Quantum Forest

For quantitative geneticists and breeders out there: ASReml runs OK in any mac with Intel processor and Parallels. You can find some comments on using it in the ASReml Cookbook.

Incidentally, SAS works OK in a mac using Parallels too. However, I am enjoying R a lot more.

(Or why do I prefer software where I do have a say)

Recently I was commenting on some software that I use for writing. I think that one of the main reasons non-strictly related to software usefulness is the quality of the community around the software. This has two elements:

• How open is the developer to feedback from the users and
• How active is the community at using the software to push the developer(s) to continue moving forward.

As an example, I like using Journler to keep track of odd ends in my mac computer. I also like using Writeroom when starting to write, because I can focus on my ideas only. Both programs have relatively active groups of users (here and here) and receptive developers, who are looking for feedback. The feeling is of people who care about a product, which in general is a necessary (although not sufficient) condition for good programs. By comparison, I struggle with Copywrite, because there is no public feedback mechanism: I do not know what other users think or what are the projects of the developer for this software. Is he (or she) still developing it or now he is moving to live in Vanuatu to enjoy the rest of his life?

An interesting element is that both Writeroom and Journler are free (sensu gratis)—although the developers ask for donations—while Copywrite costs US$30 or so. There is a psychological element on paying for software; one thinks that the programmers must be working on the product. However, there is no feedback to confirm this assumption in Copywrite. In addition, I expect more activity from smaller companies: they are supossed to be more agile than, say, Microsoft.

Thus, if you are a small company I expect you to show some changes here and there. If you are a small company and charge for your product I better should have a say on what is going on. If you are a large company, most likely I will buy your software only if I need to, because most probably you are developing not very interesting products (there are exceptions¹ of course).

¹ Wolfram’s Mathematica is an example. Insightful’s Splus is not: R is much more active, there is plenty of feedback and it is free.

It all started last week with problems coming back from sleep mode. The MBP would wake up for a few seconds and then shutdown completely. It was an annoyance, but given that I was still teaching and preparing lectures using the laptop, I just kept going. Last Monday 19^th September it was happening often enough that I sent an email to the University’s IT support, for which I received an automatic reply on Tuesday saying ‘we got your message’.

Yesterday, Wednesday 21^th September, the computer just ‘died’ four hours before my last lecture for STAT220. I would turn on and then shutdown almost immediately. I had prepared the last lecture at home, without a chance for the automatic network backup that I get at work. Therefore, I spent the last few hours frantically trying to recreate the lecture (in PowerPoint rather than Keynote) in a borrowed HP laptop. Not the best final lecture, but at least a decent end for my participation on the course.

Marcela dropped the laptop at MagnumMac, the authorised Mac reseller in Christchurch. We were presented with the following options: for normal guarantee work (which certainly was this case) I would need to wait until next week so the technicians had a look at the computer. That is, waiting at least from Wednesday until Monday so someone would touch the computer, not even repair it. The option: spend NZ$75 so the technicians would put my computer at the front of the queue—skipping another 14 computers—and start diagnosing the problem. Not having the computer is certainly worth much more than $75 per day for me, so I decided to pay, but the whole system sounds wrong:

• The computer is under warranty (and with additional AppleCare), so Why should I pay to have it fixed in a reasonable amount of time?
• MagnumMac’s technical support appears to be seriously understaffed if it takes them so long just to ‘have a look’.
• At least in theory, people that choose not to pay the extra cost can be continuously pushed down the queue to have their computers repaired.
• Apple did not offer any support so I can keep working while they repair my computer. My mechanic can lend me a car while he is fixing my vehicle, so how can that a computer company can not do the same? How do they expect me to continue working with my Keynote documents?
• Several supposedly ‘lesser quality’ brands offer a much faster turn around for repairs.

Apple has not found the problem yet: I was told—after I called a couple of times—that they have reproduced the problem but that they are still trying to figure out what is its cause. Once that happens, it will take several days for me to get back my computer (tomorrow is Friday already): normally they order the parts from Australia, which may take several days, even weeks.

This is the second time that my computer goes back to Apple: the first time was a battery problem (before the big battery recall). It has been very disappointing to have these problems, particularly when they seem to be so common place.

