Random Acts of Science

Spotify for Windows (for Linux)

2011-09-20T19:26:00.001-04:00

So Spotify is a pretty good way to listen to new albums...as long as I know the albums exist.

It turns out that Wine can run the Windows version of Spotify from either my 32-bit or 64-bit installations of Slackware Linux. Spotify can't read any of my .ogg files, but if the point is to hear new albums, then maybe that bug isn't too terrible.

The interface between Spotify and the dreaded Facebook does not work, but why would anyone care what nonsense streams from my computer anyway, right?

In the style of Twitter

2010-11-24T02:41:00.001-05:00

Slackintosh-current on a G5 iMac

Debian 5.0 for PPC is elegant and easy to use, and 6.0 will probably be even better once the installer is fixed. I wanted a more minimal system, so I returned to Slackintosh, even though it is only semi-maintained. The -current version of Slackintosh still gets updates, however. So here is how to get Slackintosh on a G5 iMac:

Partition the disk, and separate the /boot partition, so that it can be accessed by multiple Linux installations (format this partition as ext2). Give yourself at least three additional partitions of around 5 GB to work with. My disk looked like this: Partition Map, NewWorld bootblock, HFS Mac OS X installation, swap, ext2 /boot, JFS for Crux root, ext3 for initial Slackintosh root, JFS for future Slackintosh root.

So: one partition is for a temporary Slackintosh install, and can be small; another is for a chroot environment (CruxPPC), and can also be small; the last will be the long-term home for Slackintosh. Add extra partitions for /usr/local, /home, etc. as desired.

First install CruxPPC to a small partition (3 GB is plenty). Crux provides a convenient environment for building 64-bit kernels, which you will need to boot a G5. The shipped kernel (g5ppc64) for Slackintosh 12.1 works, but it is old (2.6.16?) and lacks support for several file systems.

Follow the installation instructions for Crux. Build a new kernel under Crux with whatever options you wantfilesystems, crypto, SMP support, etc. Do not count on any modules, because the modules that ship with Slackintosh (and the ones you could build with Slackintosh) are 32-bit, and so won't load on a G5. The kernel configuration under /proc/config.gz will boot as-is (copy it to /usr/src/linux-*/, gunzip it and rename it to .config), but you may wish to add more features. You can even download up-to-date kernel source and make a super-new kernel. Install the new kernel and verify that CruxPPC boots properly.

Install Slackintosh 12.1 to a different partition, but skip installation of the yaboot bootloader. I later migrated this installation to a JFS-formatted partition, but for now, just get an installation onto the hard drive. Instead of configuring yaboot from Slackintosh, reboot into CruxPPC.

Now is the tricky part. At this point, the computer can only boot into CruxPPC Linux (and possibly Mac OS, if applicable). As a test, edit /etc/yaboot.conf under CruxPPC to boot the new Crux kernel with the temporary Slackintosh installation as root; run ybin -v and boot into Slackintosh with the CruxPPC kernel. If this step works, migrate the temporary installation by mounting the other partition and umask 000 as root, then running cp -a /$dir /mnt/<mount point>/ for each $dir in the root (

) directory. The Slackware website has useful information on migrating an installation. Do not forget to create /proc, /boot, etc. directories on the new drive.

Reboot into Crux, add the new drive to /etc/yaboot.conf, and run ybin -v (daring souls can do this step from the temporary install of Slackintosh without rebooting). Reboot into the Slackintosh on the permanent partition with the new kernel. If everything has worked so far, then there is probably no need ever to boot into Crux again, but I recommend keeping it around as a chroot environment to update the kernel: remember that Slackintosh builds 32-bit binaries for userspace applications, and Crux builds 64-bit binaries like the kernel.

The Slackintosh website and changelog provide some help on upgrading from Slackintosh-12.1 to Slackintosh-current. I recommend the upgrade, but it requires rsyncing and a few GB of patience. With or without the update to -current, Slackintosh is quicker than Crux more powerful than Debian. Slack also has better logos.

For good measure

2010-02-28T19:34:00.001-05:00

I did attempt FreeBSD; it did not boot.

Goddamn it, BSD

2010-02-27T17:45:00.001-05:00

I can't help but quit you. I want to admire how BSD works and fits together, but damn it, shit doesn't work. True believers can tell me that I don't know what I'm doing, and perhaps they're right, but I've now installed OpenBSD three times and NetBSD once. NetBSD is okay, but not superior to Linux on my laptop, and not usable on this computer; OpenBSD is unreliable on the laptop and unpleasant to use on this iMac G5. From what I can gather, no BSD is appropriate for my netbook. Quo fucking vadis? I want to try this OS, but I can't justify using it if it is obviously inferior.

Inspired logon screen

2010-01-30T14:17:00.001-05:00

go6.net, freenet6.com IPv6 solution at last!

2009-11-04T12:05:00.001-05:00

Yes!

I've been bragging about how I turned a g5 iMac into a Debian server, thanks to the good people here, but my tunnel to the IPv6 internet kept dying (a common problem). At least two weeks passed while I struggled with crontab and generally fumbled towards a solution.

The main problem, I now realize, is first, that the connection is fragile and occasionally drops (obviously). To automatically reopen the connection, I added the following to root's crontab:

0,5,10,15,20,25,30,35,40,45,50,55
  * * * * /bin/pidof gw6c >/dev/null 2>&1 || /etc/network/if-pre-up.d/gw6c

Unfortunately, the script to reopen the tunnel always tried to ask a question: "do you want to add some server to your configured list, blah blah blah?" Since I was nowhere to be found, the script kept asking over and over, got no response, filled up my inbox with error messages, and finally died without reopening the connection.

The fix was to add the line always_use_same_server=yes the the gw6c.conf file. The script asks no questions, and the connection is now reasonably stable. Now I can get all all my files from anywhere.

Toxic cloud computing (ha!)

2009-11-03T11:08:00.005-05:00

The next big thing on the internet: cloud computing, even though it was the first big thing. Weren't MUDS, OLGA, and timesharing computers "cloud computing," anyway?

Now cloud computing means Google and Microsoft Azure and Amazon's computation service, or whatever. I am sure that for some companies, these solutions make sense. But wouldn't it suck if your remote data got hacked? What about that time Google Mail crashed?

Everything has its risks. Still, I am puzzled. Computing power is cheap and only getting cheaper. Plenty of people carry phones with enough space to fit every email they'll ever write. Why centralize our data? Unneeded cloud computing invites a security nightmare.

Killer app for IPv6 internet?

2009-11-01T14:53:00.007-05:00

You may have other things on your mind right now, but we are running out of internet addresses (a.k.a., version 4). Maybe it isn't really such a problem—ISPs have been pretty blase' about the whole thing. More likely, no-one is switching to new addresses (version 6), mostly because no-one knows that there is a problem, since just about everyone who cares about the internet (in its current form) already has a access through an old address.

But now hear this: non-Latin characters will soon be available to name your website. That's a lot of potential websites (hello, Iranian protestors!); where will we fit them all?

Ho, ho—IPv6 addresses will ride to the rescue of our UTF-8 brothers and sisters. How many years til the Westerners' original web becomes a parochial backwater?

I don't quite understand IPv6

2009-08-25T23:16:00.001-04:00

It sure would be cool to have a globally accessible IPv6 address on my main home computer, but the good folks at go6.net (formerly freenet6.net, or something) don't seem to have quite what I need.

My service provider at home, Time Warner/RoadRunner is not so friendly to IPv6 internet connectivity. I set up the proper tunnel and firewalls, and I can ssh over IPv6, but the connection is slow and short lived. I'll learn tomorrow whether a last-minute tweak to the firewall makes any difference...but my guess is that either go6.net or IPv6 in general is not ready for this jelly.

NetBSD.

2009-07-16T22:19:00.001-04:00

It is workable. Coming from the Linux world, I found the first steps disorienting. I am posting via wireless, and even the sound system is in pretty good shape (although I haven't figured out how to get output from the headphone jack).

Whether compiling all this stuff was really worth it, I can't quite say. Dependency resolution does have its place, though. I look forward to a version of NetBSD (or any BSD) with decent support for that hoary G5 PowerPC Macintosh.

Bolt-Bus lets me have all my toys

2009-06-20T08:42:00.001-04:00

Be sure to use secure connections when working on an open network, kids!

