[Bioperl-pipeline] Help! Stuck with setting up (mysql this time)

[Jer-Ming Chia]

Hi Peter,

I had the same problem with the distribution that I downloaded from
sunfreeware, for the solaris 8.

I noticed that certain directories seemed to be misplaced or missing in the
tar package. After much frustrating tries, I decided to try the binary
distribution  mysql-3.23.52 from mysql.com and it worked.

hope this helps,
Jer-Ming

----- Original Message -----
From: "Peter Kos" <kos@rite.or.jp>
To: <kos@rite.or.jp>; <elia@fugu-sg.org>
Cc: <bioperl-pipeline@bioperl.org>
Sent: Thursday, August 29, 2002 9:14 AM
Subject: [Bioperl-pipeline] Help! Stuck with setting up (mysql this time)


> Hi all,
>
> Sorry, it should go perhaps to a mysql list, but I am afraid, that
> other problems will follow this one, so I ask you about this one too.
>
> > and then it's easier for us to help you
> > to setup a pipeline in that direction?
> >
> > Looking forward to discuss it further,
>
> I am dead. I have stuck in the middle of installing
> the necessary components for the bioperl-pipeline
>
> I work on a Sun (SunBlade) (Ultrasparc), Solaris8
>
> I have Perl and Bioperl. (I may surely need some more
> stuff for the pipeline, but that is for later.)
>
> I have installed DBI. Tests are OK, installed fine.
>
> I downloaded the binary distribution of mysql, and later,
> as I did not have any better idea, mysql-max too.
> Both were very easy to install. But none of them work.
> Or they do, just not for me.
>
> I ran the ./configure script, which then said that it does not need
> configuration, and also said how to start the server. I followed
> that,
> OK, the server started and immediately shut down without complaining.
> (message included below as TEXT1)
>
> [(By the way, if I run ./safe_mysqld from the mysql/bin dir, rather
> than
> /bin/safe_mysqld from the mysql dir, it complains that:
>
> "The file /usr/local/mysql/libexec/mysqld doesn't exist or is not
> executable
> Please do a cd to the mysql installation directory and restart
> this script from there as follows:
> /bin/safe_mysqld."
> which makes sense as there is nothing like .../libexec directory,
> and I do not know how I could have one, why and what to have in
> there.)]
>
>
> mysql-test-run worked nicely. It skipped gemini, isolation and raid
> tests,
> but otherwise it was perfect:
>
> "Ending Tests
> Shutting-down MySQL daemon
>
> Master shutdown finished
> Slave shutdown finished
> All 139 tests were successful."
>
>
> The reason why I am panicking is that I can not keep the daemon
> alive.
> I strongly suspect that the designers of the mysql may know something
> about mysql, that I don't.
> I hope, you too.
>
> For running run-all-tests in sql-bench, I need DBD, but for the
> 'make test'
> of DBD I need the server running, but again according to the text
> below,
> it just starts and ends for me.
>
> Although the 'configure' says that I do not need to configure
> anything,
> I tried to do that in lack of any better idea. And moreover since
> throughout
> hours of agony one of the manuals suggested to try the
> port (number whatever) via telnet, and that did not work either, and
> I am
> completely and fully unaware how to handle the ports.
>
> 'bench-init.pl' in the sql-bench directory "Can't locate /server-cfg
> in @INC"
> which really made me mad, as the corresponding line is
>
> require "$pwd/server-cfg" || die "Can't read Configuration file:
> $!\n";
>
> - where (although require) it should have looked to the current dir,
> where that damn file is smiling at me,
> - moreover the error message in this line is different from what I
> get
> (perhaps some built-in Perl message, rather than the 'die'-text,
> - and moreover I prepended the current directory to @INC as follows,
> and still
> had the error message as follows. (TEXT2)
> I guess that perhaps "$pwd" is empty, so it looks at the root dir.
> Well, whatever.
>
>
> SO, IN BRIEF,
>  could anyone tell me what on earth to do in order to keep the
> safe_mysqld alive?
>
> The text from ./configure is completely shameless. It kindly tells me
> how to
> start the MySQL daemon, and how to test it being up and functioning
> nicely,
> but nothing about why it immediately ends.
> Similarly all the installation instructions and other manuals that
> I've seen
> troubleshoot serious issues of .so and .h files but this problem is
> never mentioned.
>
> Your kind help would therefore be highly appreciated.
> Cheers
> Peter
>
> .................................................................
> .........
> Peter B. Kos,
> (RITE)
> E-mail: kos@rite.or.jp
>
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