[Biopython-dev] Missing files in Biopython 1.22

[Michiel Jan Laurens de Hoon]

Thomas Hamelryck wrote:
 > Hi Michiel,
 >
 > Did you compile the KDTree module too? Some time ago somebody
 > asked for it for Windows. It's uncommented in setup.py because
 > of a bug in distutils on some platforms.

I just tried to compile KDTree on Windows. It seems that the file 
Bio/KDTree/_KDTree.swig.C is missing in the source distribution. I 
picked it up from CVS, however I was not able to compile KDTree on 
Cygwin/MinGW (which I am using to build the Windows installer) nor using 
Microsoft's compiler. It seems that distutils doesn't realize that this 
is a C++ file, but I don't know how to fix that. Changing the file 
extensions to .cpp or .cc didn't help.

--Michiel.

C:\cygwin\usr\local\bin\gcc.exe -mno-cygwin -mdll -O -Wall 
-Ic:\Python22\include -c Bio/KDTree/_KDTree.C -o 
build\temp.win32-2.2\Release\_kdtree.o
In file included from /usr/local/include/c++/3.3/bits/locale_facets.h:166,
                  from /usr/local/include/c++/3.3/bits/basic_ios.h:44,
                  from /usr/local/include/c++/3.3/ios:51,
                  from /usr/local/include/c++/3.3/ostream:45,
                  from /usr/local/include/c++/3.3/iostream:45,
                  from Bio/KDTree/_KDTree.h:1,
                  from Bio/KDTree/_KDTree.C:1:
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:46: error: 
`_U' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:47: error: 
`_L' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:48: error: 
`_U' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:48: error: 
`_L' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:49: error: 
`_N' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:50: error: 
`_X' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:50: error: 
`_N' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:51: error: 
`_S' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:52: error: 
`_P' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:52: error: 
`_U' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:52: error: 
`_L' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:52: error: 
`_N' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:52: error: 
`_B' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:53: error: 
`_P' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:53: error: 
`_U' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:53: error: 
`_L' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:53: error: 
`_N' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:54: error: 
`_C' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:55: error: 
`_P' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:56: error: 
`_U' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:56: error: 
`_L' was not declared in this scope
/usr/local/include/c++/3.3/i686-pc-cygwin/bits/ctype_base.h:56: error: 
`_N' was not declared in this scope
Bio/KDTree/_KDTree.C: In member function `void
    KDTree::neighbor_simple_search(float)':
Bio/KDTree/_KDTree.C:914: warning: comparison between signed and 
unsigned integer expressions
Bio/KDTree/_KDTree.C:923: warning: comparison between signed and 
unsigned integer expressions
error: command 'gcc' failed with exit status 1


> 
> Regards,
> 
> -Thomas
> 
> ---
> Thomas Hamelryck
> Computational modeling lab (COMO)
> Vrije Universiteit Brussel (VUB)
> Belgium
> http://homepages.vub.ac.be/~thamelry
> 
> 

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon