2012 is going to my best year thus far.

I just decided that it will be so it better be.

Top 10 lessons that I learnt in 2011.

1. Data analyses is 95% data cleaning and variable definition.

2. R is fun and liberating.

3. Perl is even more fun but it's funny and weird and super tough to learn.

4. I have a massive crush on Hadley Wickham. Mostly because he is the ggplot2 creator. And maybe also because he has a website of family recipes and oh, a really informative website manual for ggplot2. Is this as impractical a crush as the Rahm Emanuel phase? Well... slightly less because I might actually get to meet him someday... but on the whole, big check.

5. ggplot2 is a fascinating way to think about data.

6. FlowingData is one of my favourite inspirations. It replaces aldaily (which, unfortunately, I have been steadily ignoring).

7. There is always light at the end of the tunnel. You just need to find the switch - which is often right on the darkly shrouded wall behind you.

8. Linux is not so much a monster as a friendly devil. I prefer linux as my primary OS. Surprise.

9. I love my family. They are the best anyone could ever hope for and of course, the only ones I have.

10. Surprisingly, I like documentaries way more than movies.

I need to burn this into my mind:

Ctrl-D

After I make some unfortunate mistake at the prompt, bash patiently waits for my next move... when I really just want to get back to the home prompt and start all over again. Ctrl-D curtly tells it not to wait anymore and it exits with:

> bash: unexpected EOF while looking for matching `''
bash: syntax error: unexpected end of file

You have to love those quoted adjectives in trailers.

"Delightful"
oh, was the popcorn tasty?

"Terrific"
oops terrible?

"Stunning"
had a cataract surgery
"WONDERFUL!"
We were stoned.
"Masterful"
full of what?

"Spendid!"
you didn't!

"INTOXICATING"
say no more
"Charming!"
give it a rest already

"Captivating!!!"
drunk. no doubt

"Seductive"
so you have a crush on the actress

---
PS: wish there was a way to float words right. would have made it even more authentic. heh.

Another view of gorgeousness*

That is going to be my philosophy this date onwards.

In the year 2000...
2012...

I will

1. Work all year in pomodoros and squash as many tomatoes as I can.

1. Publish. Publish. Publish

1. Master R and Perl.

1. Learn how to manipulate and code in Bioconductor

1. Analyze and publish on least one public dataset in genetics.

1. Transition into more genetics and bioinformatics.

1. Write more science. Make future-oriented useful notes.

1. Be more in contact with my family.

1. Be less confused, Be more mentally organized

1. Set priorities and stick with them regardless of what comes in between.

1. Reach a better place and work on feeling less guilty

For Paul, Matt and Terry. :-)



---
NB: (e:matthew), check out the illustrations here:

My new deadline is December 31. I am dead serious about this and want to finish it once and for all. Even if lake Erie burst into flames right now and it was a grand public spectacle, I wouldn't want to go see it more than I want to finish my dissertation writing.

So I am taking off the internets and (e:strip) till the next year.

All of you, happy holidays and behave yourselves.

cheerio,
TP

rpm -qa *\nvidia\*  *\kernel\*|sort;uname -r;lsmod |grep -e nvidia -e nouveau;cat /etc/X11/xorg.conf

Hmmm.. that doesn't look so good

rpm -qa *\nvidia\* *\kernel\*|sort;uname -r;lsmod |grep -e nvidia -e nouveau;cat /etc/X11/xorg.conf

nouveau;cat /etc/X11/xorg.conf
abrt-addon-kerneloops-2.0.6-1.fc16.x86_64
kernel-3.1.4-1.fc16.x86_64
kernel-3.1.5-1.fc16.x86_64
kernel-3.1.5-2.fc16.x86_64
kernel-headers-3.1.5-2.fc16.x86_64
libreport-plugin-kerneloops-2.0.7-1.fc16.x86_64
texlive-l3kernel-2011-4.SVN_2966.svn24657.fc16.noarch
3.1.5-2.fc16.x86_64
nouveau 754554 0
ttm 61533 1 nouveau
drm_kms_helper 30277 2 i915,nouveau
drm 213647 7 i915,nouveau,ttm,drm_kms_helper
i2c_algo_bit 5572 2 i915,nouveau
i2c_core 28203 7 videodev,i2c_i801,i915,nouveau,drm_kms_helper,drm,i2c_algo_bit
mxm_wmi 1743 1 nouveau
video 12388 2 i915,nouveau
cat: /etc/X11/xorg.conf: No such file or directory

PS: I would like a decent lighter background code box for christmas.
With

• Inconsolata monospace font
• line-wrapping
• syntax highlighting (even without syntax highlighting is fine really)
• for perl and bash.

