[Bioperl-l] bioperl-db and MySQL again
Barry Moore
bmoore at genetics.utah.edu
Wed Nov 30 10:31:39 EST 2005
Chen-
It looks to me like all your failed tests are due to the fact that the
test scripts can't connect to your MySQL database as 'root'. You could
su to an account that is set up for access to your database for make
test and then back to root for make install, you give root a MySQL
account, or you could just skip the tests and force the install
(probably what I'd do since I'm lazy, and haven't gotten burned for not
testing that group of modules yet).
I think all of those options should work, and hopefully Hilmar or
someone else will correct me if I've led you astray.
Barry
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
> bounces at portal.open-bio.org] On Behalf Of chen li
> Sent: Wednesday, November 30, 2005 4:45 AM
> To: Hilmar Lapp
> Cc: bioperl-l at bioperl.org
> Subject: [Bioperl-l] bioperl-db and MySQL again
>
> 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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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;
ho
> st=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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