OpenBSD lives

2009-06-18T00:09:00.001-04:00

Looks like I got it working-on x86_64, not ppc64, but whatever. It's all pretty much the same anyway.

To BSD? Not to BSD.

2009-05-15T22:14:00.001-04:00

What a disaster.

I thought I was hardcore, and I wanted to try BSD, the better-than-Linux Ur-Open-Source alternative, but I failed. (More accurately, the fact that I have an iMac G5 test machine failed me.)

FreeBSD is the most popular BSD, and therefore lies beneath my consideration. Turns out that FreeBSD does not support this computer anyway, so my elitism was accidentally justified.

NetBSD prides itself on being endlessly portable to a wide variety of processors, and such flexibility appeals to me a lot. In zanier times, I even tried to get a Slackware laptop running with the NetBSD package management, but that configuration was approximately as painful as Gentoo Linux. So I stuck with Slackware on that machine.

Ha ha! Despite running on a wide assortment of pocket watches, NetBSD does not run on this particular PowerPC (i.e., non-Intel) Macintosh. Fine. Everyone says that the truly hardcore only use ...

OpenBSD, noted for impressively oppressive security and for being the only BSD to support this computer! So I have an excuse to use "the difficult one" after all, since the other BSDs can't run on this machine. Grand.

The installation went smoothly enough, although the software mirrors tend to call these machines macppc for installation, but then label all the auxilliarly sofware in the ports system as powerpc. I was pleased how quickly packages installed over the network, and how compact even all of GNOME was.

Oh, except for two gigantic problems: OpenBSD ran slower than OS X (or Debian 5.0), and the fan made horrible noises. Online documentation hinted that OpenBSD developers new about the fan control noise in the G5, but apparently they figured that cranking the fan to the maximum speed was the safest-cum-easiest solution.

Debian it is, then. At least until Slackintosh ships with a 64-bit kernel that supports the JFS file system.

iTunes stares into the abyss

2009-03-20T23:04:00.001-04:00

I had to quit iTunes months ago, because some update had rendered it completely unusable. Of late, a subsequent update has mostly fixed things, but it's come too late for me: I have abandoned iTunes (which I never much liked) for Vox, which at least supports the Ogg Vorbis format.

Vox does not allow playlists, though. The website promises real playlists soon, but there is a simple solution: create a new folder and fill it with symbolic links to your music.

localhost:~/Music/Voxlinks daWreck$ for file in
~/Music/*/*.{wmv,ogg,mp3} ; do ln -s "$file" $(basename $file | sed
's/ /_/g'); done

I needed several different layers of /*/ to make all the needed links, but it worked just fine, and OS X politely declined to make any links that already existed because of duplicate files or whatever. Die, iTunes, die.

Props to Debian 5.0

2009-02-23T22:14:00.001-05:00

Yeah, sure, I love the Slackware, but the sad fact is that the Slackintosh port to powerpc (nee ppc) does not deal well with 64-bit machines. I wanted JFS support in a 64-bit kernel, and Slackintosh did not deliver. The boot setup failed, too.

Now that I have a working boot sequence, I suppose I could re-attempt Slackintosh, but Debian 5.0 is working pretty well for me so far. In the last year or so, then, I've infected 3 computers with Slackware, two with Slamd64 (64-bit biarch Slackware port-good stuff), one with Ubuntu (it was a request), and one with Debian 5.0.

Good times.

Slackware Linux and baroque partitioning

2009-01-17T14:48:00.001-05:00

I like Linux. For my computers I especially like Slackware Linux. I have also used Puppy Linux, PCLinuxOS (from 0.92), Ubuntu (from 5.10), OpenSuSE (10.1 and 10.2), and Ututo/Gentoo (with paludis). I wandered a bit before settling on Slackware.

I learned a lot while wandering, and I concluded that to become comfortable in Linux requires a fast internet connection and the option of trying different flavors. To have Windows or a Mac OS to fall back on is also helpful.

Here is the problem: simply installing Linux requires . . . experimentation. Becoming a proficient user needs even more research and more trial-and-error. A bumpy installation can be terribly demoralizing, and a naive partitioning scheme complicates trying anything new.

So, I can only recommend a new plunge Linux to two people:

The victim of a Linux zealot, who will watch as said zealot performs the installation and setup
The patient tinkerer with a fast connection for the main computer and an extra deskop box to try Linux

Anyone else ought at least to read the rest of this post, but you have been warned.

Slackware Linux is somewhat daunting to install. The process is aggressively text-only, and the hard drive must be partitioned (with fdisk or cfdisk) before running the setup script. To make up for these minor challenges, the Slackware installer provides more control and transparency than Ubuntu or OpenSuSE. I easily installed Slackware 12.2 onto a Pentium IV with 512 MB memory that resisted the other two distributions.

Two issues complicated the last few times I've installed Linux (Slackware or Ubuntu) for people: one because of Windows, and another related (I think) to the manufacturers of the computers.

First, impatient users get into the habit of shutting down Windows "the hard way," by holding the power button. Windows duly flags the native NTFS file system on the hard disk, and repartitioning programs then choke. The solution to this problem is to reboot Windows and shutdown nicely, and perhaps to run CHKDSK if prompted.

The second issue is related to Windows, but has more to do with manufacturers' "Recovery" partitions, which are usually invisible to Windows. I do not understand how these work, so I never mess with them. However, installing a new operating system requires new partitions, and there are constraints on where those partitions can go. For example, Windows XP must be on a primary partition on the main boot device, and only three primary partitions are allowed on each physical disk.

The point is that the presence or absence of a recovery partition affects where everything else will go, and graphical partitioners are not the most reliable. I have tried to write a serious set of rules for partitioning the way I like it, but some guidelines are the best I can do:

On machines that also run Windows, put a medium-large partition for data right after the Windows partition - I format this partition FAT32 (vfat), and usually mount it at /data on the Linux side with the options user,users,rw. Users can read from or write to this partition from any OS. It's not very secure, but extremely helpful while switching from Windows to Linux. If you require more security, encrypt the partition with Truecrypt
The entire Linux installation on one partition is the simplest solution, but not the best - Simplify future upgrades or reinstallations by partitioning intelligently
In general, I like to format partitions as JFS - No deep reasons. The performance of JFS, XFS, and ReiserFS are all excellent (I'm told), but ReiserFS has an uncertain future, and XFS seems slighly less reliable than JFS.
Always put /home on its own partition, or as a symlink to /usr/local/home -
Make separate partitions for / and /usr/local - Upgrades are then much easier
10 GB is plenty for the / partition, and 20 GB can fit the kitchen sink - This computer (no KDE, GNOME, or Xfce) uses less than 4 GB of 5.5 GB on the / partition. For my parents, I barely filled 10 GB with all of Slackware 12.1 and all of GnomeSlackBuild
If the hard disk is truly gigantic, you might as well keep /home and /usr/local on separate partitions
Make /usr/src and /opt symlinks to /usr/local/src and /usr/local/opt - As ever, for easier upgrades and reinstallations without losing data or compiled programs
Make /boot a separate partition of 50-100 MB - For extra security, format this partition ext2 and put the option noauto in the /etc/fstab file
Modern computers probably require no swap partition, but put one next to a partition like / or /usr/local, so you can delete it and expand into it if desired
Servers probably deserve separate /tmp and /var partitions - Perhaps of 100-1000 MB is size, and also for security reasons, but I have not worked seriously on a server

I have rarely partitioned two disks the same way, and I am often uncomfortable recommending Linux as a result. Generic solutions break and are difficult to upgrade; complicated schemes are painful to explain to a new user. Unless you are vert patient or willing to get a lot of help, Linux is probably not worth it.

Upgrade misery

2008-10-13T15:28:00.001-04:00

I have learned my lesson.

After many happy months with Slackware 12.0, I grew jealous of the pretty bootscreen (idiot) with 12.1, and I tried to upgrade my hand-me down Toshiba P4 via Slackpkg. It was a disaster---the internet and (especially) Emacs were hopelessly slow, and several GTK-based programs did not work.

