[Bioperl-l] bioperl-db and MySQL again
chen li
chen_li3 at yahoo.com
Wed Nov 30 06:44:52 EST 2005
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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