Scott Cain | 20 Feb 00:39 2013
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Re: BioGraphics: Bio::SCF installation through cpan fails

Hi Peyman,

I have no idea what might be required to get staden and Bio::SCF installed on a windows machine; you have my
sympathies for having to go through it. 

But what I wanted to touch on was what you wrote, that is, that you "need" it for Bio::Graphics. I just wanted
to point out that you don't need it unless you want to be able to display traces from ABI sequencers (which
most people don't really care to do these days). Bioi::SCF is listed as a recommended module, not a
required one.

Scott

Sent from my iPad

On Feb 19, 2013, at 4:16 PM, peyman alavi <peymanalavi <at> yahoo.com> wrote:

> 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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> Bioperl-l <at> lists.open-bio.org
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