peyman alavi | 19 Feb 22:16 2013
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BioGraphics: Bio::SCF installation through cpan fails

Hello,
I am having
problems for a while trying to install the Bio::SCF module on my Vista32. Now, I know that Bio::SCF isn't
really a Bioperl module, but I need it for Bio::Graphics, and I thought perhaps other people had
experienced the same problem before.  I
have installed zlib and io_lib (both their last available versions), but it
looks like sth. (presumably with io_lib) is missing. I should be very grateful
if someone could tell me what still needs to be done!
Here are
the paths where the io_lib "library" and "include" directories are installed, and I
set them to cpan before trying to install Bio::SCF:
o conf
makepl_arg “LIBS=-Lc:/MinGW/msys/1.0/local/lib INC=-Ic:/MinGW/msys/1.0/local/include”
And the
following is what I get on the STDOUT:
 
Set up gcc environment - 4.7.2
[32m
cpan shell -- CPAN exploration and modules installation (v1.9800)
Enter 'h' for help.[0m
 
[32m    makepl_arg         [LIBS=-Lc:/MinGW/msys/1.0/local/lib
INC=-Ic:/MinGW/msys/1.0/local/include][0m
[32mPlease use 'o conf commit' to make the config permanent![0m
 
[32m[0m
[32mReading 'D:\Perl\cpan\Metadata'[0m
[32m  Database was generated on
Sun, 17 Feb 2013 12:17:02 GMT[0m
[32mRunning install for module 'Bio::SCF'[0m
[32mRunning make for L/LD/LDS/Bio-SCF-1.03.tar.gz[0m
[32mChecksum for
D:\Perl\cpan\sources\authors\id\L\LD\LDS\Bio-SCF-1.03.tar.gz ok[0m
[32mScanning cache D:\Perl/cpan/build for sizes[0m
[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32m.[0m[32mDONE[0m
[32mBio-SCF-1.03/[0m
[32mBio-SCF-1.03/t/[0m
[32mBio-SCF-1.03/t/scf.t[0m
[32mBio-SCF-1.03/eg/[0m
[32mBio-SCF-1.03/eg/write_test_obj.pl[0m
[32mBio-SCF-1.03/eg/write_test_tied.pl[0m
[32mBio-SCF-1.03/eg/read_test_obj.pl[0m
[32mBio-SCF-1.03/eg/read_test_tied.pl[0m
[32mBio-SCF-1.03/SCF/[0m
[32mBio-SCF-1.03/SCF/Arrays.pm[0m
[32mBio-SCF-1.03/DISCLAIMER[0m
[32mBio-SCF-1.03/README[0m
[32mBio-SCF-1.03/SCF.pm[0m
[32mBio-SCF-1.03/SCF.xs[0m
[32mBio-SCF-1.03/Changes[0m
[32mBio-SCF-1.03/test.scf[0m
[32mBio-SCF-1.03/Makefile.PL[0m
[32mBio-SCF-1.03/META.yml[0m
[32mBio-SCF-1.03/INSTALL[0m
[32mBio-SCF-1.03/MANIFEST[0m
[32m
  CPAN.pm: Building
L/LD/LDS/Bio-SCF-1.03.tar.gz[0m
 