By the way, I am still waiting to receive an email written by humans from the University’s IT support.

P.S. 2006-09-27. I received my laptop back on Monday 25^th. Apple’s technician explained to me that they were able to replicate the problem but not to pinpoint the cause. They replaced 512MB of third party RAM for Apple brand and that seems to have temporarily fixed the problem. Today I had a shutdown when running on battery (with supposedly 67% of charge). It may be that the battery needs calibration; however, it may also be the same problem coming back. We’ll see.

P.S. 2006-09-28. Random shutdowns are back. Called tech support and they will order the next potentially problematic part.

P.S. 2006-10-05. The left I/O board was replaced on Monday 2^nd October, got the computer back yesterday and it failed again tonight. I am returning it tomorrow and will ask for a replacement computer. The issue is now how to get a bit over 10GB of data backed up (mostly the multimedia part, the rest—around 2GB—is already safely stored in our network), while the computer is working. If it is not possible, we will need to access the hard drive from somewhere else.

P.S. 2006-10-10. I received a new Macbook Pro, which did not present any of the problems of the previous one. Annoyances aside, I received a faster computer (2GHz instead of 1.86GHz) and I used the opportunity to upgrade RAM from 1Gb to 1.5GB. All in all, I am a lot happier with the new computer. Apple was not very keen on exchanging the computer, but I refused to accept back the old one. At least some times it pays to be a real pain in the butt.

Following my Another mac update post I will cover a few small applications that have made a big difference on the way I do things.

DigitalColor Meter: One of the common tasks that I perform when updating my web sites is to change the CSS files. I keep the same templates, but I do play a fair amount with the design; particularly colours. When I was using mostly a PC I would find a nice colour in a page, take a screenshot (with Shift-Print Screen), open the screenshot in The Gimp and use the color picker to get the hexadecimal representation of the colour. Moving to the mac I had the temptation of doing the same, but using Grab (which comes by default under Applications, Utilities, Grab.app) and The Gimp for mac or—a simplified version of it—Seashore. Then I discovered that the mac ships by default with Digital ColorMeter (under Applications, Utilities, DigitalColor Meter.app) a small piece of software that lets you hover above any screen and get the hexadecimal color. One can even modify the aperture size, to change the number of pixels being included in the average colour measurement. Now it is simply ‘Hover with my mouse, Shift-Command-C’ and I get the hexadecimal values.

Dictionary: The other one is simply Dictionary. Yes, I have a problem, I like dictionaries and related books. I do own a copy of ‘Webster’s New World’, ‘Oxford Advanced Learners’, ‘Roget’s International Thesaurus’, ‘Brewer’s Dictionary of Phrase & Fable’ and ‘Fowler’s Dictionary of Modern English Usage’. This is covering English only. I do have a similar set of books in Spanish, starting with ‘Diccionario del Español Actual’ by Manuel Seco, Olimpia Andrés and Gabino Ramos (4,666 pages), followed by a large number of smaller dictionaries and books on the use of Spanish. I used to go and look for words all the time, but now there is Command-Spacebar Di (in Quicksilver) and the word. That’s it and I love it. I now only need something like that for Spanish.

Still trying on writing tools

Writeroom keeps growing on me, but I need to store all the bits and pieces that I am writing for different reasons. Although I tried Mori (from the same makers as Writeroom), I still do not feel quite comfortable with it. Journler, on the other hand, it is a nice journaling application, although its full screen mode is still a bit clunky.

So, I wrote my first ever piece of Applescript:


tell application "WriteRoom"
set docName to the name of front document
set docContent to the text of front document
end tell
tell application "Journler"
set newEntry to (make new entry with properties {name:docName, plain text:docContent})
end tell


Writeroom assigns automatically the content of the first line as document name. Thus, the script grabs the name and content of a WriteRoom window and creates a new entry in Journler with that title and content.

Yes, I did buy a copy of Copywrite before, but I can not make it fit in my workflow yet. I will keep trying it for a while, and see if it ‘just clicks’ with me in the near future.