Thanks! :)

Thankfully, I waited for a complete 5 minutes (took (e:metalpeter)'s advice and went to get tea) instead of jumping on the power button. It recovered after taking its own sweet time.

Dec 17 20:20:26 why udevd[11705]: timeout: killing '/sbin/blkid -o udev -p /dev/sdb1' [12021]
Dec 17 20:20:27 why udevd[11705]: timeout: killing '/sbin/blkid -o udev -p /dev/sdb1' [12021]
Dec 17 20:20:28 why udevd[11705]: timeout: killing '/sbin/blkid -o udev -p /dev/sdb1' [12021]
Dec 17 20:20:28 why dbus-daemon[1173]: dbus[1173]: [system] Activating service name='net.reactivated.Fprint' (using servicehelper)
Dec 17 20:20:28 why dbus[1173]: [system] Activating service name='net.reactivated.Fprint' (using servicehelper)
Dec 17 20:20:28 why dbus-daemon[1173]: Launching FprintObject
Dec 17 20:20:28 why dbus[1173]: [system] Successfully activated service 'net.reactivated.Fprint'
Dec 17 20:20:28 why dbus-daemon[1173]: dbus[1173]: [system] Successfully activated service 'net.reactivated.Fprint'
Dec 17 20:20:28 why dbus-daemon[1173]: ** Message: D-Bus service launched with name: net.reactivated.Fprint
Dec 17 20:20:28 why dbus-daemon[1173]: ** Message: entering main loop
Dec 17 20:20:29 why udevd[11705]: timeout: killing '/sbin/blkid -o udev -p /dev/sdb1' [12021]
Dec 17 20:20:30 why udevd[11705]: timeout: killing '/sbin/blkid -o udev -p /dev/sdb1' [12021]
Dec 17 20:20:31 why udevd[11705]: timeout: killing '/sbin/blkid -o udev -p /dev/sdb1' [12021]

This is the tail of the /var/log/messages. With all those mentions of killings and daemons, it totally looks like notes from a homicidal maniac with a medieval tilt.

Farther back the log has these entries:

Dec 17 16:17:19 why dbus-daemon[1173]: dbus[1173]: [system] Successfully activated service 'org.freedesktop.PackageKit'
Dec 17 16:26:35 why kernel: [65687.762948] CPU6: Package power limit notification (total events = 2)
Dec 17 16:26:35 why kernel: [65687.762956] CPU2: Package power limit notification (total events = 2)
Dec 17 16:26:35 why kernel: [65687.762956] CPU1: Package power limit notification (total events = 2)
Dec 17 16:26:35 why kernel: [65687.762965] CPU0: Package power limit notification (total events = 2)
Dec 17 16:26:35 why kernel: [65687.762969] CPU4: Package power limit notification (total events = 2)
Dec 17 16:26:35 why kernel: [65687.762972] CPU7: Package power limit notification (total events = 2)
Dec 17 16:26:35 why kernel: [65687.762977] CPU5: Package power limit notification (total events = 2)
Dec 17 16:26:35 why kernel: [65687.762977] CPU3: Package power limit notification (total events = 2)
Dec 17 16:26:35 why kernel: [65687.773971] CPU5: Package power limit normal
Dec 17 16:26:35 why kernel: [65687.773975] CPU2: Package power limit normal
Dec 17 16:26:35 why kernel: [65687.773982] CPU4: Package power limit normal
Dec 17 16:26:35 why kernel: [65687.773984] CPU6: Package power limit normal
Dec 17 16:26:35 why kernel: [65687.773988] CPU3: Package power limit normal
Dec 17 16:26:35 why kernel: [65687.773992] CPU7: Package power limit normal
Dec 17 16:26:35 why kernel: [65687.773997] CPU1: Package power limit normal
Dec 17 16:26:35 why kernel: [65687.773999] CPU0: Package power limit normal
Dec 17 16:26:48 why kernel: [65700.686031] [Hardware Error]: Machine check events logged
Dec 17 16:26:48 why mcelog[1166]: Hardware event. This is not a software error.
Dec 17 16:26:48 why mcelog[1166]: MCE 0
Dec 17 16:26:48 why mcelog[1166]: CPU 2 THERMAL EVENT TSC 7740a8dc9110
Dec 17 16:26:48 why mcelog[1166]: TIME 1324157195 Sat Dec 17 16:26:35 2011
Dec 17 16:26:48 why mcelog[1166]: Processor 2 below trip temperature. Throttling disabled
Dec 17 16:26:48 why mcelog[1166]: STATUS c0000000881b0c00 MCGSTATUS 0
Dec 17 16:26:48 why mcelog[1166]: MCGCAP c09 APICID 4 SOCKETID 0
Dec 17 16:26:48 why mcelog[1166]: CPUID Vendor Intel Family 6 Model 42
Dec 17 16:26:48 why mcelog[1166]: Hardware event. This is not a software error.
Dec 17 16:26:48 why mcelog[1166]: MCE 1
Dec 17 16:26:48 why mcelog[1166]: CPU 1 THERMAL EVENT TSC 7740a8dcb633
Dec 17 16:26:48 why mcelog[1166]: TIME 1324157195 Sat Dec 17 16:26:35 2011
Dec 17 16:26:48 why mcelog[1166]: Processor 1 below trip temperature. Throttling disabled
Dec 17 16:26:48 why mcelog[1166]: STATUS c0000000881b0c00 MCGSTATUS 0
Dec 17 16:26:48 why mcelog[1166]: MCGCAP c09 APICID 2 SOCKETID 0
Dec 17 16:26:48 why mcelog[1166]: CPUID Vendor Intel Family 6 Model 42
Dec 17 16:26:48 why mcelog[1166]: Hardware event. This is not a software error.

It killed something in cold blood and is now gloating over it?

Apparently it is some bios issue as described here:

According to the followup to that post, it's a kernel issue that sprang up after 2.6.38.7 The kernel is not able to balance loads on the CPU/GPU well in processors with a sandy bridge and gives rise to these errors. Updating the bios does not solve the issue.

---

Why does it ALL have to happen in my machine?! Seriously, this is not even my super-sucky original machine. It's a machine from my bro. Does the linux universe hate me or what?!

VLC is misbehaving on my system. The GUI doesn't start up unless I invoke it on the terminal. I can't find a solution to the error that comes up and I don't have time to look. I just erased it out of frustration.

Here's the crazy error, (e:paul). Knock yourself out.

$ vlc
VLC media player 1.1.12 The Luggage (revision exported)
Blocked: call to unsetenv("DBUS_ACTIVATION_ADDRESS")
Blocked: call to unsetenv("DBUS_ACTIVATION_BUS_TYPE")
[0x13216c0] [rc] lua interface: Listening on host "*console".
VLC media player 1.1.12 The Luggage
Remote control interface initialized. Type `help' for help.
> vlc: could not connect to socket
vlc: No such file or directory
[0x13497d0] lirc interface error: lirc initialisation failed
[0x13497d0] main interface error: no suitable interface module
[0x134e1d0] oldtelnet interface: using the VLM interface plugin...
[0x134e1d0] oldtelnet interface: telnet interface started on interface localhost 4212
[0x121d120] main libvlc: Running vlc with the default interface. Use 'cvlc' to use vlc without interface.
Blocked: call to setlocale(6, "")
Blocked: call to setlocale(6, "")
(process:12794): Gtk-WARNING **: Locale not supported by C library.
	Using the fallback 'C' locale.

{and then VLC gui starts. It's insane to have to pull it up with the terminal.}

Which meant I looked for alternatives, and I found the beyond perfect replacement.


DeaDBeeF


It sounds gruesome but it is fantastic.


It has cuesheet support, a smashing 10 channel equalizer, tabbed playlist support, customizable colours, plays every lossless format and submits information to last.fm.

I suddenly and completely stopped missing foobar2000.

More importantly, the programs I miss from Windoze is now down to exactly 1.
PDFXchange Reader.