Set up gcc environment - 4.7.2
Checking if your kit is complete...
Looks good
Writing Makefile for Bio::SCF
Writing MYMETA.yml and MYMETA.json
cp SCF.pm blib\lib\Bio\SCF.pm
cp SCF/Arrays.pm blib\lib\Bio\SCF\Arrays.pm
D:\Perl\bin\perl.exe D:\Perl\site\lib\ExtUtils\xsubpp  -typemap
D:\Perl\lib\ExtUtils\typemap  SCF.xs > SCF.xsc &&
D:\Perl\bin\perl.exe -MExtUtils::Command -e mv -- SCF.xsc SCF.c
Please specify prototyping behavior for SCF.xs (see perlxs manual)
c:/MinGW/bin/gcc.exe -c  -Ic:/MinGW/msys/1.0/local/include              -DNDEBUG
-DWIN32 -D_CONSOLE -DNO_STRICT -DHAVE_DES_FCRYPT -DUSE_SITECUSTOMIZE
-DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -DUSE_PERLIO -D_USE_32BIT_TIME_T
-DPERL_MSVCRT_READFIX -DHASATTRIBUTE -fno-strict-aliasing -mms-bitfields -O2        
  -DVERSION=\"1.03\"         -DXS_VERSION=\"1.03\"  "-ID:\Perl\lib\CORE" 
-DLITTLE_ENDIAN SCF.c
In file included from c:/MinGW/msys/1.0/local/include/io_lib/scf.h:31:0,
                 from SCF.xs:12:
c:/MinGW/msys/1.0/local/include/io_lib/mFILE.h:23:0: warning:
"MF_APPEND" redefined [enabled by default]
In file included from
c:\mingw\bin\../lib/gcc/mingw32/4.7.2/../../../../include/windows.h:55:0,
                 from
D:\Perl\lib\CORE/win32.h:61,
                 from
D:\Perl\lib\CORE/win32thread.h:4,
                 from
D:\Perl\lib\CORE/perl.h:2825,
                 from SCF.xs:5:
c:\mingw\bin\../lib/gcc/mingw32/4.7.2/../../../../include/winuser.h:131:0:
note: this is the location of the previous definition
SCF.xs: In function 'XS_Bio__SCF_get_scf_pointer':
SCF.xs:35:2: warning: passing argument 3 of '(*Perl_ILIO_ptr((struct
PerlInterpreter *)Perl_get_context()))->pNameStat' from incompatible pointer
type [enabled by default]
SCF.xs:35:2: note: expected 'struct _stati64 *' but argument is of type
'struct stat *'
Running Mkbootstrap for Bio::SCF ()
D:\Perl\bin\perl.exe -MExtUtils::Command -e chmod -- 644 SCF.bs
D:\Perl\bin\perl.exe -MExtUtils::Mksymlists \
     -e
"Mksymlists('NAME'=>\"Bio::SCF\", 'DLBASE' => 'SCF',
'DL_FUNCS' => {  }, 'FUNCLIST' =>
[], 'IMPORTS' => {  }, 'DL_VARS' =>
[]);"
Set up gcc environment - 4.7.2
dlltool --def SCF.def --output-exp dll.exp
c:\MinGW\bin\g++.exe -o blib\arch\auto\Bio\SCF\SCF.dll -Wl,--base-file
-Wl,dll.base -mdll -L"D:\Perl\lib\CORE" SCF.o   D:\Perl\lib\CORE\perl512.lib
c:\MinGW\lib\libkernel32.a c:\MinGW\lib\libuser32.a c:\MinGW\lib\libgdi32.a
c:\MinGW\lib\libwinspool.a c:\MinGW\lib\libcomdlg32.a c:\MinGW\lib\libadvapi32.a
c:\MinGW\lib\libshell32.a c:\MinGW\lib\libole32.a c:\MinGW\lib\liboleaut32.a
c:\MinGW\lib\libnetapi32.a c:\MinGW\lib\libuuid.a c:\MinGW\lib\libws2_32.a
c:\MinGW\lib\libmpr.a c:\MinGW\lib\libwinmm.a c:\MinGW\lib\libversion.a
c:\MinGW\lib\libodbc32.a c:\MinGW\lib\libodbccp32.a c:\MinGW\lib\libcomctl32.a
c:\MinGW\lib\libmsvcrt.a dll.exp
Warning: resolving _VirtualQuery <at> 12 by linking to _VirtualQuery
Use --enable-stdcall-fixup to disable these warnings
Use --disable-stdcall-fixup to disable these fixups
Warning: resolving _VirtualProtect <at> 16 by linking to _VirtualProtect
Warning: resolving _EnterCriticalSection <at> 4 by linking to
_EnterCriticalSection
Warning: resolving _TlsGetValue <at> 4 by linking to _TlsGetValue
Warning: resolving _GetLastError <at> 0 by linking to _GetLastError
Warning: resolving _LeaveCriticalSection <at> 4 by linking to
_LeaveCriticalSection
Warning: resolving _DeleteCriticalSection <at> 4 by linking to
_DeleteCriticalSection
Warning: resolving _InitializeCriticalSection <at> 4 by linking to
_InitializeCriticalSection
SCF.o:SCF.c:(.text+0xf35): undefined reference to `mfreopen'
SCF.o:SCF.c:(.text+0xf4b): undefined reference to `mfwrite_scf'
SCF.o:SCF.c:(.text+0xf6a): undefined reference to `mfflush'
SCF.o:SCF.c:(.text+0xf72): undefined reference to `mfdestroy'
SCF.o:SCF.c:(.text+0x1138): undefined reference to `write_scf'
SCF.o:SCF.c:(.text+0x16ac): undefined reference to `scf_deallocate'
SCF.o:SCF.c:(.text+0x17b1): undefined reference to `mfreopen'
SCF.o:SCF.c:(.text+0x17c1): undefined reference to `mfread_scf'
SCF.o:SCF.c:(.text+0x19bd): undefined reference to `read_scf'
c:/mingw/bin/../lib/gcc/mingw32/4.7.2/../../../../mingw32/bin/ld.exe:
SCF.o: bad reloc address 0xa4 in section `.rdata'
c:/mingw/bin/../lib/gcc/mingw32/4.7.2/../../../../mingw32/bin/ld.exe:
final link failed: Invalid operation
collect2.exe: error: ld returned 1 exit status
dmake.exe:  Error code 129, while
making 'blib\arch\auto\Bio\SCF\SCF.dll'
[32m  LDS/Bio-SCF-1.03.tar.gz[0m
[31m  D:\Perl\site\bin\dmake.exe
-- NOT OK[0m
[32mRunning make test[0m
[32m  Can't test without successful
make[0m
[32mRunning make install[0m
[32m  Make had returned bad
status, install seems impossible[0m
[32mFailed during this command:
 LDS/Bio-SCF-1.03.tar.gz                      : make NO[0m
[32m[0m
[31mWarning: Configuration not saved.[0m
[32mLockfile removed.[0m
 
 
 Thanks in advance for any useful
suggestions/help!!
Peyman

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