Making a progress bar for long R programs

From : http://ryouready.wordpress.com/2009/03/16/r-monitor-function-progress-with-a-progress-bar/

total <- 20
# create progress bar
pb <- txtProgressBar(min = 0, max = total, style = 3)
for(i in 1:total){
Sys.sleep(0.1)
# update progress bar
setTxtProgressBar(pb, i)
}
close(pb)

How to concatenate a list of data.frames to obtain a data.frame in R

From http://stackoverflow.com/questions/2851327/r-converting-a-list-of-data-frames-into-one-data-frame :

df <- do.call("rbind", listOfDataFrames)

extract maps in sp format from the maps package in R

from the doc of the package spacetime :

library(maps)
states.m = map('state', plot=FALSE, fill=TRUE)
IDs <- sapply(strsplit(states.m$names, ":"), function(x) x[1])
library(maptools)
states = map2SpatialPolygons(states.m, IDs=IDs)
class(states)
[1] "SpatialPolygons"
attr(,"package")
[1] "sp"

reading numeric data from a string variable in R

use textConnection :

strin_var = readLines(textfle)
tc=textConnection(string_var)
df = read.table(tc,colClasses="numeric")


http://www.r-bloggers.com/example-8-27-using-regular-expressions-to-read-data-with-variable-number-of-words-in-a-field/

Backing up or moving a Silverstripe website

http://silverstripe.org/installing-silverstripe/show/4581#post251271

Flushing cache in Silverstripe

go to the link http://silverstripe.website.org/?flush=1

Hand Typed Path in Nautilus – Ubuntu

Try Ctrl-L

Accessing a postgresql database in OpenOffice or libreoffice

If you have ubuntu, install :

sudo apt-get install libreoffice-sdbc-postgresql


In LibreOffice, create a new database. Then, in connection parameters, specify the URL : dbname=XXX host=abc.net and then the username and the password.

Graphical file diff editor for Linux

Meld is a wonderful little graphical program for Linux that helps differentiate between text files :

sudo apt-get install meld

geodjango object has no attribute 'geo_db_type

Following the geodjango tutorial https://docs.djangoproject.com/en/dev/ref/contrib/gis/tutorial/

While building the application called world, one has to run the following command to initialise the database :

python manage.py sqlall world
....
AttributeError: 'DatabaseOperations' object has no attribute 'geo_db_type'

The error is solved by editing settings.py and replacing the line
'ENGINE': 'django.db.backends.postgresql_psycopg2', # Add 'postgresql_psycopg2',
with
'ENGINE': 'django.contrib.gis.db.backends.postgis', # Add 'postgresql_psycopg2',

Thanks to http://stackoverflow.com/questions/3567352/geodjango-syncdb-errors-from-geodjango-tutorial

GIMP: Replace image backgrounds with transparency

Save the image in a format that handles transparency (GIMP pcx or PNG).

Create an alpha channel : Layer-Transparency-Add Alpha Channel

To replace a single given color with transparency : Layer-Transparency-Color to Alpha

Ubuntu : too many open files

From http://www.zimbra.com/forums/administrators/16066-solved-too-many-open-files-error.html

To set the maximum limit allowed for open files, as sudo or root, edit the /etc/security/limits.conf file. At the end of the file just above “# End of File” enter the following values:
* soft nofile 65535
* hard nofile 65535
Save the file. This will set the number of open files to unlimited.

An R package : sun-methods Methods for sun ephemerides calculations

sun-methods Methods for sun ephemerides calculations

Description :
Functions for calculating sunrise, sunset, and times of dawn and dusk, with flexibility for the various formal definitions. They use algorithms provided by the National Oceanic & Atmospheric Administration (NOAA).

Plotting error bar with polygons in R

A very nice presentation by Edzer Pebesma showing the spatio-temporal capabilities of R (spacetime package). Includes a nice way of plotting error bars as polygons :

http://ifgi.uni-muenster.de/~epebe_01/inpe.pdf

Startup manager for Ubuntu for boot options

"sudo apt-get install startupmanager"

GuitarPro6 segmentation fault Ubuntu 64 bits

http://askubuntu.com/questions/41920/why-i-am-getting-a-segmentation-fault-opening-guitar-pro

mv ~/.ArobasMusic ~/.ArobasMusicbkp

If this does not work (Ubuntu 11.04), and the error is :

GdkPixbuf-CRITICAL **: gdk_pixbuf_get_height: assertion `GDK_IS_PIXBUF (pixbuf)' failed
Segmentation fault

then downgrade the ia32-libs package :
(from http://getsatisfaction.guitar-pro.com/arobas_music/topics/after_ubuntu_11_04_upgrade_i_cant_open_gp6)

It seems a bug in the latest ia32-libs causes some trouble to applications that uses 32bit libraries (GP6 use 32 bit libraries too).