On the bright side, I resurrected the computer with a fresh install of 12.1, and everything is running quickly again (except Xe, but I might be better off that way). The best part about the new regime is my new partitioning scheme:

/dev/hda1 (not mounted; /usr/local from the old install) (12 GB)
/dev/hda2 /usr/local jfs  defaults 1 2 (10 GB)
#/dev/hda3 /boot      ext2 defaults 1 2 (not mounted) (50 MB)
/dev/hda5 swap       swap defaults 0 0 (1 GB)
/dev/hda6 /          jfs  defaults 1 1 (6 GB)

For one thing, I am now using JFS filesystem instead of ReiserFS, which is no longer cool. More importantly, the next time I break everything, all I need to do is reinstall to the sixth partition without touching anything else. All programs and files for this computer are on /usr/local. The directories /home, /opt, and /usr/src symbolically link to /usr/local/home, /usr/local/opt, and /usr/local/src, and only official Slackware packages install to /usr (via ./configure). Everything I compile gets installed to /usr/local, although I've kept a fair amount of extra space on the root (/) partition, just in case.

Facebook mobile --- yes.

2008-09-23T15:02:00.001-04:00

I swear that I am not addicted to Facebook, but I am relieved finally to have a way to post to Facebook from Emacs. I had tried to get facebook.el, a rather obscure application to work, but clearly the secret is simply to login here.

This computer lacks cURL?

2008-09-23T13:57:00.001-04:00

Apparently it did. Now cURL is in effect, and I presume that blogging with g-client works now.

Mobile Facebook to the rescue

2008-09-23T09:01:00.001-04:00

And I'll write more about it if this post works.

FlashBlock be damned.

2008-07-07T16:04:00.001-04:00

A follow-up to my months-old post below on stopping pop-up dialogs in 64-bit browsers:

Move libnullplugin.so out of the plugins folder. I learned that months ago, but I had forgot about it until updating Seamonkey.

Unsent letter from 2006

2008-07-01T15:59:00.001-04:00

Russ (one of the great figures in my life) made fun of me about ten years ago for not building my own computer. I think it was right about the time that I bought the Micron. Russ had already long been a hardcore geek--I recently wrote to you about his internet adventures before there was much of an internet out there.

So, anyway--I put a computer together today. It was pretty fun.

I know you already managed this yourself--at least, you figured out the hard part, which is getting a new hard drive in there. I found some slow old thing, jacked it up with all the spare parts I could find, and started installing some badassery on it. The plan is to make it somewhat useful for science in the near future--we'll see.

From albahaca

2008-06-30T22:08:00.001-04:00

Are we beginning to get the hang of this? I sure do not understand what dependency I'm missing on my remote machine, but at least I can set up g-client quickly with any local installation of emacs. BIG HINT: use emacs-22 at least, or run around looking for time-date.el and other bits of emacs-lisp code.

Think remote, post local

2008-06-30T16:08:00.001-04:00

It looks like I cannot post to blogger from a remote account. Posting to Wordpress remotely was easy.

del.icio.us and emacs

2008-06-30T14:14:00.005-04:00

Posting directly to del.icio.us from emacs is pretty cool. Some quick changes to dp.pl make it even better:

#!/usr/bin/perl
use strict;
use lib "/path/to/perlmodule/dependencies";
use lib "/path/to/other/dependencies";
use Net::Delicious;
use Log::Dispatch::Screen;
my ($url,$dsc,$notes,$tag) = @ARGV;
my $USER='your_del.icio.us_name';
my $PASSWORD='your_del.icio.us_password';
die "use: dp.pl url title notes tag" unless (defined($tag));
my $del = Net::Delicious->new({'user'=>$USER,'pswd'=>$PASSWORD});
my $result = $del->add_post({'url'=>$url,
                             'description'=>$dsc,
        'extended'=>$notes,
                             'tags'=>$tag,
                             'shared'=>'yes'});
die "post failed\n" unless $result;
1;

Then, slip the following into .emacs:

(defun delicious-post-url ()
  (interactive)
  (if (null (w3m-anchor))
      (message "no anchor at point")
    (let ((url (w3m-anchor))
          (title (buffer-substring-no-properties
                  (previous-single-property-change (1+ (point)) 'w3m-href-anchor)
                  (next-single-property-change (point) 'w3m-href-anchor))))
      (if (w3m-url-valid url)
          (progn
     (setq delicious-notes (read-string "post notes: "))
            (setq delicious-tags (read-string "post tags: "))
            (setq delicious-cmd (concat "~/bin/dp.pl \"" url 
                                        "\" \"" title 
     "\" \"" delicious-notes
                                        "\" \"" delicious-tags "\""))
            (shell-command (concat delicious-cmd)))
        (message "no URL at point!")))))

All code only slightly modified from here.

Yahoo Pipes

2008-06-25T11:28:00.003-04:00

Here's an interesting idea: combine several RSS feeds into one, and then subscribe to that one. The interface is strange, and most people interested in doing this could probably figure out how to do it themselves, but after some struggling, it seems like a sensible way to aggregate blogs on different topics for submission to a certain website.

NoScript Extension

2008-04-16T11:59:00.002-04:00

Sometimes, I use a 64-bit operating system (Slamd64, that is), and there is no good Flash option for me. Flash and Shockwave are usually unneeded distractions, so I don't mind.

Alas, sometimes I visit a webpage that features the hated Flash. The Flashblock extension largely solves the problem, but I do sometimes have to tell the browser not to download Shockwave or whatever else I don't (can't) have.

So I got greedy, and I tried to install NoScript, which I knew worked well on Firefox, and thereby prevent those annoying dialogs in Seamonkey

Uh, no. Had to clean out all of my Mozilla settings (in .mozilla/) to get Seamonkey working again at all. Now I am back to annoying dialogs that I can never satisfy, plus I've lost my installed extensions and whatnot. *Pthbbttt*

Back to Slack

2008-04-05T11:36:00.001-04:00

OS X lets me do what I want on my Lady Friend's computer, but over here it's strictly Slackware.

Nothing to do . . .

2007-10-23T23:04:00.001-04:00

. . . and too many ways to do it. Does this post through Tor (via curl)? We'll see.

Getting out of my way

2007-10-15T20:37:00.001-04:00

Today I got out of my own way by drinking a couple of beers. My productivity (post-alcohol) far outclassed that of earlier in the day. I fretted through the morning. By evening, though, I had got out of my own way. Now I can get something done. (And I dig music.)

Please, Financial Times

2007-10-14T21:02:00.001-04:00

Don't give in! Don't shrink your pages! The New York Times looks ill (in a bad way), and the Wall Street Journal looks more like B-school USA Today (I mean, uh, Investor's Business Daily) every day. Fight! FIGHT!

(As far as I know, the FT is safe and sound and not in danger of getting ugly. To be safe, though: buy a copy today. Even Noam digs it. I resubscribed.)

Little helpers

2007-10-14T16:19:00.001-04:00

Some of these installed with fink, others with darwinports. Here I present the definitive list of my favorite open-source software for making a Macintosh into an acceptable machine:

Oroborus - Window manager for XDarwin; can't do much without one
Sylpheed - my mail client of choice
Liferea - RSS reader to keep track of news
Easytag - For tagging .ogg files that I ripped with OggDrop. Using .ogg files on a Mac is mighty annoying.
Epiphany - my favorite web browser. I hear this preference is strange.
Emacs-gtk - Aquamacs is okay, I guess, but I prefer GNU.
emacs-w3m - Text-mode web-browser from inside of emacs. Extra nerdy.
Pybliographer - For managing TeX/LaTeX/BibTeX bibliographies. Not needed if there's a decent Emacs to be found, but easy to use

I also brought my .emacs file and .emac.d folder from my Linux computers; the former worked with only minor changes. As noted below, I needed a .xmodmap file to map the Alt keys on the Mac keyboard to Meta for use in Emacs.

EDIT 15/10/2007 11h00: Also need Bogofilter, without which my work email is hopeless

Something like victory

2007-10-14T13:06:00.000-04:00

In this file, I would like to create a number of natural line breaks, which I will then make go away by some simple command. I hope to be able to i) compose text with line breaks, then ii) run a script on that text to make it postable through a Blogger API (or something), even though I do not remember what API stands for.

Also: I'd like to preserve double line breaks, as occurs between this fake paragraph and the previous one.

