[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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>
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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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