Sour Milk

A co-worker has an HP xw8000 for a workstation. It runs XP, and if you leave XP going, it starts getting slower and such, so she rebooted it.

And it wouldn't start.



That's the beep she got. This is where I came in. I moved it, opened the case, unplugged it, made sure all the cards were in tight — the last time there was a problem with this box, it was a loose video card — and began to check the beep code index.

There's no entry for no beeps.

What am I supposed to do for no beeps? "Hey, guys? I have a problem, so I won't start. No, I won't tell you what the problem is."

So, I told the other tech guy.

He unplugged it and waited until the green light on the power supply went out. I am sure that happened in my picking up and moving, too. Then he plugged it in and started it.

And it started.

The co-worker wanted to know what the problem was, what she did to upset the silicon god on her desktop.

For the life of me, I can't understand what the problem was, much less explain it to someone else. Although, I think I have a start.

Other Broken Things in Ubuntu Koala

This is Gnome System Monitor. In an ugly pink punk tartan.

Thing is, it's usable, except it's not. I mean, I can right-click and I get a drop-down in some other indecipherable pattern. I can double-click where the angry pink tartan should have a menu and have it roll up like any other window. I just can't see it!

Any thoughts as to how to fix this?

Configuration: The Devil is in the Details

I work in a lab. The simple fact is that, in the 21st Century, all science is computer science, and that's especially true here. We have several computers whose entire purpose is to control scientific instruments and handle the data that comes from them. But we don't want the data to be on the instrument machine. We want it to be on the server.

This is where FTP, and especially the Perl module Net::FTP, come in. We try to keep it locked down, configured at the firewall so that only the server can FTP into the instrument and even then can only move instrument->server, not the other way around.

One specific machine was set up with Windows 2000 and the FileZilla FTP server. The software, we were told, wanted 2K, and so we ran with that. FileZilla was about the first Google result I hit when I searched on "windows ftp server", and I cannot say there was ever a point where I regretted using FileZilla for all my FTP needs.

Then there was a necessary upgrade that needed Windows XP. The machine had 2 HDs in it, so I installed XP on disc 2 and made it dual boot. And, since it was XP Pro, I had IIS already. I may have had it on the 2K, I never thought to check. Anyway, the machine now spends most of the time under XP. I have had to change the upload-and-munge script to handle the new, and I'm not sure how much is IIS-vs-FileZilla and how much is Instrument-Software 1.3 vs Instrument-Software 2.0.

Where the story threatens to become interesting is this: The person who runs on that instrument, she makes a CSV config. Normally, she copys it, changes it, and seemingly, as long as the Excel file was open, it wouldn't upload. This was the 2K and FZ behavior.

Windows XP and IIS, it seems, FTP anyway, no matter if the Excel file is still open. And I had to clean up after it because of it. Not a problem, to be sure, but something to be aware of.

Oz never gave nothin' to the Tin Man...

Tinman is the name of my Compaq Mini netbook. Twiki^* is the name I gave to my wife's netbook, which is an EeePC. Both, at this point, run Windows XP. Yeah, I'm the big Linux guy, but as a web developer, I find it useful to have a machine running Internet Explorer that I can test against.

We got the Mini with a deal with Sprint. We get the card Bill Kurtis has been pushing, which would allow someone to use the Internet when far away from wireless access points, using the Sprint cell network for data. It also provides good and useful GPS information like location and speed and the way to the closest Sprint store. I got a netbook out of the deal (yay) but I live in a house with Wi-Fi and work in a dank sub-basement with Wi-Fi and sufficient network cables. I don't find the need to check email much when I'm not either at work or at home. However, K spends her day running around a lot. It therefore makes reasonable sense for her to use it. So she asked me if she could have it.



Let me cut to the end, of the story, just for a moment. The dingus, once set up, is set up. You have to reinstall the interface software, sure, but anything you plug it into should be able to quickly get online, because by plugging it in you've done all you have to do to log onto the network.

Unless you have some sort of problem with your USB. Which Twiki seems to have.

* In the beginning of the Mystery Science Theater take on Catalina Caper, Joel has the bots say their prayers, even for Twiki. My eldest asked "Who is Twiki?" This is the description I gave.

There was a show in the late 70s and early 80s called Buck Rogers. There was a character whose name I don't recall, who was a hyperintelligent computer which takes the form of a of a blinged-out hubcap. Being a hubcab, that character cannot move, so there's Twiki, who looks like a cartoon seven-year-old with a bowl cut frozen in carbonite, who wears the blinged hubcap like Flavor Flav wears a clock.

This caused my son to laugh out loud.

I know the time, boieee

The installer comes with the Sprint card, and I have installed it four times. I have talked to the Sprint helpdesk. I have tried this process on three (3) computers ( Twiki, Tinman and Maria, named after the evil Maria from Metropolis ) and the problem comes up only on Twiki. Yeah, I have other Windows machines I can test against, sure. But the take-away seems that there's something wrong with K's machine.