#!/bin/sh # txt2blog.sh - translates auto-filled plain text (possibly with hyperlinks) into a single, blog-ready line with (angle-bracket p angle-bracket) tags and everything basename=$(echo $1 | sed 's/\..*//') echo "Basename of $1 is $basename" echo "Removing /tmp/$basename.txt" rm /tmp/$basename.txt echo "Creating /tmp/$basename.txt" touch /tmp/$basename.txt echo "(angle-bracket p angle-bracket)" >> /tmp/$basename.txt cat $1 >> /tmp/$basename.txt echo "(angle-bracket slash p angle-bracket)" >> /tmp/$basename.txt cat /tmp/$basename.txt | sed 's/^$/(backslash angle-bracket backslash slash p backslash angle-bracket backslash angle-bracket p backslash angle-bracket)/g' | while read line ; do echo -n "$line " ; done | sed 's/(backslash angle-bracket p backslash angle-bracket [backslash angle-bracket backslash slash p backslash angle-bracket backslash angle-bracket p backslash angle-bracket]+/backslash angle-bracket p backslash angle-bracket/g' > $basename.blog echo "Here is the blog-ready file:" echo "" cat $basename.blog

That will do for now.

I think we've got it.

2007-10-14T01:24:00.001-04:00

Yes! Put (add-hook 'tex-mode-hook 'turn-on-auto-fill) in .emacs, so that I can write happily in LaTeX, but leave ugly line breaks out of whatever games I play while posting to blogger. Productive Saturday.

The final straw

2007-10-14T00:39:00.001-04:00

It comes down to this: I have abandoned auto-fill-mode on this computer, and I fully expect gblogger-mode to work properly now. It's not such a big deal; I can add auto-fill-mode as a tex-mode-hook. You've won this round-but I'm ready to write now, with no more futzing.

Ok, that didn't do it

2007-10-13T21:13:00.001-04:00

But maybe if I sneak on into to customize-variables and do a little magic there, maybe then I'll have a sufficiently customized xsltproc . . . but I doubt it.

But can I choose my stylesheet?

2007-10-13T21:10:00.001-04:00

Well, my guess is that I can't; still, I have now edited g-utils.el to call

xsltprog
        betteratom.css

instead of just xsltprog, but I fully expect nothing but a mess.

I am trying to surrender

2007-10-13T21:02:00.001-04:00

Since my last effort was a failure, I have been trying (and still failing) to turn off auto-fill-mode in sgml-mode/gblogger-mode, but I am not having much luck. Semi accidentally, I might have found the proper wat to switch stylesheets; let's see if the audience notices the difference.

Now I'm really screwing

2007-10-13T20:51:00.001-04:00

around with things I do not understand-I found the css stylesheet that gblogger.el runs each post through; I saved it locally and removed the phrase convertLineBreaks, then I switched the call to atom-view.xsl to hit my new file instead, which (in turn-I hope) will call the local stylesheet. Assuming approximately 74581905 contingencies work the way I want, maybe this post will look better.

Now I'm really screwing

2007-10-13T20:50:00.001-04:00

What if

2007-10-13T20:23:00.001-04:00

What if (he grumbled), the whole problem is that I've been adding sgml-mode-hooks left and right, when what I really need to do is add a gblogger-mode-hook, since everything that I do to post here is in (surprise) gblogger-mode? I'd be a bit annoyed that it took so long to get it right, but at least there would be some semblance of sanity to it all. And now, I shall add a linkto another sucker's webpage.

What if

2007-10-13T20:20:00.001-04:00

What if

2007-10-13T20:18:00.001-04:00

I guess I just can't stop

2007-10-13T20:11:00.001-04:00

At this point, I'll settle for a situation where my text does not suffer a needless linebreak in the middle of a tag. Even thought this advice suggests that my version of Emacs should not commit these unsightly gaffes, it does. So I have inserted the Lisp that they suggest into my .emacs file. Hopeful? No.

Desperation sets in

2007-10-13T19:27:00.001-04:00

I appear to be the only person the internet with this problem: gblogger.el adds tons of irritating line breaks when I compose in auto-fill-mode, even though sgml-mode allegedly ignores such nonsense. In this post, I attempt to fix things by activating sgml xml mode in customize-group : sgml, but my hopes are not high.

Desperation sets in

2007-10-13T19:25:00.001-04:00

sgml xml
        mode

in customize-group : sgml, but my hopes are not high.

Still struggling

2007-10-13T18:16:00.001-04:00

Sure, I could always forget about using auto-fill-mode, and simply type-type away in one gigantic line every post, or I could stop worrying about making the whitespace in these posts look acceptable, but my entire world rests on being able to vomit out my techie/geeky thoughts without having to resort to a web browser, and still have everything look neat. Save me, Emacs-you're my only hope. Memo to self: two hyphens do not an en-dash make. I cribbed some suggestions from this site, but I doubt that this try will look any more acceptable. *sigh*

Still struggling

2007-10-13T18:13:00.001-04:00

Coming to terms with OS X

2007-10-13T13:12:00.001-04:00

I have hated before, but it's beginning to look like OS X is quite totally acceptable--as long as one registers as a "Mac developer" (HA!) and juices up the computer with Linux applications from fink and darwinports.org

There's also a good chance that a bit of EmacsLisp modified from here has finally solved my problems with sgml-mode putting ugly line-breaks into my posts:

(defun local-sgml-mode-hook ()
  (setq indent-tabs-mode nil
 next-line-add-newlines nil
 standard-indent 4
 sgml-indent-data t)
  (auto-fill-mode t))
(add-hook 'sgml-mode-hook
   '(lambda () (local-sgml-mode-hook)))

Also: fooling around in GTK Emacs (Not AquaMacs--*pthbbttt*) was a chore until I learned this neat trick:

put these lines in a file called .xmodmap:

keysym Alt_R = Meta_R
add Mod2 = Meta_R

Now add this line to .profile:

 xmodmap ~/.xmodmap

Brilliant!

UPDATE: No, had to go back and fix this via the web. Still: almost there. Emacs will do what I want, as long as I ask properly

jpeg problems (mostly) SOLVED

2007-10-08T15:09:00.001-04:00

I still cannot view inline images with emacs-w3m, but that is probably just as well. The important problem was that many of my programs--including Liferea and Eye of Gnome, but not including Epiphany or Gimp--could not open jpeg files. I cannot find the forums post that saved me here, but the problem went away after adding tiff to the first line (*/*) of /etc/paludis/use.conf, and re-compiling gtk+. I already had the jpeg USE flag activated, but that had never solved the problem. (I like some Gnome programs, though I run Enlightenment. *pthbbttt*)

is not a symbolic link SOLVED

2007-10-08T14:59:00.001-04:00

Another minor issue is finally fixed. A number of *.so.* files--some in /usr/lib, most in /usr/local/lib--got flagged as not a symbolic link during compilation. Well, I finally got around to looking at these files. It turns out that in each case, the not a symbolic link file was identical to another file in the same directory with a slightly longer name--for example, libORBit.so.3 and libORBit.so.3.0.1, or something like that. I moved the former file to a safe place (in case it was hard-linked or something else that might cause trouble if deleted), then created a symlink: sudo ln -s /usr/local/lib/libORBit.so.3.0.1 /usr/local/lib/libORBit.so.3. And now all is beautiful. ALSO: Often during compilation, gcc vomits out a warning that [FILENAME] seems to be moved; as long as this doesn't hurt the compilation (it usually does not), then this is an ignorable warning due to a minor bug in libtool or gcc. Cool.

docbook-sgml-utils compile error SOLVED

2007-10-07T14:35:00.001-04:00

Egad, it took forever to fix this problem. I had seen lots of

jade:../../doc/docbook-utils.sgml:1:55:W: cannot generate system identifier for public text "-//OASIS//DTD DocBook V3.1//EN"

While trying to compile docbook-sgml-utils. The package in question does not seem to be required for much, so I usually just skipped it and updated the rest of my (Ututo/Gentoo) system with paludis. The problem turns out that I was missing part of '=app-text/docbook-sgml-dtd-3.1-r3::gentoo', so a quick paludis -i '=app-text/docbook-sgml-dtd-3.1-r3::gentoo', followed by paludis -i docbook-sgml-utils finally solved my problem. It sure did take forever, though. I found other references to this problem, but no straight-forward solution.

