[Bioperl-l] bioperl-db and MySQL again
Hilmar Lapp
hlapp at gmx.net
Wed Nov 30 12:28:46 EST 2005
Not astray - only that forcing the install won't help if the downloaded
version is 0.1 from CPAN - it needs to be from CVS. Provided it is,
then you might choose to force the install and go back to running the
tests once you encounter errors running the
load_{seqdatabase,ontology}.pl scripts or one of your own.
-hilmar
On Nov 30, 2005, at 7:31 AM, Barry Moore wrote:
> 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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--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
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