Additional Comments From diego <at> conysis.com  2004-05-04 08:50 -------
If you use python2.3, probably, you are working with the testing branch of Debian 
(sarge). Sarge use python2.3 by default, so that it is no necesary to specify
the version.

The package python-dev will install python2.3-dev, that has distutils.

Just: apt-get install python-dev

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Marc Colosimo | 4 May 15:14 2004
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Re: [Bug 1630] Install errors on debian


On May 4, 2004, at 7:03 AM, bugzilla-daemon <at> portal.open-bio.org wrote:

> http://bugzilla.bioperl.org/show_bug.cgi?id=1630
>
> hoffman <at> ebi.ac.uk changed:
>
>            What    |Removed                     |Added
> ----------------------------------------------------------------------- 
> -----
>              Status|NEW                         |RESOLVED
>          Resolution|                            |INVALID
>
>
>
> ------- Additional Comments From hoffman <at> ebi.ac.uk  2004-05-04 07:03  
> -------
> Biopython requires Python 2.2 or later. Please install the latest  
> version of
> Python and try again.
>

NO it requires python 2.3. I posted this the other day, I guess I'll  
submit a bug report. The Disutils with 2.2 do not have  
Extentions.language.

> Hint: in some distributions there might be a newer version of Python  
> called
> python2, python2.3, or something similar.
>
(Continue reading)

Michael Hoffman | 4 May 15:19 2004
Picon
Picon

Re: [Bug 1630] Install errors on debian

On Tue, 4 May 2004, Marc Colosimo wrote:

> NO it requires python 2.3. I posted this the other day, I guess I'll
> submit a bug report. The Disutils with 2.2 do not have
> Extentions.language.

I remember that e-mail but I thought that was only the CVS version,
not the 1.24 release. I consider your previous issue to still be open
and was waiting for a response from Brad on that.

Either we need to upgrade the requirement to 2.3 or come up with an
ever-more-kludgy workaround.
--

-- 
Michael Hoffman <hoffman <at> ebi.ac.uk>
European Bioinformatics Institute
bugzilla-daemon | 4 May 15:25 2004

[Bug 1631] New: setup.py does not run

http://bugzilla.bioperl.org/show_bug.cgi?id=1631

           Summary: setup.py does not run
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: trivial
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: mcolosimo <at> mitre.org

setup.py uses fetures of distutils not found in python 2.2 (details below). Therefore, biopython now 
requires python 2.3 or a newer version of distutils.

An easy solution is to change the .C files to correct extention endings (.cpp or .c++ or .cc)

 python setup.py build
Traceback (most recent call last):
  File "setup.py", line 392, in ?
    language="c++"
TypeError: __init__() got an unexpected keyword argument 'language'

Removing this from:

    Extension('Bio.KDTree._CKDTree',
              ["Bio/KDTree/KDTree.C",
               "Bio/KDTree/KDTree.swig.C"],
(Continue reading)

Marc Colosimo | 4 May 16:15 2004
Picon

Re: [Bug 1630] Install errors on debian


On May 4, 2004, at 9:19 AM, Michael Hoffman wrote:

> On Tue, 4 May 2004, Marc Colosimo wrote:
>
>> NO it requires python 2.3. I posted this the other day, I guess I'll
>> submit a bug report. The Disutils with 2.2 do not have
>> Extentions.language.
>
> I remember that e-mail but I thought that was only the CVS version,
> not the 1.24 release.

Opps, I missed the line on the right of the screen about the version. 
Mine is with the CVS and I've added it to bugzilla (as we now all know) 
so that it can be tracked.

> I consider your previous issue to still be open
> and was waiting for a response from Brad on that.
>
> Either we need to upgrade the requirement to 2.3 or come up with an
> ever-more-kludgy workaround.

I think just changing the file name endings is all we have to do. Okay, 
maybe there is more. I'll send that on the other one.
> -- 
> Michael Hoffman <hoffman <at> ebi.ac.uk>
> European Bioinformatics Institute

Gmane