Linuxified

2007-09-29T20:40:00.001-04:00

The ugly truth, I think, is that Linux is mostly a huge waste of time. It is not a waste of time for me, of course (at least, not anymore); now that I can use Linux reasonably well (only took me a year and a half), I find Linux superior for text processing. Learning how to use teTeX and emacs were brilliant decisions. I probably didn't need to take the detour into the arcane worlds of Slackware and Ututo/Gentoo, but I regret nothing. I even suspect that friendlier distributions would not have forced me to learn some useful bash scripting so soon. The more important question, I think, is who should switch to Linux. Answer: Almost no-one. Work in an office? Windows is probably the only way to roll, unless you are unusually interested in computers. Virus problem? Use a Macintosh (though I don't like them). I mean, automated text processing is wonderful for building websites, and GnuPG is fun, if not terribly necessary (for me). Normal productivity requires old, solid technology. YouTube and friends are time thieves, just like TV, but if the people want them, then the people are better off without Linux. Bottom line: want to learn about computers? Use Linux. Want to build or revive a cheap (well below $100) computer? Use Linux. Anyone with sufficiently simple requirements for computing (web, mail, word processing, playing music) will do fine with a friendly Linux, but there is no compelling reason to switch. Think Microsoft is evil? Read a book.

YES.

2007-09-28T13:32:00.001-04:00

Everything is in place except the content. Ho ho ho.

Round and round

2007-09-28T13:28:00.001-04:00

and round and round we go.

Well?

2007-09-28T13:26:00.001-04:00

Now we have something a bit prettier. I suspect that I'll line-wrap with significant wackness, however.

Well?

2007-09-28T13:25:00.003-04:00

Now we have something a bit prettier. I suspect that I'll line-wrap with significant wackness, however.

Well?

2007-09-28T13:25:00.001-04:00

Now we have something a bit prettier. I suspect that I'll line-wrap with significant wackness, however.

Finite regress

2007-09-28T13:21:00.001-04:00

Now we look tighter . . . maybe.

Direct to you

2007-09-28T13:15:00.001-04:00

I reckon that the fact I am still testing things out over here, despite the fact that this blog has been up for years, is probably a bad sign.

Damn shame

2007-09-28T13:01:00.001-04:00

It is a damn shame that gblogger/g-client is so inferior to weblogger.el. I rather prefer the latter, but sure can't use it with Blogger.

Damn shame

2007-09-28T13:00:00.001-04:00

It is a damn shame that gblogger/g-client is so inferior to weblogger.el.

My first useful, original script

2007-07-23T20:07:00.001-04:00

LaTeX is wonderful, but it clutters up my folders with .aux, .bbl, and other files. So I wrote this script for one-part articles:

#!/bin/bash

# q-tex - takes a .tex file, copies it to a hidden directory, runs
# pdflatex (and later, bibtex), and writes a symlink to the .pdf in
# the original directory.

workdir=".q-tex"

if [ $# -eq 0 ] ; then
    echo "Usage: $0 basefilename (no .tex extension)" >&2
    exit 1
fi

if [ $(echo $1 | grep '.tex') ] ; then
    echo "Usage: 0$ basefilename (OMIT .tex EXTENSION)"
fi

basefilename="$(echo $1 | sed 's/.tex$//g')"

if [ ! -d $workdir ] ; then
    echo "q-tex directory does not exist yet; creating it."
    mkdir .q-tex
fi

if [ -s ${basefilename}.pdf ] ; then 
    rm ${basefilename}.pdf ; 
elif [ -f ${basefilename}.pdf ] ; then
    echo "There is already ${basefilename}.pdf in this directory.  Delete or rename it to use $0"
    exit 1
fi

cp $1 $workdir/
cd $workdir
pdflatex $basefilename
cd ..
ln -s $workdir/${basefilename}.pdf ${basefilename}.pdf

exit 0

# TODO: use the same basic plan with .bib file: copy it to .q-tex, run
# stuff there, return to original directory. This way, I can have my
# RCS directories in the original directory without screwing things
# up.  Where should I keep my .sty files, though?  bibq-tex.sh

In the interest of science

2007-07-19T12:13:00.001-04:00

Well, if you'll permit me to group finance with the sciences: I present this chart, which details the performance of a mutual fund premised on active (not to say frantic) churning according to William J. Oneil's rules. Investor's Business Daily is an interesting paper (I just started I trial subscription), and I hope to share more thoughts about it soon.

SuSE 10.1 minus Gnome

2007-07-19T11:59:00.001-04:00

Fvwm sure looks strange. Well, no--it looks like Unix used to look in 1998. However, since I have so many important documents on this computer that I am afraid to upgrade, and since Gnome was so slow, Fvwm (OliCha theme) seems an appropriately conservative choice. Navigating the Fvwm menus is less intuitive, but the overall gain in speed more than makes up for a little fumbling.

(Side note: I would have preferred to compile IceWM on here, but gave up after a few tries. How annoying.)

Now: is it really the case that mirrors stop hosting releases of OpenSuSE after a couple of years? 10.1 is not that old, but I can't seem to get updates anymore. Slackware mirrors still have pretty much every release ever. I suppose I don't really understand how these things work. OpenSuSE still makes a good workstation, though.

Compiling Gnucash 2.1.5 on Slackware 12.0

2007-07-08T15:35:00.000-04:00

No more Ubuntu for me! Too many of my favorite applications (Claws-mail, Pybliographer, Gnucash) ran much better on Gnome, and so I could not switch completely over to Slackware. After much fighting, I think I have what I want now. Claws-mail was the easiest to get working . . . I think Slackware repositories had most of what I needed. I still don't have Pybliographer, but Kbibtex compiled after adding a patch, so the only thing left to do was fix Gnucash. It was hard, but not as hard as I expected. I compiled the required bits of Gnome (plus a couple other things), and that was that: a complete Gnome installation is totally unnecessary, and Gnucash looks great under XFCE or KDE. This list is probably not quite complete, but a useful desktop system probably has most other dependencies (mine did, after all). Unless otherwise noted, I compiled the newest version supplied by gnome.org, available as of 7 July 2007. From Slackware depositories pcre From gnome.org libbonobo ln -s /usr/local/lib/libbonobo-activation.la /usr/lib/libbonobo-activation.la ln -s /usr/local/lib/libbonobo-2.la /usr/lib/libbonobo-2.la ORBit ln -s /usr/local/lib/libORBitCosNaming-2.la /usr/lib/libORBitCosNaming-2.la ln -s /usr/local/lib/libORBit-2.la /usr/lib/lorbORBit-2.la gconf ln -s /usr/local/lib/libgconf-2.la /usr/lib/libgconf-2.la libgnome libbonoboui gnome-keyring libgnomecanvas ln -s /usr/local/lib/libcairo.la /usr/lib/libcairo.la gail gtkhtml-3.x (not the 1.x package that Slackware provides) libgnomeprint goffice Then Gnucash will ./configure && make, sudo make install as hoped. I realize that the symbolic links are not the proper and elegant way to do things; I did eventually add /usr/local/lib to /etc/ld.so.conf, but the procedure given above got me running. Still no Pybliographer, though, but I think Kbibtex is probably worth giving a try, anyway.

Ah so, w3m-buffer

2007-05-12T14:55:00.001-04:00

Not, I think that it matters much . . . but I did install the cvs versions of w3m and emacs-w3m.

Needed curl

2007-05-12T12:19:00.001-04:00

How about now? That wasn't so bad at all. I needed to install curl and byte-compile/load time-date.el on my Ubuntu 7.04 machine, but other than that, things seem okay.

Get w3m working as a browser
Make sure that the other gblogger functions work, particularly gblogger-blog
Why are my sgml tags unhighlighted?
Customize gblogger.el and ~/.emacs

The new plan

2007-05-11T11:53:00.001-04:00

Ok. I've tweaked, I've overhauled, I'm ready to port my modified ~/.emacs and gblogger.el files over to my home computer(s) and check whether I have this all correct or not. If that miniproject goes reasonably well, then this nerdy little weblog might be about ready to press forward. Next things to add:

The configuration files that made it all possible, and some notes on the programs I needed (don't forget to run autoconf, kids)
Essay on the look of my least favorite newspaper
$100 Computing
Fearful authenticity
Tufte vs. even more obscure nerds

Whoa . . . that should be plenty for now.

I owe it

2007-05-10T19:26:00.001-04:00

To you all to delete some of the more inane posts. And so I shall.

Crazy pops

2007-05-10T19:23:00.001-04:00

Now I think we're beginning to get it right . . . just maybe. Who can ever really say.

Is the white space really gone?