After using the Macbook Pro for a few more weeks, I have been settling on my final software selection:

• Quicksilver: which is a great launcher and keeps learning about my preferences. Additional plugins installed: del.icio.us, dictionary, firefox and iphoto.
• Office: well, I do exchange a lot of documents with colleagues and friends that use the Windows version. In general works quite well, although compatibility is not perfect. My main issues have been spreadsheets containing lots of VBA or embedded Activex controls and compressed graphics in PowerPoint, which show that puzzling ‘QuickTime and a TIFF/JPEG decompressor are required to view this picture’ message. In addition, Microsoft has not released a Universal binary for Office, and will not do it until they have the next version available, whenever that is.
• Thunderbird: after trying Mail.app and Entourage, my experience was disappointment with how unreliable Mail.app was (missing emails and crappy IMAP support) and found Entourage too big and clunky.
• Firefox and Camino: Firefox is a great browser, but it feels a bit un-Macintosh. Camino uses the same engine, but with a nicer interface. I like the ability of closing the tabs just next to their names (a la Safari). However, it does not have (yet) incremental search, which is something that I love in Firefox (PS 2006-06-29. It is possible to have a close button in the tabs of Firefox through the use of the Tab X add-on. PS 2006-06-30. Bob Cantoni points out ‘to close Firefox tabs, just middle-click on the tab to close it; i.e., click the scroll wheel’).
• R: a great cross-platform (and free) statistical software. I do most exploratory analysis using it, and only go to SAS, using Parallels (see below), when strictly necessary for working with other people.
• Parallels: allows running windows and I currently use it only to run SAS. It still feels a bit slow, but for writing and prototyping SAS code is good enough. I bought the pre-release copy at US$50.
• Copywrite: I normally become very easily distracted when using a word processor to write. All the options, fonts and formats become a real nightmare. Enter Copywrite, which is a simple writer’s editor. It allows only basic formatting, so it is very good for the first couple of drafts.
• Devonthink: after reading Merlin Mann’s comment on 43 folders, I decided to give it a try. I am quite tempted to use it in a continuous basis. It is a good brain dump, where I can put all odds and ends that I normally loose. The current version still has some bugs and missing features, like that the full screen editor works only for plain text and that changing the colours of text may have effects on other parts of the program. Anyway, searching and connecting notes seems to work quite well. I still think that Copywrite’s full screen editor is much better and less distractive. PS 2006-06-30: I have decided to wait until the next version before buying Devonthink: still too buggy for my taste.
• Writeroom: I just started testing this great full screen writing system. Just write there, no need to save. If I want something a bit more complex, I can type using Markdown and convert it to HTML using Humane.Text service. PS 2006-06-30. Jers Novel Writer is another writing program that supports full screen mode and that deserves a try.
• TeXShop a highly polished LaTeX distribution, that I am using for writing lectures notes for STAT220 (Biometry I).

Sharing printers in a mixed network

I can not remember another time when I have been using so many computers in such a regular basis. My main work machine is Mastropiero¹ (Macbook Pro 15”), although there is an exception for simulation work, where I use Nutcracker (a.k.a. Black Box, a generic 3GHz, Windows XP machine, which just happens not to be beige). In addition, at home I also use Happy Meal², a Power PC Mac Mini that acts as back up and has the printer connected. Last—and certainly least—I keep Beige Box (a generic 1GHz Windows XP machine) still functional at home, just in case we need some extra simulation capability when time is not an issue.

Last weekend, we bought another cheap windows laptop for Plus Tree, our consulting arm. It is a Compaq Presario V2000, temporarily named Lucrezia Borgia³.

Given that the printer is attached to Happy Meal and that we some times need to access it from either Mastropiero or Lucrezia Borgia using wi-fi, we:

• Shared the printer (using System Preferences, Sharing), which works for any Mac computer in the network, including Mastropiero.
• Allowed access from Windows machines—like Lucrezia Borgia—installing Bonjour for Windows, which has a handy ‘Bonjour Printer Wizard’. Use the Wizard and the printer is now available to Windows too. Piece of cake!

Incidentally, after using the Compaq laptop for a while, I can say that it feels as warm as the Macbook Pro on the top surface. The exception is the part above the function keys in the MBP, which is bloody hot.

