Re: DB_File, windows and config.in

[marto]

Which version of Perl are you using? Here you state DWIM perl, which is Strawberry 5.14.2.x which has DB_File as standard.

[Arthfael]

Hi guys,

Yes, I have DWIM Perl, but apparently it failed to properly install DB_File. This is what I get when I try to install BioPerl:

 Checking optional features...
 DB_File Tests.........disabled
 requires:
 ! DB_File is not installed
 
 ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the 
+versions of the modules indicated above before proceeding with this i
+nstallation
Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live
+ database tests? y/n [n]

Any ideas what may be the problem? I can remove-reinstall DWIM Perl and see what happens.

[marto]

Do you have more than one installation of Perl? What does perl -V show?

[Arthfael]

This is really weird, when I look at installed packages in PPM DB_File is really listed, however when I try to install BioPerl through CPAN or the PPM gui the install complains about DB_File (and other packages) not being here:

In PPM:

 ERROR: Can't find any package that provides Ace:: for Bundle-BioPerl-
+Core
Can't find any package that provides DB_File:: for Bundle-BioPerl-Core
Can't find any package that provides IPC::Run for GraphViz

The result of perl  -V is:

 Set up gcc environment - 4.6.3 20111208 (prerelease)
Summary of my perl5 (revision 5 version 16 subversion 3) configuration
+:

  Platform:
    osname=MSWin32, osvers=5.2, archname=MSWin32-x64-multi-thread
    uname=''
    config_args='undef'
    hint=recommended, useposix=true, d_sigaction=undef
    useithreads=define, usemultiplicity=define
    useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=und
+ef
    use64bitint=define, use64bitall=undef, uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='C:\PROGRA~1\Rtools\GCC-46~1.3\bin\gcc.exe', ccflags ='-DNDEBUG
+ -DWIN32 -
D_CONSOLE -DNO_STRICT -DWIN64 -DCONSERVATIVE -DPERL_TEXTMODE_SCRIPTS -
+DUSE_SITEC
USTOMIZE -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -DUSE_PERLIO -DHA
+SATTRIBUTE
 -fno-strict-aliasing -mms-bitfields',
    optimize='-O2',
    cppflags='-DWIN32'
    ccversion='', gccversion='4.6.3 20111208 (prerelease)', gccosandve
+rs=''
    intsize=4, longsize=4, ptrsize=8, doublesize=8, byteorder=12345678
    d_longlong=undef, longlongsize=8, d_longdbl=define, longdblsize=8
    ivtype='__int64', ivsize=8, nvtype='double', nvsize=8, Off_t='__in
+t64', lsee
ksize=8
    alignbytes=8, prototype=define
  Linker and Libraries:
    ld='C:\PROGRA~1\Rtools\GCC-46~1.3\bin\g++.exe', ldflags ='-L"C:\Pe
+rl64\lib\C
ORE"'
    libpth=\lib
    libs=-lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 
+-lshell32
-lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion 
+-lodbc32 -
lodbccp32 -lcomctl32 -lmsvcrt
    perllibs=-lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvap
+i32 -lshel
l32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lvers
+ion -lodbc
32 -lodbccp32 -lcomctl32 -lmsvcrt
    libc=msvcrt.lib, so=dll, useshrplib=true, libperl=perl516.lib
    gnulibc_version=''
  Dynamic Linking:
    dlsrc=dl_win32.xs, dlext=dll, d_dlsymun=undef, ccdlflags=' '
    cccdlflags=' ', lddlflags='-mdll -L"C:\Perl64\lib\CORE"'


Characteristics of this binary (from libperl):
  Compile-time options: HAS_TIMES HAVE_INTERP_INTERN MULTIPLICITY
                        PERLIO_LAYERS PERL_DONT_CREATE_GVSV
                        PERL_IMPLICIT_CONTEXT PERL_IMPLICIT_SYS
                        PERL_MALLOC_WRAP PERL_PRESERVE_IVUV PL_OP_SLAB
+_ALLOC
                        USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
                        USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
                        USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
                        USE_SITECUSTOMIZE
  Locally applied patches:
        ActivePerl Build 1604 [298023]
  Built under MSWin32
  Compiled at Apr 14 2014 15:29:45
  @INC:
    C:/Perl64/site/lib
    C:/Perl64/lib
    .