[Bioperl-l] bioperl-db and MySQL again

Hilmar Lapp hlapp at gmx.net
Wed Nov 30 12:22:07 EST 2005


Chen, you can't download bioperl-db from CPAN and have it work with the  
current BioSQL version (and possibly not even with the current Bioperl  
version - it's very old). Sorry for this inconvenience. Download from  
CVS the main trunk, then issue the usual triple of

	$ perl Makefile.PL
	$ make
	$ make test

followed possibly by 'make install' if you do have root access on the  
machine. Otherwise point PERL5LIB at the directory to which you  
downloaded bioperl-db/

	-hilmar

On Nov 30, 2005, at 3:44 AM, chen li wrote:

> Hi Himar,
>
> There are so many problems working with Perl under
> Windows XP so I have  linux Fedora core 1 installed on
> my computer. I already install all necessary compoents
> on my computer without any problem. But when I install
> bioperl-db. I still have problems: the installation
> can't make test.  The following is the message I
> got(sorry for the lengthy post). What is really going
> on here?  It seems there are some configuration
> problems but I am sure how to fix it.
>
>
> Thanks,
>
> Li
>
> message from the screen:
>
>
>
> cpan> install B/BI/BIRNEY/bioperl-db-0.1.tar.gz
> Running make for B/BI/BIRNEY/bioperl-db-0.1.tar.gz
> CPAN: LWP::UserAgent loaded ok
> Fetching with LWP:
>
> ftp://ftp.perl.org/pub/CPAN/authors/id/B/BI/BIRNEY/bioperl-db 
> -0.1.tar.gz
> CPAN: Digest::MD5 loaded ok
> CPAN: Compress::Zlib loaded ok
> Checksum for
> /root/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-db-0.1.tar.gz
> okScanning cache /root/.cpan/build for sizes
> Deleting from cache: /root/.cpan/build/DBI-1.49
> (11.3>10.0 MB)
> bioperl-db-0.1/
> bioperl-db-0.1/Bio/
> bioperl-db-0.1/Bio/DB/
> bioperl-db-0.1/Bio/DB/Map/
>
> (many are deleted here for short)
> ...................................................
> ...................................................
>
>
>   /usr/bin/make  -- OK
> Running make test
> PERL_DL_NONLAZY=1 /usr/bin/perl
> "-MExtUtils::Command::MM" "-e" "test_harness(0,
> 'blib/lib', 'blib/arch')" t/*.t
> t/comment..........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42351 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/comment..........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> Scalar found where operator expected at (eval 155)
> line 1, near "'int'  $__val"
>         (Missing operator before   $__val?)
> DIED. FAILED tests 1-6
>         Failed 6/6 tests, 0.00% okay
> t/dbadaptor........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42361 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/dbadaptor........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-3
>         Failed 3/3 tests, 0.00% okay
> t/dblink...........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42371 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/dblink...........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-7
>         Failed 7/7 tests, 0.00% okay
> t/ensembl..........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42381 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/ensembl..........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-14
>         Failed 14/14 tests, 0.00% okay
> t/ePCRdb...........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42391 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/ePCRdb...........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-3
>         Failed 3/3 tests, 0.00% okay
> t/map..............DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42401 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/map..............dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-6
>         Failed 6/6 tests, 0.00% okay
> t/marker...........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42411 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/marker...........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-19
>         Failed 19/19 tests, 0.00% okay
> t/remove...........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42421 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/remove...........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-22
>         Failed 22/22 tests, 0.00% okay
> t/seqfeature.......DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42431 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/seqfeature.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-9
>         Failed 9/9 tests, 0.00% okay
> t/seqfeaturekey....DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42441 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/seqfeaturekey....dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-11
>         Failed 11/11 tests, 0.00% okay
> t/seqlocation......DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42451 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/seqlocation......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-10
>         Failed 10/10 tests, 0.00% okay
> t/simpleseq........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42461 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/simpleseq........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-20
>         Failed 20/20 tests, 0.00% okay
> t/species..........DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42471 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/species..........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-6
>         Failed 6/6 tests, 0.00% okay
> t/swiss............DBI
> connect('host=localhost;','root',...) failed: Can't
> connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm
> line 186
>         (in cleanup) DBI
> connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42481 
> ;host=localhost','root',...)
> failed: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2) at
> t/DBTestHarness.pm line 212
> t/swiss............dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-16
>         Failed 16/16 tests, 0.00% okay
> Failed Test       Stat Wstat Total Fail  Failed  List
> of Failed
> ----------------------------------------------------------------------- 
> --------
> t/comment.t        255 65280     6   12 200.00%  1-6
> t/dbadaptor.t      255 65280     3    6 200.00%  1-3
> t/dblink.t         255 65280     7   14 200.00%  1-7
> t/ePCRdb.t         255 65280     3    6 200.00%  1-3
> t/ensembl.t        255 65280    14   28 200.00%  1-14
> t/map.t            255 65280     6   12 200.00%  1-6
> t/marker.t         255 65280    19   38 200.00%  1-19
> t/remove.t         255 65280    22   44 200.00%  1-22
> t/seqfeature.t     255 65280     9   18 200.00%  1-9
> t/seqfeaturekey.t  255 65280    11   22 200.00%  1-11
> t/seqlocation.t    255 65280    10   20 200.00%  1-10
> t/simpleseq.t      255 65280    20   40 200.00%  1-20
> t/species.t        255 65280     6   12 200.00%  1-6
> t/swiss.t          255 65280    16   32 200.00%  1-16
> Failed 14/14 test scripts, 0.00% okay. 152/152
> subtests failed, 0.00% okay.
> make: *** [test_dynamic] Error 255
>   /usr/bin/make test -- NOT OK
> Running make install
>   make test had returned bad status, won't install
> without force
>
>
>
>
>
>
>
>
>
>
> 	
> 		
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>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------




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