[DAS] mysql.sock trouble

[Leonardo Marino-Ramirez]

Steve,

I think that I found something that could be useful to you:

http://www.mysql.com/doc/C/a/Can_not_connect_to_server.html and
http://www.mysql.com/doc/P/r/Problems_with_mysql.sock.html

in synthesis you can try to symlink it: "ln -s /var/lib/mysql/mysql.sock
/tmp"

I hope it works for you.

Leonardo


On Fri, 17 May 2002, Steve Chervitz wrote:

> DAS folks,
>
> This may be more of a mysql issue than a DAS issue, and is more of an FYI since
> I have a mostly satisfactory resolution, but I was getting a connection error
> when using the ldas_load.pl script:
>
> $ ldas_load.pl --create --database dicty test.das
> DBI->connect(dicty) failed: Can't connect to local MySQL server through socket
> '/tmp/mysql.sock' (111) at
> /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
> line 140
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Can't connect to database: Can't connect to local MySQL server through
> socket '/tmp/mysql.sock' (111)
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/Root/Root.pm:315
> STACK: Bio::DB::GFF::Adaptor::dbi::caching_handle::new
> /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:90
> STACK: Bio::DB::GFF::Adaptor::dbi::new
> /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/dbi.pm:74
> STACK: Bio::DB::GFF::Adaptor::dbi::mysql::new
> /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/dbi/mysql.pm:253
> STACK: Bio::DB::GFF::Adaptor::dbi::mysqlopt::new
> /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm:149
> STACK: Bio::DB::GFF::new
> /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF.pm:550
> STACK: /usr/local/bin/ldas_load.pl:50
> -----------------------------------------------------------
>
> I could succesfully connect to the dicty database using mysql on the
> command-line, so my mysql setup appeared OK.
>
> My /tmp/mysql.sock was apparently defunct, probably from an old mysql install
> that I did over a year ago. The real socket from the latest mysql installation
> was at /var/lib/mysql/mysql.sock and wasn't been recognized. I tried deleting
> /tmp/mysql.sock and re-installing LDasServer, but still no go.
>
> Problem was solved by restarting mysqld with --socket=/tmp/mysql.sock
>
> This however created another annoyance in that the mysqladmin now requires that
> I specify the --socket, since it defaults to /var/lib/mysql/mysql.sock.
>
> So it seems I have to use /tmp/mysql.sock to appease the LDasServer, but it
> complicates my mysql installation. Any suggestions from the mysql jocks out
> there?
>
> Here's my version info:
> mysqladmin  Ver 8.23 Distrib 3.23.49a, for pc-linux-gnu on i686
>
> Steve
>
>
> =====
> Steve Chervitz
> sac@bioperl.org
>
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-- 

___ _/ _______________________________________________________________
   _/
  _/    _/      _/_/_/    Leonardo Marino-Ramirez   lmarino@tamu.edu
 _/    _/_/  _/_/    _/  Biochemistry Department, Texas A&M University
_/_/_/_/  _/  _/_/_/    2128 TAMU, College Station, TX 77843-2128, USA
     _/      _/     _/ Voice: (979) 862-4055   Fax: (979) 845-9274
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