Posts from January 2012

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: @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 @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, @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.

I think I am going to document all the "transactions" of updates here so I can go back and see what changed when.

I also found out recently that someone called Ben Williams uploads updated Fedora livecds and images when kernels are updated. I think I will be using his images from now on if I do any new install so that all updates are incorporated in the newly installed system.

Starting with the update today:

Installing:
 kernel                    x86_64    3.1.5-2.fc16             updates      26 M
Updating:
 createrepo                noarch    0.9.9-9.fc16             updates      97 k
 dhclient                  x86_64    12:4.2.3-4.P1.fc16       updates     258 k
 dhcp-common               x86_64    12:4.2.3-4.P1.fc16       updates     273 k
 dhcp-libs                 x86_64    12:4.2.3-4.P1.fc16       updates     123 k
 diffutils                 x86_64    3.2-5.fc16               updates     259 k
 dracut                    noarch    013-20.fc16              updates     164 k
 folks                     x86_64    1:0.6.5-2.fc16           updates     440 k
 fprintd                   x86_64    0.4.1-1.fc16             updates      56 k
 fprintd-pam               x86_64    0.4.1-1.fc16             updates      13 k
 gnome-python2             x86_64    2.28.1-7.fc16            updates      46 k
 gnome-python2-bonobo      x86_64    2.28.1-7.fc16            updates      79 k
 gnome-python2-canvas      x86_64    2.28.1-7.fc16            updates      32 k
 gnome-python2-gconf       x86_64    2.28.1-7.fc16            updates      42 k
 gnome-python2-gnome       x86_64    2.28.1-7.fc16            updates      74 k
 gnome-python2-gnomevfs    x86_64    2.28.1-7.fc16            updates      78 k
 gtk2                      i686      2.24.8-3.fc16            updates     3.2 M
 gtk2                      x86_64    2.24.8-3.fc16            updates     3.2 M
 gtk2-immodule-xim         x86_64    2.24.8-3.fc16            updates      62 k
 kernel-headers            x86_64    3.1.5-2.fc16             updates     772 k
 libfprint                 x86_64    0.4.0-1.fc16             updates     114 k
 libimobiledevice          x86_64    1.1.1-3.fc16             updates     101 k
 mdadm                     x86_64    3.2.2-15.fc16            updates     317 k
 memtest86+                x86_64    4.20-4.fc16              updates      77 k
 openssh                   x86_64    5.8p2-23.fc16            updates     257 k
 openssh-clients           x86_64    5.8p2-23.fc16            updates     396 k
 openssh-server            x86_64    5.8p2-23.fc16            updates     313 k
 tracker                   x86_64    0.12.8-2.fc16            updates     1.2 M
 vte                       x86_64    0.28.2-2.fc16            updates     349 k
 vte3                      x86_64    0.30.1-3.fc16            updates     317 k
Removing:
 kernel                    x86_64    3.1.2-1.fc16             @updates    112 M
Installing for dependencies:
 pyliblzma                 x86_64    0.5.3-5.fc15             fedora       44 k

Transaction Summary
================================================================================
Install       2 Packages
Upgrade      29 Packages
Remove        1 Package

I really wish the code box were lighter and easier on the eye. :(

I don't like bananas. They are not really high on my fruits from heaven list (topped by papaya, btw).

But the minute bananas are looking sad, black, almost ready to mould, I develop an inordinate amount of love for them because they make the MOST amazing banana bread aroma when I bake them. Even if the bread itself turns out a mild disaster (it mostly does since I cut out everything remotely luxurious, including butter), the ripe baking banana aroma is quite enough for me to love any bread... however poorly it might have turned out.

So if you are about to toss some black bananas, you know who wants them.

ME.
Signed,
The black spotty over-ripe banana bread experimenter supreme.

---
NB: today's experiment
2 black over-ripe bananas
1 cup plain low-fat yogurt
1¾ cup Whole Wheat Bread flour
¼ cup Wheat bran
Nutmeg
Fig Butter
½ cup Applesauce
Splash of vanilla essence
One BIG thumbs-sized (your thumbs, not mine) fresh ginger chopped.
Some ground black pepper
A tsp and a ½ of salt.

When there is no chocolate on walgreens shelves. Well... there is chocolate but not MY favourite chocolate.

I realize I eat chocolate like it were popcorn or something but still... they are out of *my favourite* chocolate today. They say it will be re-stocked soon. But I want it now, dammit.

Ominous plus plus