Installing bioperl-ext - on windows xp... (Jul/24/2008 )

Hello,

I am trying to install the latest version of bioperl-ext (Bio::Ext::Align, for Smith Waterman alignment function)
on Windows xp.
(I already have the following packages installed up to date: bioperl core,
bioperl db, bioperl gui, bioperl network, bioperl run.)
In the bioperl-ext-1.5.1\Bio\Ext\Align directory, I get the following output
from 'perl Makefile.PL'.

C:\Perl\bioperl-ext-1.5.1\Bio\Ext\Align>perl Makefile.PL
Note (probably harmless): No library found for -lm
Note (probably harmless): No library found for oldnames.lib
Note (probably harmless): No library found for kernel32.lib
Note (probably harmless): No library found for user32.lib
Note (probably harmless): No library found for gdi32.lib
Note (probably harmless): No library found for winspool.lib
Note (probably harmless): No library found for comdlg32.lib
Note (probably harmless): No library found for advapi32.lib
Note (probably harmless): No library found for shell32.lib
Note (probably harmless): No library found for ole32.lib
Note (probably harmless): No library found for oleaut32.lib
Note (probably harmless): No library found for netapi32.lib
Note (probably harmless): No library found for uuid.lib
Note (probably harmless): No library found for ws2_32.lib
Note (probably harmless): No library found for mpr.lib
Note (probably harmless): No library found for winmm.lib
Note (probably harmless): No library found for version.lib
Note (probably harmless): No library found for odbc32.lib
Note (probably harmless): No library found for odbccp32.lib
Note (probably harmless): No library found for msvcrt.lib
Writing Makefile for Bio::Ext::Align

When I proceed anyways with 'nmake', I get the following errors:

C:\Perl\bioperl-ext-1.5.1\Bio\Ext\Align>nmake
Microsoft ® Program Maintenance Utility Version 1.50
Copyright © Microsoft Corp 1988-94. All rights reserved.
DEFINE='-DPOSIX -DNOERROR'; CC='cl'; CFLAGS='-nologo -GF -W3 -MD -Zi
-DN
DEBUG -O1 -DWIN32 -D_CONSOLE -DNO_STRICT -DHAVE_DES_FCRYPT -DNO_HASH_SEED
-DUSE_
SITECUSTOMIZE -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -DUSE_PERLIO
-DPERL_MS
VCRT_READFIX'; export DEFINE INC CC CFLAGS; cd libs && nmake CC='cl'
CFLAGS='-n
ologo -GF -W3 -MD -Zi -DNDEBUG -O1 -DWIN32 -D_CONSOLE -DNO_STRICT
-DHAVE_DES_FCR
YPT -DNO_HASH_SEED -DUSE_SITECUSTOMIZE -DPERL_IMPLICIT_CONTEXT
-DPERL_IMPLICIT_S
YS -DUSE_PERLIO -DPERL_MSVCRT_READFIX -DPOSIX -DNOERROR' DEFINE='-DPOSIX
-DNOERR
OR' libsw.lib -e
'DEFINE' is not recognized as an internal or external command,
operable program or batch file.
NMAKE : fatal error U1077: 'C:\WINDOWS\system32\cmd.exe' : return code '0x1'
Stop.


I get the same error as above when I run 'nmake test' and 'nmake install' as
well.
Does anyone know how to solve this problem?
I heard that installing is much easier on Linux or unix...

Thanks in advance for any help.

hi jayn,

indeed, i find it much easier in linux. if you need windows you can make a separate partition on your computer to install any linux distro you like (i personally like ubuntu, it's free, popular, lots of support on ubuntuforums.org and now even dell sells their computers with this os)

instead of bioperl you could alternatively install emboss, its smith waterman alignment program is called "water". the new version of ubuntu (8.04, long term support, don't use the experimental versions in between!) has the necessary repositories for these programs.

I agree with perlmunky -- use PPM (if you're using ActiveState Perl) after adding "http://bioperl.org/DIST" to your repositories. For further info, see here.