bioperl-db and MySQL again

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bioperl-db and MySQL again

Li Chen-2
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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RE: bioperl-db and MySQL again

Barry Moore
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: [hidden email] [mailto:bioperl-l-
> [hidden email]] On Behalf Of chen li
> Sent: Wednesday, November 30, 2005 4:45 AM
> To: Hilmar Lapp
> Cc: [hidden email]
> 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
>
>
>
>
>
>
>
>
>
>
>
>
> __________________________________
> Yahoo! Mail - PC Magazine Editors' Choice 2005
> http://mail.yahoo.com
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

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Re: bioperl-db and MySQL again

Hilmar Lapp
In reply to this post by Li Chen-2
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
>
>
>
>
>
>
>
>
>
>
>
>
> __________________________________
> Yahoo! Mail - PC Magazine Editors' Choice 2005
> http://mail.yahoo.com
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


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Re: bioperl-db and MySQL again

Hilmar Lapp
In reply to this post by Li Chen-2
In fact it also appears the connection attempt to mysql already fails.  
Make sure you have the Biosql instance instantiated, and make sure you  
followed the instructions and copied t/DBHarness.conf.example to  
t/DBHarness.biosql.conf while editing it to reflect your setup,  
username, and password.

This is another reason why using the CPAN shell won't work for  
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
>
>
>
>
>
>
>
>
>
>
>
>
> __________________________________
> Yahoo! Mail - PC Magazine Editors' Choice 2005
> http://mail.yahoo.com
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


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Re: bioperl-db and MySQL again

Hilmar Lapp
In reply to this post by Barry Moore
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: [hidden email] [mailto:bioperl-l-
>> [hidden email]] On Behalf Of chen li
>> Sent: Wednesday, November 30, 2005 4:45 AM
>> To: Hilmar Lapp
>> Cc: [hidden email]
>> 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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Hilmar Lapp                            email: lapp at gnf.org
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bioperl-db and MySQL

Li Chen-2
Very special thanks to Hilmar and Barry who help me
out for installing bioperl-db.


The follwoings are my experience for installing
bioperl-db:

1) Have a Linux operation system (in my case)
2) Use anonymouse CVS to install bioperl and follow
the HOWTO
3) the CPAN method doesn't work in my case



Li




               
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