Just had a thought. K might not be running as Admin. In general, that's good, but if she is, she can't install the drivers in the protected places and thus can't get networking going. I thought she was running with Admin privs, but I do not recall. Still, that's worth a look. ETA I checked, and she's running as Admin. It isn't that.

And the jQuery is just that simple!

$(document).ready(function(){
     $("legend").click(function(event){
          if ( $(this).parent().children('div').is('.hidden') ) {
              $(this).parent().children('div').removeClass('hidden') ;
              }
          else {
              $(this).parent().children('div').addClass('hidden') ;
              }
          });
      });

Except I think I will want an external link, so I'll have to add another level of parent(). But jQuery is hardly distinguishable from magic.

Investigating jQuery

So, you have a bunch of HTML elements. Let's say they're Fieldsets.

  
 x 
  XXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXX


  
 x 
  XXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXX


  
 x 
  XXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXX

Now, you want to be able to hide some of those fieldsets. You could make the legend clickable.

  
 x 
  XXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXX

hide_element() is dead easy. I do it in five lines. I could drop one if I wanted. Just a bit of stylesheet manipulation. But there's a problem. As written, that hides the fieldset for good. I really want to toggle. So, something must remain.

  
 x 
  
 XXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXX 

This is better, but you have to name every single fieldset. There should be a way to address everything anonymously. And there is. jQuery. Which I don't quite grok yet. But that's where my head is.

Noting Peculiarities ...

K's laptop decided it didn't have a camera anymore.

It did, of course. It is built onto the EeePC 900HA. But it claimed it didn't.

Took me 90 minutes of looking to find out that, hey, the BIOS turned it off.

If you look for hardware in the hardware list, and the BIOS turned it off, it doesn't show up.

But now it works. So, good night.

Exercising futility ...

Run within R, it works. Run from test_R.pl, it doesn't. Why?

jacoby@oz:~/Desktop$ cat test_R.pl 
#!/usr/bin/perl

use 5.010 ;
use strict ;
use warnings ;
use Carp ;
use Cwd ;
use File::Copy ;
use Statistics::R ;

my $cwd = getcwd ;

my $R = Statistics::R->new( ) ;
say 'starting R' ;
$R->startR ;

while (  ) {
    chomp ;
    my $line = $_ ;
    next if $line =~ m{^q}mx ;
    say $line ;
    $R->send( $line ) ;
    sleep 1;
    }

$R->stopR() ;
say 'stopped R' ;


__DATA__
png(file="~/Desktop/plot.png")
plot(pressure)
postscript(file="~/Desktop/plot.ps")
plot(pressure)
jpeg(file="~/Desktop/plot.jpg")
plot(pressure)
q("no")
jacoby@oz:~/Desktop$ R

R version 2.7.1 (2008-06-23)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> png(file="~/Desktop/plot.png")
> plot(pressure)
> postscript(file="~/Desktop/plot.ps")
> plot(pressure)
> jpeg(file="~/Desktop/plot.jpg")
> plot(pressure)
> q("no")
jacoby@oz:~/Desktop$ ./test_R.pl 
starting R
png(file="~/Desktop/plot.png")
plot(pressure)
postscript(file="~/Desktop/plot.ps")
plot(pressure)
jpeg(file="~/Desktop/plot.jpg")
plot(pressure)
stopped R
jacoby@oz:~/Desktop$ ls plot.*
plot.jpg  plot.png  plot.ps
jacoby@oz:~/Desktop$ twitter.pl "It works from R but not via Statistics::R. It does not make sense."
It works from R but not via Statistics::R. It does not make sense.
OK
jacoby@oz:~/Desktop$ 

Rage Taking Over ....

The current job is to create an Electronic Lab Notebook. Basically, you need to be able to access it via the web, you need to be able to link to images and import tables from Excel and the like. I started doing wiki on a UseMod wiki, so when I started rolling my own, I looked to UseMod, which was abandoned, and then to OddMuse. OddMuse has a few things I like. It's modular, it's Perl, and you don't have to use a whole host of odd modules and root access to make it work.

So, when it came time to make an Electronic Lab Notebook, I thought wiki. I thought OddMuse Wiki.

There's an add-on for tables. There's an add-on for simple image linking.

But....

The suggested WSYWIG editor is FCKeditor. And "fck!" is pretty much how I'm feeling about said editor. Because it isn't writing acceptable output, and I do not for the life of me know why.

Either that, or it isn't interpreting the saved output once the page is rendered again.

Edited To Add: That was it. The outputted wiki-text was incompatable with the wiki, so by using a module that speaks that kind of output, I got it to work. Yay me.

Specifically, I used the Markup.pl extension, in case that helps someone.


Edited To Add: Using Markup.pl kills tables.

Blowing it again ...

Or perhaps still.

Fuse went right as I walked through the door. So, I spent my time wondering how I was going to get anything done, rather than getting something done.

Sometimes, I think I should get a laptop.

Then again, you don't get 2560x1024 on a laptop.

So, this means I did nothing today.

"Nothing" include "not reviewing Beautiful Code".

However, I did read some Bioinformatics and Computational Biology Solutions using R and Bioconductor. Which is pretty much what I do here. But I couldn't try any examples, which sucks.