P.S. 2006-06-30. Welcome to 43 folders’ readers. Five hundred visits in two days; not bad for a small sidebar link.

¹ Homage to the (in)famous composer so many times presented by Les Luthiers (and English article in Wikipedia).

² Its volume is actually a bit smaller than a MacDonald’s Happy Meal box.

³ Obvious reference to this Renaissance woman.

After playing for a little while, I managed to connect my Macbook Pro to the internet using my mobile phone via bluetooth. I have a small Samsung ZV10 and my service provider is Vodafone New Zealand. The steps are quite simple:

• Click the bluetooth icon in the topbar and select ‘setup bluetooth device…’.
• Check that the phone is running bluetooth and that is discoverable (Under settings, connectivity).
• Select mobile phone in the list of available devices.
• The computer will search and—we hope—find your mobile phone.
• The computer will generate a numeric passkey that has to be keyed in and accepted in the phone.
• Select ‘Access the Internet with your phone’s data connection’ in the next menu.
• The settings to connect to Vodafone in New Zealand are:
  • username: vodafone.
  • password: vodafone.
  • GPRS CID string: *99#
  • Modem script: Vodafone VC701SI

This explanation is based on the excellent—and illustrated—version by Pukupi.

I am a bit late with this post, but I have been very busy the last ten days. Yes, I managed to run SAS inside Parallels in my Macbook Pro. I have not yet had the time, nor the need, to try ASReml inside Parallels.

I have had two issues with the new laptop (a.k.a. Mastropiero), one that seems to be not mac related while the other is pretty much central to high performing laptops with little ventilation (in the name of silence).

First, my computer was freezing at start up at home, but not at work. Initially I thought that it could be that the configuration at the university meant that the computer was looking for the network all the time and that it would crash in its absence. That was proved false when Bruce tested the computer at the university but disconnected from the network. With Bruce’s help we pinpointed that the culprit was my wireless router (a D-Link DSL G604T). It seems that the router could not allocate a proper IP address and it would conflict with my mac mini (aka Mini Me) at home. I first contacted D-Link’s tech support, which was completely useless and denied any possibility of problems caused by the router. I then contacted my ISP (iHug), where tech support suggested assigning a fixed IP for the laptop and now it works. Well, it still takes a long time to boot, but when it does everything seems to go OK. By the way, my macbook pro connects without any problems to other wireless networks.

The second issue was heat. The laptop tends to get quite hot, because it is using the titanium chassis and cover to dissipate heat from the inside. I used speedit to monitor the CPU heat, which was about 60 degrees C when idle and would go up under load. Before getting in to ‘thermal grease removal’ mode (and voiding the warranty on the process) I had a look around and found iLap, which seemed worth a try. Well, the idea seemed OK but would I spend US$50 plus postage to New Zealand for a fancy piece of Aluminium?

I had a chat with my mate Nigel, which went like this:
—Do you have a piece of Aluminium sheet?
—Would a 3mm one be OK?
—Yep. Could you make a stand for me if I sent you the dimensions and a quick drawing?
—No worries, mate.

I emailed to him the links to the iLap site. A couple of hours later he came back with a rough approximation, but that works great and it does not look that bad either. Cost? I owe him a beer (or two). The laptop is now 10 degrees C cooler, and the new position makes typing and looking at the screen a lot more comfortable.

A few updates on my previous post on buying a Mac mini.

• Microsoft Office has a nicer feeling in the Mac than under Windows, which is a nice surprise but says a lot about how crappy the Windows version is.
• Why would you call an email program just Mail? It makes very hard to look for help with such a generic name. Using ‘Apple Mail’ and Mail.app helps a bit, but it is such a silly name, like calling a browser ‘Web’ or a spreadsheet program ‘Spreadsheet’.
• We started using Mail for email, but we just hit a few undesirable ‘features’, like disappearing email. It happens like this: there are some messages in the Inbox and, suddenly, they are not there anymore. Probable cause: data corruption, but I am not willing to experiment with my email. Ended up using Entourage, which comes with my copy of Office, so no extra expense there.
• Most hyped and useless feature: dashboard. I am really hard pressed to find any useful widgets. We use some times the calculator and the egg timer for cooking.
• I still have not made a firm choice between Safari and Firefox. Some times I use one some times the other. I do not care much about sharing or losing bookmarks, because I keep them in delicious.
• I am using SubEthaEdit as editor, which is quite nice (and love the logo). The interface is simple, and I have most of what I need at hand.
• We do not use any client-side email filtering: we just redirect personal email from our server (uncronopio.org) to Gmail, let Google filter it and read it from there with any email program. As a side effect we get all incoming and outgoing email backed up in the Gmail account.
• The keyboard is very nice and the mighty mouse is quite comfortable. I love the tiny scroll wheel!

