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

[Peter Kos]

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