2007-05-10T19:21:00.001-04:00

One wonders just how much time is being saved by doing everything the hard, text-only emacs way . . .

The end of auto-fill-mode

2007-05-10T12:39:00.001-04:00

UPDATED--white space begone!

It is my great hope that I have vanquished this disgusting pox forever from gblogger-mode/sgml/nxml/whatever-I'm-using by changing the line in gblogger.el that read

(auto-fill-mode 1))

(auto-fill-mode 0))

. . . and it looks like I did.

Thank you, sness

2007-05-10T12:03:00.001-04:00

Just what I needed.

Some fixed, some broken

2007-05-10T11:47:00.001-04:00

AT LAST! Four lines of LaTeX code have saved me. I needed

1. To render bibliograpies as sections inside of individual chapters 2. To make the bibliographies appear in the table of contents (toc)--ideally, as numbered sections (that is, \section, not \section* 3. To prevent bibliography "chapters" from appearing in the toc 4. To suppress any silly errors while running pdflatex

I needed the chapterbib.sty and natbib.sty packages. Once I had those files where I needed them--and after many failed experiments--I added these lines to the preamble of my root LaTeX file (the file that has all the \include commands to call all of the chapters):

\usepackage[]{chapterbib} \usepackage[sectionbib,square,comma,sort(ampersand)compress]{natbib} \renewcommand\bibsection{\section{\refname}} \def\newblock{\hskip .11em plus .33em minus .01em}

Success! Of course, I've somehow broken posting here from my SuSE box, and I've never got it to work from my Ubuntu machine. Working on it.

How I wish

2007-05-08T17:48:00.001-04:00

I didn't have to retype my feed URL everytime I posted here.

Planner, Diary, etc.

2007-05-08T12:17:00.001-04:00

This post seeks two things: 1. The ability to save locally without ruining my ability to post. I have noticed that when I save posts with .xhtml or .xml extensions, the GNU Emacs/g-glient command M-x gblogger-publish fails. Thus, I'll try to save this without an extension. 2. A simple ~/.emacs file. The meaning of the LISP code is gradually making sense, but opposing forces are battling for my (computer's) soul--I want to understand what I'm doing, but I want things to work, so I add lots of junk I don't understand to the settings file (~/.emacs). Who wins? Memo to self: Set whatever variable is needed to keep word-wrap from breaking off my text. Do I want to recompile planner-el with icalendar? I think I'd really like to post my diary and schedule and planner to Google Calendar or some such place without effort.

Unchecking word wrap

2007-05-07T11:45:00.001-04:00

I hope that by unchecking the word wrap box under the Options menu, I can prevent the disgusting appearance of my posts below. Oh, I see that I have not fixed the problem yet. Perhaps it had something to do with Auto-Fill? Now I feel all guilty about publicly dissing xemacs, when I took for granted the fact that my lines would not get broken all stupid-like. Now, all my work seems to be for naught. OR IS IT??? Apparently, all I needed to do was to toggle auto-fill in the Options menu. That feels so much better.

Those linebreaks are still hideous

2007-05-07T11:31:00.001-04:00

This attempt is my third--I seem to have lost my ability to post, and right after I had discovered it, too. It seems that saving the entry is a no-no. UPDATE 10 May 2007: I think I just edited this old post through emacs. I needed to install the newest cvs of w3m-emacs (actually, maybe I didn't need to do that, but I did do it), and then I commented out my g-html-handler line of .emacs -- weird stuff.

A breakthrough with GNU Emacs

2007-05-07T11:21:00.001-04:00

EDITED 10 May 2007 (mostly just to show off)

After a protracted battle, I guess I can post to my blog from GNU Emacs (xemacs did not work, and is kind of ugly, anyway).

I downloaded g-client and installed it to my emacs load-path. Be sure to make config all instead of simply make. Some other things I needed: psgml and time-date.el. For good measure, I installed a few other emacs extensions from the openSuSE 10.1 respository.

With those changes, I could run M-x gblogger-new-entry and start typing. The important thing is to enter the URL of your feed, not of your blog. Thus, I entered http://www.blogger.com/feeds/numberoffeedhere/posts/default instead of errorbar.blogspot.com. VERY IMPORTANT.

After typing away, I ran M-x gblogger-publish, and all seems well. Unfortunately, I am certainly leaving out several other important details. Maybe I'll be able to get this set up in reasonable time on my Ubuntu box at home, but I am not so sure . . . I am beginning to think that Ubuntu does what it does quickly and easily, but those things that it does not do, it does not do. We'll see.

IT IS SUPPOSED TO BE EASY

2007-05-07T11:11:00.001-04:00

But is it?

Blank incoming encrypted messages with Enigmail/Seamonkey

2007-03-07T18:25:00.000-05:00

Enigmail was almost unusable on my laptop until today (Enigmail 0.94, Seamonkey 1.0.5 and 1.1.0). Set-up went fine: it was easy to install and import my keys, and adding my email accounts went as planned. I was able to send encrypted and signed messages with either secret key (I have two). Annoyingly, one of my secret keys—the “work” key—behaved oddly in Enigmail. I could decrypt messages at the command line with GnuPG, but any encrypted message that I tried to read in Seamonkey appeared completely blank. If I downloaded the message without Seamonkey and decrypted with the command line, the message appeared. Even stranger, Enigmail handled my other secret key without difficulty. After upgrading to Seamonkey 1.1.1, Enigmail (0.94) is, finally, working. I have found no information about this problem anywhere else. My ancient laptop proudly runs Slackware 11.0, a custom 2.6.17.13 kernel, and Xfce. ---UPDATE 11 March 2007--- Well, I had it working. Now, though, the GnuPG-Seamonkey interface seems broken. I can see the encrypted messages in their encrypted form (better than before), but I cannot decrypt them without saving the file separately. I surely brought this upon myself when I updated my Slackware patches. After much fiddling with dependencies, I have switched to Claws-mail (Sylpheed) with the GPG plug-ins. Claws-mail is fast, but the SpamAssassin plug-in seems to slow things down an awful lot. I am optimistic about Claws so far. A whiny note in closing: I irrationally find the Netscape-style buttons on Seamonkey repulsive. Opera is pretty, but does not seem to work as well, and is slow on my hobbling $100 laptop. Despite my kissing Seamonkey mail goodbye, it looks like the browser will stay.

PDF, PostScript Viewer for Slackware 11

2007-03-04T18:28:00.000-05:00

I am writing in LaTeX a lot these days, and I decided that my old laptop¹ needed a versatile document viewer: something to read .pdf, .ps, perhaps .dvi files. Xpdf lacked certain fonts, and Evince seemed the obvious choice, but there were too many dependencies².

Ghostscript compiled without too much trouble, but I wanted to spoil myself with a graphical user interface. Problems began—I was not able to get the GV program to compile, and GSView compiled but could open no files.

Here is what to do, and why:

Tweak a Ghostscript sourcefile if you use gcc 3.4.6 on i686-pc-linux-gnu. I had never played in C before . . . scary. Due to

http://www.tutorials-blog.com/postscript/report-does/

Edited ghostscript-8.54/src/gdevpdfe.c line 27 to read

typedef unsigned long long uint64_t;

Compile GhostScript with shared object files.

tar -xzvf ghostscript-8.54.tar.gz

cd ghostscript-8.54

GSView requires libgs.so, but the default compile for Ghostscript does not create them. So, in accordance with

http://www.cs.wisc.edu/~ghost/doc/cvs/Make.htm

Do the following in ghostscript-8.54 directory:

ln -s src/unix-gcc.mak makefile

make so

make soinstall

(I always run make and subsequent commands as root. It's amateur night in Linuxia.)

Install the Ghostscript fonts.

tar -xzvf ghostscript-fonts-std-8.11.tar.gz

cd fonts

mkdir /usr/local/share/ghostscript/8.54/Resource/Font

cp * /usr/local/share/ghostscript/8.54/Resource/Font

Install GSView.

tar -xzvf gsview-4.8.tar.gz

cd gsview-4.8

cp srcunx/unx.mak Makefile

make

make install

Before running make, I edited line 52 of Makefile to read

XINCLUDE=-I/usr/local/lib

But I am pretty sure that this made no difference.