In all, transition has not been difficult. It helped to have a copy of Mac OS X: The Missing Manual, Tiger Edition. It is a good resource for newbies playing with Macs under OSX. The only software I miss at home: Picasa. Hey, Google guys, when are you going to release a Mac version? It is way better than iPhoto, and forking out ~US$500 for Aperture is just too much for a hobby.

This post continues documenting the switch from my PC at home to a Mac Mini. After the basic setup of the new computer, it was important to move all the data across platforms. I did a quick web search to find out how to move all the mail from the Windows version of Microsoft’s Outlook Express to Apple’s Mail. Unfortunately, I did not find a straightforward way to do it (PS 2005-12-20: There is a US$25 product called Emailchemy that does the same as Thunderbird below), although I found out at least two ways to move mail from the full version of Microsoft Outlook (see, for example, Entourage cross platform issues).

Outlook Express has its own mail format and very few export options. After having a look at mail formats, I opted for using Mozilla Thunderbird as an intermediate step.

I installed Thunderbird in the windows box, which automatically imported all Outlook Express mail and stored the emails in Unix format at: C:\\Documents and Settings\\your account\\Application Data\\Thunderbird\\Profiles\\Your account\\Mail\\Local Folders. I saved the files contained in that directory in a CD and then put the CD in the Mac.

Then run Mail and go File, Import Mailboxes, Import data from: Other, and then specify the location of the mailboxes to import (in my case the CD in the superdrive). And that was it.

Importing pictures in to iPhoto was extremely easy too. Just File, Add to library and then specify the location of the pictures (CD again). However, I have not been able to find a Picasa importer, so I need to go again over all pictures and retouch them. I would certainly pay for an importer Picasa to iPhoto or, even better, a Picasa version for Mac that were able to directly import everything from the windows version.

Last weekend I started using our new Mac mini. Some first impressions:

• It was very easy to connect (not that PCs are that difficult either).
• Installing the printer was just plugin in to the computer and it was autodetected. I liked that.
• I love the good quality (almost photographic) icons. I don’t like that much the brushed metal windows. They look a bit tacky compared with the rest of the system.
• I installed Mighty mouse’s driver, which installed an evaluation copy of Office 2004. Because I did not remember deleting it, I had trouble when installing my own legal full version of Office 2004. So I needed to uninstall both versions and then reinstalled my copy of Office. Everything is working fine.
• Email and web browsing are working fine. I have to find how to import messages from Windows’ ‘Outlook express’ to Mail.
• I really like putting the system to sleep and how responsive is when coming back to life.
• iPhoto is sort of nice, but I am used to Picasa and the thought of importing the pictures and redoing all the work touching up thousands of pictures is more than a bit annoying. Picasa is faster and does not keep duplicates of the pictures. I may have to look for an alternative to iPhoto, without the price tag (US$500) of something like Aperture.

In general it has been a good experience. Starting work from scratch in the mac is quite easy. Thus, most of the pending issues are related to ‘legacy files’, where I want to move things from Windows and do as little as possible to get exactly what I used to have in my old machine.

P.S. 2005-12-08: I forgot to mention; only two USB ports in the Mac Mini is not enough (considering its size, no wonder there are no more ports on the little thing). The two ports allowed me to connect the printer and keyboard, with the mouse connected to one of the two keyboard ports. The other keyboard port can be used to plug the digital camera, while the video camera can be pluged to the single firewire port on the back of the mini. However, if one wants to plug an iPod, the keyboard port can not charge it. It was a good thing that I had a USB hub in my old PC. I am using it with quite good results in the Mac and can then plug everything in one go, including my Palm T3.