[Bioperl-l] installing bioperl-1.5.2 errors:DB_File

Chris Fields cjfields at uiuc.edu
Fri Apr 4 16:07:12 EDT 2008


I think you have to use the cygwin installer to install DB_File (it  
also installs dependencies, such as BDB).  According to 'perldoc  
perlcygwin':

....
Optional Libraries for Perl on Cygwin

Several Perl functions and modules depend on the existence of some  
optional libraries. Configure will find them if they are installed in  
one of the directories listed as being used for library searches. Pre- 
built packages for most of these are available from the Cygwin  
installer.
....

chris
On Apr 2, 2008, at 12:52 PM, Pan Zheng wrote:

> Hi,
>
>  I am installing bioperl-1.5.2_102 under cygwin on my Windows XP and  
> having some errors during the process.
>
>  When I was running "perl Build test", one major error is the error  
> about DB_File. I tried to install DB_File from cpan and rpm without  
> any luck.
>
>  ++++++++++++++++++++++++
>  CPAN: File::Temp loaded ok (v0.16)
> CPAN: YAML loaded ok (v0.62)
>    CPAN.pm: Going to build P/PM/PMQS/DB_File-1.817.tar.gz
>  Parsing config.in...
> Looks Good.
> Checking if your kit is complete...
> Looks good
> Note (probably harmless): No library found for -ldb
> Writing Makefile for DB_File
> cp DB_File.pm blib/lib/DB_File.pm
> AutoSplitting blib/lib/DB_File.pm (blib/lib/auto/DB_File)
> gcc -c  -I/usr/local/BerkeleyDB/include -DPERL_USE_SAFE_PUTENV -fno- 
> strict-alias
> ing -pipe -Wdeclaration-after-statement -DUSEIMPORTLIB -O3   - 
> DVERSION=\"1.817\"
> -DXS_VERSION=\"1.817\"  "-I/usr/lib/perl5/5.8/cygwin/CORE"  - 
> D_NOT_CORE  -DmDB_
> Prefix_t=size_t -DmDB_Hash_t=u_int32_t   version.c
> version.c:30:16: db.h: No such file or directory
> make: *** [version.o] Error 1
>  PMQS/DB_File-1.817.tar.gz
>  /usr/bin/make -- NOT OK
> Running make test
>  Can't test without successful make
> Running make install
>  Make had returned bad status, install seems impossible
> Failed during this command:
> PMQS/DB_File-1.817.tar.gz                    : make NO
>  +++++++++++++++++++++++++++++++++++++++++++++++
>
>
>  I can't remember I had this kind error while installing earlier  
> version.
>
>  Would you please help me on DB_File installation ?
>
>  Thanks.
>
>  Pan
>
>
> ---------------------------------
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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