[Bioperl-l] Installing bioperl-ext on windows

Eileen Heo tiarua at gmail.com
Wed Jul 23 02:05:56 EDT 2008


Hello,

I am trying to install the latest version of bioperl-ext (Bio::Ext::Align)
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 (R) Program Maintenance Utility   Version 1.50
Copyright (c) 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.
How can this problem be solved so that installing bioperl-ext is successful?

Thank you in advance for any help.


More information about the Bioperl-l mailing list