Run GSView on a test file. In my case, I got two types of errors:

GSView needed the (installed) libgs.so file, but could not find it
GSView also could not find the fonts

Close the error windows with “Ok,” and click to Options-->Advanced Configure

Update Ghostscript Version

854

Give the correct location of Ghostscript Shared Object

/usr/local/lib/libgs.so

Ghostscript Program as gs is fine

Add the fonts to the Ghostscript Include Path (see Step 3, above)

/usr/local/share/ghostscript/8.54/Resource/Font

After closing the Advanced Configure dialog, you should be able to open your test file again.

----------

1A $100 laptop, it turns out. More on this point to come.

2Since I run xfce.

Digital Camera Woes

2007-02-19T14:15:00.000-05:00

My work requires photographs, and digital photographs have totally replaced film here. Like so many other new technologies, digital cameras seem easy to use, and so the demand for the shared cameras is impossibly high. As a result, the cameras are frequently broken or missing. Simply bringing a digital camera from home does not solve the problem. The Windows machines at work cannot mount the foreign camera without administrative access (which I lack). Can Linux save the day? My Ubuntu 6.10 box at home mounts my borrowed Kodak EasyShare V530 without a problem--the camera plugs into a charging pedestal (whatever this thing is called), and the pedestal plugs into the wall and the USB port. After physical connection, a button on the pedestal puts the camera and computer in virtual connection. The OpenSuSE 10.1 box at work did not detect the camera, even with the F-Spot program. According to the website, OpenSuSE supports this camera with gphoto2, so I installed gphoto2 and libgphoto2. Installation went fine, but I could not get the CLI to do what I wanted. The key program was gtkam (and libexif), both available from the repository. I could only access the camera through F-Spot (Ubuntu treated the camera as a disk drive), but all is working now. What I would really like is an easy way to use old CCD cameras with any of my Linux computers at work--then I could take endless pictures through microscopes and dissection-scopes.

Taxes: e-file with GNU/Linux

2007-02-11T12:48:00.000-05:00

Keywords: IE4Linux, Wine, Ubuntu 6.10 Shamefully, I've been in the habit of using Turbotax on the web since I began filing my own taxes. I say "shamefully," because I have been paying needlessly for this service, except for the first year or two. It has never been expensive, and I've always found the service worth the price (especially in years when I could not find my W-2--Turbotax accessed the information for me). I was thrilled, then, when the IRS website offered a free version of Turbotax on the web under certain conditions. Last week was the earliest I had ever started to file my taxes. The Turbotax website, alas, is not Linux-friendly--it supports Firefox on Windows and Mac OS X, but not on my Ubuntu 6.10 or OpenSuSE 10.1 Dells (Epiphany was a non-starter). In both cases, I could not get past a Turbotax error page. On the Ubuntu machine, the Wine Windows-compatibility program and the trememdously useful Internet Explorer 6 for Linux package saved the day. Via IE4Linux, the website ran smoothly and I was able to file electronically. The only remaining wrinkle involved Adobe Acrobat Reader: some of the website's functionality required Acrobat, and even though I had the program on both computers, the website could not recognize it. This problem was particularly annoying for digitally signing the forms for submission--I needed to consult my 2005 tax returns to verify my identity, but Turbotax would not allow me to download the files, since it did not recognize that I had Acrobat (or any other PDF reader) installed. After downloading my returns on another computer, everything else proceeded as expected. I grimly emphasize that IE4Linux did not help on the OpenSuSE 10.1 machine. Were I feeling more scientific, I would have attempted the experiment on my OpenSuSE 10.2 PPC, but that computer is from 1999 and not worth the hassle. Minor note: IE4Linux, unfortunately, has never allowed me to use Lotus Notes on the web, which I need to be completely Windows-free at work. My positive experience with Turbotax has renewed my enthusiasm for IE4Linux--thank you! Disclosure: I own a small amount of stock in Novell, who publish OpenSuSE. Maybe my hopes for the company will prompt me to upgrade 10.1 (which has well-known problems, but my box now runs fine after minor tweaking) to the much slicker 10.2.

The new face of RAOS

2007-01-14T17:24:00.000-05:00

All joking aside—to change, improve, or control anything, one must first be able to measure it. The original point of this weblog was to broaden my reading (and understanding) of scientific articles by recording what I read. I also planned to make Random Acts of Science a public document of my dedication, and I hoped that my need to show off would keep me reading and updating. The original impulse obviously failed, but that is okay. I have not met my barely ambitious goal of reading and recording one scientific article per day, either. Still, my failure is not as naked as my updates here suggest. The trick is this: I have found a better way to document and organize my reading. For Windows, Mac, Slackware Linux: JabRef For Gentoo, OpenSuSE 10.1-10.2, Ubuntu/Debian: Pybliographer Pybliographer is my favorite tool for managing bibliographies, and it requires fewer system resources than JabRef to run. It is graphical, and greatly resembles Endnote (for PCs) or Tellico (for KDE-based GNU/Linux). I keep several separate bibliographies in BibTeX format: one for work, one for general interest, and one for financial matters. Since the BibTeX bibliographies are text files, it is easy to edit, manipulate, or combine them at will. For TeX cognoscenti, it is trivial to cite elements of these bibliographies in Emacs or some other text editor; for my purposes, it suffices to have a searchable record of citations. JabRef requires Java, but it does not require any compiling—I was never able to get Pybliographer to compile on Slackware 11, and so I turned to the readily downloadable JabRef. JabRef is not as minimal as Pybliographer, but it can also save bibliographies in BibTeX format, and JabRef integrates readily with OpenOffice (export the bibliography to an OpenOffice Calc file, then use that file as the bibliography database Tools:Bibliography Database:Choose Data Source). You can even use a strictly web-browser based version of JabRef. While there are other tools for similar purposes, I find that Pybliographer and JabRef meet all of my record-keeping needs. Eventually, I hope to learn enough Python to tweak Pybliographer into a tool for keeping a laboratory notebook in TeX format, complete with inserted figures and other supplementary files . . . but not right now.

The No-Sh*t Principle

2007-01-06T20:25:00.000-05:00

Writing is hard, and so people write badly. There are several ways that young writers (in particular) make writing difficult for ourselves: we tend not to read enough, we rarely pre-write, and almost no-one drafts and revises properly. For many of us—scientists, for example—writing seems secondary to our main task, whether that task is research or something else. Writing therefore becomes a chore, and we fail to allow it enough time and care.

This essay does not suggest that up-and-coming writers read more, pre-write more, or revise better; we already know all that, and we each must wrestle with those issues ourselves, forever. Here, I only consider my own minute-to-minute problems with how one sentence follows another. I usually see three main problems in my own writing:

Lack of clarity, especially within sentences. Strunk & White offer excellent advice for writing clearly—I read The Elements of Style every year¹, and it shames me to admit that I really do learn something each time (even if I still disagree with some of their suggestions and find many others completely unnecessary for anyone literate). I further propose three additional rules, particularly for scientists:

The word this must be followed immediately by the noun that is modifies.

When used to refer to a noun, the words that or which must be explicitly preceded as immediately as possible by the simplest possible noun phrase to which they refer.

Adjectival gerunds (ending in -ing) must always explicitly modify nouns, not whole phrases.

The purpose of all three rules is the same: to leave no doubt in the reader's mind as what you are discussing. Far too frequently we write “This demonstrates . . . “ or “We walked together to buy the ring, proving that I loved her.” What demonstrates—the last thing you mentioned, or the events described in the last paragraph, or the entire preceding text? Does the ring prove that you love her, or does walking together prove it, or did you otherwise manage to prove your love while out shopping? Clear writing is unambiguous, so we must make the relationship between the words obvious.

Lack of logical connection between sentences or paragraphs. I think that most writers have fewer difficulties here, if only because so many of us write very slowly or revise heavily for “flow.” I can't recommend any guidelines here, other than to urge you to read your text aloud. Where you naturally pause, check for punctuation. Where you do not pause, there should likely be no punctuation. As long as you use common sense, the pacing will seem natural, and the reader will never think, “Why did you say that thing, there?”

In all seriousness, I do not know many writers who have trouble with point two, above. Some of us may stumble over the odd comma or semicolon (see S&W), but in general I believe my friends and colleagues structure paragraphs and pages logically. Writers, particularly those of us who consider ourselves writers, pay a great deal of attention to “flow,” I think because we believe that attending to it helps us to develop our own voice. Our pride depends on smooth prose.

