[BioPython] 1.21 installation difficulty

[Michiel Jan Laurens de Hoon]

I made a Biopython installer for python 2.2 on windows; it is available at
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/biopython-1.21.win32-py2.2.exe.

I ran into some difficulties building this installer. During the
bdist_wininst command, it cannot find the file
build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs. This is probably a
problem with Python's distutils for Windows; I don't run into this
problem when compiling on Unix. So on Windows, I created that directory
by hand and copied the files from Bio\EUtils\DTDs into it. That seems
like the right thing to do, but I am not sure; does anybody know?

The "python setup.py install" command works fine with Python 2.2.3 on
Windows, so you can also install Biopython yourself using Cygwin. I put
some explanation of how to do that on
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/index.html

On Unix, I get the following warning:

*** Martel *** is either not installed or out of date.

This package is required for many Biopython features.  Please install
it before you install Biopython.
You can find Martel at http://www.biopython.org/~dalke/Martel/.

Isn't Martel included with Biopython? Btw, the link is dead.


One more issue: with Python 2.3, mxTextTools (and therefore Biopython)
cannot be compiled. The gcc compiler on Cygwin gets farther than
Microsoft's cl.exe. With cl.exe, it fails at

C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe /c /nologo /Ox
/MD /W3 /GX /DNDEBUG /O2 /Gf /GB /GD -DBAD_STATIC_FORWARD=1
-UHAVE_STRPTIME -UHAVE_TIMEGM -Imx/DateTime/mxDateTime
-Ic:\Python23\include -Ic:\Python23\PC /Tcmx/DateTime
/mxDateTime/mxDateTime.c
/Fobuild\temp.win32-2.3\Release\mx\DateTime\mxDateTime\
mxDateTime\mx/DateTime/mxDateTime/mxDateTime.obj
mxDateTime.c
mx/DateTime/mxDateTime/mxDateTime.c(163) : error C2133:
'mxDateTime_Methods' : ?
?????????
mx/DateTime/mxDateTime/mxDateTime.c(166) : error C2133:
'mxDateTimeDelta_Methods
' : ??????????

(My Microsoft Visual Studio is in Japanese, I can't read the compiler
messages
either).

With gcc, the problem occurs in the final linking stage:

C:\cygwin\usr\local\bin\gcc.exe -mno-cygwin -shared -s
build\temp.win32-2.3\Rele
ase\mx\TextTools\mxTextTools\mxTextTools\mx\texttools\mxtexttools\mxtexttools.o
build\temp.win32-2.3\Release\mx\TextTools\mxTextTools\mxTextTools\mx\texttools\m
xtexttools\mxte.o
build\temp.win32-2.3\Release\mx\TextTools\mxTextTools\mxTextTo
ols\mx\texttools\mxtexttools\mxbmse.o
build\temp.win32-2.3\Release\mx\TextTools\
mxTextTools\mxTextTools\mx\texttools\mxtexttools\mxTextTools.def
-Lc:\Python23\libs -Lc:\Python23\PCBuild -lpython23 -o
build\lib.win32-2.3\mx\TextTools\mxTextTools\mxTextTools.pyd
build\temp.win32-2.3\Release\mx\TextTools\mxTextTools\mxTextTools\mx\texttools\m
xtexttools\mxte.o(.text+0x1200):mxte.c: undefined reference to
`__imp__mxBMS_Type'
collect2: ld returned 1 exit status

The same error occurs with Python 2.2, but then I can compile it with
Microsoft's cl.exe.


--Michiel, U Tokyo.

Brad Chapman wrote:

>>Are there plans for a Windows installer version?
> I am definitely planning on making one. My access to Windows
> computers that I have admin permissions on sucks right now, but I
> hope to have one made over the next couple of days. If you beat me
> to making it, the instructions for making Windows installers are
> here:
> 
> http://www.biopython.org/docs/tutorial/Tutorial006.html#toc26
> 
> Someone who uses Windows regularly who wants to make and maintain
> the windows installer would be great (hint, hint :-).
> 



-- 
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