Too much attention to “flow” leads to another problem. Rather than simply state our case and back it up, we tend to get wrapped up in unnecessary phrases and verbal acrobatics. We end up repeating ourselves (for emphasis, naturally) or stating the obvious. I now present the third problem I find in my writing:

Stretches of needless text that dare the reader to think, “Well, no sh*t.”

It is easy to see how excessive concern for “flow” leads to this sort of difficulty.² To many of us, it seems incredibly boring to string a series of simple declarative sentences together—after all, a list of facts may constitute a plot, but it cannot be a story without style. Our vanity leads us to discard clarity in search of this phantom, style, and along the way we lose our readers, as well. From where, then, does this vanity come?

I propose that school created the problem, and that the internet aggravates it: we no longer write to communicate; instead, we write to fill space. When a student brags that she “bullsh*tted” her way through an essay exam, what does she mean? She wrote, and she duly filled space, but she actually communicated little information. In fact, she is really bragging that her style successfully hid an absence of content. Forums on the internet, like public journals and personal ads, give millions of prose stylists limitless opportunities to write whatever comes to mind . . . and nearly everyone realizes, once on stage, that they in fact have very little to say. Vanity, however, demands that something fill the space—and so something does.

The fear that unadorned writing will be boring is a genuine fear. My job requires writing, and I often try too hard to avoid bland prose, and I probably cause myself trouble here. To paraphrase Tolstoy, every good writer writes differently, but nearly all bad writing is the same: tangled, pretentious, and nonsensical. Too often, “style” and “flow” are code-words for a lack of ideas: pith is the best style. Frankfurt³ and Fish⁴ join Strunk and White in offering sound advice—if you first master clear writing, your style can emerge. Without clarity, you can have only admirers, not readers.

SAT tutors share obscure points of grammar and vocabulary. Writers share ideas.

1As suggested by Edward R. Tufte

2I apologize for spoiling my own punchline by setting off the word flow throughout this essay.

3Frankfurt, Harry. On Bullsh*t.

4Fish, Stanley. “Devoid of content.” New York Times, 2005.

Still digging out . . .

2006-04-10T01:17:00.000-04:00

Controllable Snail-Paced Light in Biological Bacteriorhodopsin Thin Film Physical Review Letters 2005, 95:253601 KEYWORDS: physics, optics, ultraslow light, cute science, photonic, optical switch, halobacteria, refractive index VOCAB: group velocity, optical density NOTES: -"electromagnetically induced transparency" -"The induced dipole moment interferes with the dipole driven directly by the probe field, leading to a redution in the absorption of the probe with an extremely narrow frequency interval (~1/tao). This indicates that the refractive index increases rapidly over the same spectral region . . . " -quantum yield of 65% -". . . we are able to control teh group velocity from the order of 10^-4 m/s to normal light speed." -what polymer is the matrix? -does this only work for 568 nm light? Decatenation checkpoint deficiency in stem and progenitor cells Cancer Cell 2005, 8:479 KEYWORDS: biology, checkpoint, wound-healing, stem cell, cancer VOCAB: decatenation (disentanglement by topoisomerase II of chromosomes during cell division), aneuploidy, aneuploid, pseudomitosis ("spindle formation and kinetochore poleward movement in the presence of entangled chromosomes, which results in aberrant chromosome segregation") NOTES: -"checkpoint efficiency increased when embryonic cells were induced to differentiate . . " -->are stem cells part of the cancer problem? -->the "SIGNIFICANCE" box in this journal is a fine, fine touch. -"chromosome gain and loss have been observed during the ex vivo culture of human and mouse ES cells and could be a consequence of the inefficient decatenation checkpoint." DRUGS: retinoic acid, colchicine, KRF-193 (Topoisomerase II inhibitor) Sipa1 is a candidate for underlying the metastasis efficienty modifier locus Mtes1 Nature Genetics 2005, 37:1055 KEYWORDS: metastasis, bioinformatics, confluence, adherence VOCAB: transgene, locus, orthologous, multiple cross mapping, MCM, variable tandem repeat, VTR, minisatellite, PDS domain ("frequently implicated in protein-protein interactions"), nephrogenic, missense, bromodomain NOTES: -"The control Mut1 cell line produces many rounded cells when grown to confluence compared with the flat sheet observed in the shRNA knock-down cell line" --> normal (less prone to metastasis) cells die when grown to confluence in vitro -rounded cells at confluence "suggestive of strong cellular adherence"

Photonics, Wow!

2006-04-10T01:01:00.000-04:00

Design, fabrication, and optical characterization of quantum cascade lasers at terahertz frequency using photonic crystal reflectors Optics Express 31 October 2005 13(22):8960 KEYWORDS: physics, photonic, photonic crystal, terahertz, THz VOCAB: lensed mirrors, stop-band NOTES: -applications for THz: imaging, chemical sensing, astronomy -photonic crystals at "stop-band" energies = reflectors -"single plasmon waveguide (sic) are easily fabricated and enable high power structures with little out-of-plane losses -lases at 77 K PROTOCOLS: -5 nm Ti/50 nm Au --> surface plasmon -alloy at 400 deg C for 1 minute: 10 nm Ni/20 nm Ge/50 nm Au/20 nm Ni/200 nm Au

Notes on style.

2006-04-10T00:44:00.000-04:00

I plan to render titles as given. Keywords and other notable text will follow British spelling conventions (typos aside). Links will lead to Google search results (safesearch off, on principle) except where I thought it worth pointing somewhere specific. Please note in comments if any links are dead--maybe the equilibrium state will be all links leading simply to Google search results.

Two old biology papers

2006-04-10T00:28:00.001-04:00

The effect of surgical wounding on tumour development Eur. J. Surg. Oncol. 1999 25:231-243 KEYWORDS: biology, wound-healing, extra-cellular matrix, ECM, hypoxia, hypoxic VOCAB: cytokine, autochthonous (originating where it is found), stroma (connective tissue existing for support alone), mitogen (a chemical that triggers mitosis, i.e. cell division) NOTES: -growth factors: EGF (epidermal growth factor), TGF-a (transforming growth factor), TGF-b, bFGF (basic FGF), IGF I (insulin-like growth factor), IGF II, PDGF (platelet-derived growth factor) -wounding stimulates some cell lines (How? Via what factors?) -wound healing stages: inflammatory, proliferative, repair & remodeling -“wound macrophages phagocytose wound debris” and trigger the next stage (proliferation) -“fibroblasts produce many of the extracellular matrix (ECM) components that result in scar tissue formation” -p53 is a tumor-suppressor -fibrinogen (via transglutamation) --> cross-linked fibrin -kDa = 1.1(residue count)/10 -bFGF (basic FGF) is highly angiogenic -this article considers treats as hypoxic concentrations below 50 ppm oxygen (presumably in medium) -ECM components: fibronectin, laminin, collagen, vitronectin, fibrinogen, thromospondin

Oxygen Tension Regulates the Expression of Angiogenesis Factor by Macrophages Science 23 Sept 1983 KEYWORDS: biology, wound-healing, angiogenesis, hypoxia VOCAB: debridement, Permanox culture dishes, lactalbumin hydrolysate, mitogen, mitogenic NOTES: -“sealed culture chambers”? -oxygen concentration in atmosphere reported -cultured cells at 20%, 10%, 5%, 2%, 0% oxygen in air --> corresponds to what in media? are some of these points saturated/otherwise indistinguishable? -“near-anoxia” = “sealed” chamber is not so sealed?

Walk the Planck length

2006-04-09T17:42:00.000-04:00

No doubt we're jumping the gun here, but this link leads to some science books I'd like to read one of these days.

Pour one out for nerd.dartmouth.edu and wrjva2

2006-02-27T23:06:00.000-05:00

From 1 August 2001 to 28 February 2006, at an average rate of one post on one article per day . . . that would be one thousand, six hundred, and seventy-four scientific journal articles. Let's add another demerit for each successive day. Each post will include a citation (with title), and set of keywords. Any new terminology that appears in the article will get a definition or a relevant link. I might also add other commentary, like a synopsis, follow-up questions for later research, further links, possibly a link to the original article (if available). Bonus posts on anything else, while charming, do not count against the 1674+ challenge. The format will probably vary a little . . . eventually, I hope for something compatible with and complementary to Endnote. In any case, it'll do me good to build an electronic annex to the notebook on the old scientific literature. I welcome the revolution before it starts in my town.