A workaround exists, simply downgrade the ia32-libs package.

Follow these guidelines to downgrade ia32:
- download the package from this page http://packages.ubuntu.com/maverick/amd64/ia32-libs/download
- execute this command line: sudo dpkg --force-downgrade -i ia32-libs_20090808ubuntu9.1_amd64.deb

Mounting SeaGate GoFlex from Linux

Download the driver from :
http://download.pogoplug.com/install/linux/pogopluginstall.tar.gz

Create a conf file .pogoplugfs.conf under the same directory as the driver :

svcuser=your_email_registered_with_pogoplug.com
svcpassword=PASS

To mount the file system in a non-empty direcory :
./pogoplugfs --mountpoint /home/acizmeli/Pogoplugfs/

use lapply to modify a list of lists in R

modifyList package:utils R Documentation

Recursively Modify Elements of a List

Description:

Modifies a possibly nested list recursively by changing a subset
of elements at each level to match a second list.

querying a samba server and mounting a share

smbclient -L server

sudo /sbin/mount.cifs //server/Data /home/me/mountplace -o user=acizmeli%pass,rw

Stream an image file from a web server and restore it to a partition:

Stream an image file from a web server and restore it to a Linux partition:

wget -qO - http://server/backup.img | \
ntfsclone --restore-image --overwrite /dev/hda1 -

python : To create a separate list

To create a separate list, you can use slicing or the list function to quickly create a copy:

L = []
M = L[:] # create a copy

# modify L only
L.append(obj)

grep with the find command with the Linux bash shell

use grep's command line option -H to print the filenames when used within the command "find"

find . -name \*.py -exec grep -Hn string_to_search {} \;

UbuntuOne client crashes with the non-UTF filenames

Detect the files with a bad name with : python /home/acizmeli/Downloads/utf8-filename-check.py

and rename the files


https://bugs.launchpad.net/ubuntuone-client/+bug/368626

GuitarPro missing fonts

http://getsatisfaction.guitar-pro.com/arobas_music/topics/_font_missing_after_updating

Hi, try to remove these files :
C:\ProgramData\Guitar Pro 6\GuitarPro.dat
and
C:\Users\nmartin\AppData\Roaming\Guitar Pro 6\GuitarPro.dat

Linux :
sudo rm /opt/GuitarPro6/GuitarPro.dat

How to install Google Earth in Ubuntu 10.10 Maverick 64 bits

from http://www.ubun2.info/2010/10/how-to-install-google-earth-in-ubuntu.html?showComment=1287937450936

nstalling Google Earth in Ubuntu Maverick is very simple. For Ubuntu Maverick 64 bit users,they need to install the dependance package: ia32-libs and lib32nss-mdns.

Open up a terminal window from Applications -> Accessories menu and run:
sudo apt-get install ia32-libs lib32nss-mdns

After the installation of ia32-libs and lib32nss-mdns complete.
Then install googleearth-package from the default repository using this command:
sudo apt-get install googleearth-package

Then run the command:
make-googleearth-package --force

it will take a moment and finally generate a deb package.
Install the deb by the command (change the package name to yours):
sudo dpkg -i googleearth.deb

Finally,launch Google Earth from Applications – > Internet menu.

How to Install GuitarPro6 on 64-bit Ubuntu

From http://ubuntuforums.org/showthread.php?t=1458626

How to Install Guitar Pro 6 on 64-bit install.
1) Download the latest .deb from Guitar Pro's website.
2) Goto http://frozenfox.freehostia.com/cappy/ and install getlibs-all.deb
3) Run this in terminal
Quote:
sudo dpkg -i --force-architecture Downloads/GuitarPro6-r7840.deb
You will get some errors but ignore.
4) Run this in terminal
Quote:
getlibs /opt/GuitarPro6/GuitarPro

Moving a thunderbird profile to another machine

http://support.mozillamessaging.com/en-US/kb/Profiles#_Moving_a_profile

Installing Rstudio in Ubuntu : ignoring a depending package

The installer of rstudio complains : Package r-base is not installed. But in ubuntu, that package exists under the name r-base-core.

Simply install the package with the following command :

sudo dpkg -i --ignore-depends=r-base rstudio-0.92.23-i386.deb

To debug R code

Either :
* put the command browser() : will stop where the command "browser" was called
* or call the function debug : debug(name_function_to_debug) : will stop at the start of the script
* options(error=recover)

Type "Q" to exit the browser. Type "n" to execute the next line. Type "c" or ENTER to continue running and exit the function.

Installing RNetCDF (ncdf) in R

Taken from https://stat.ethz.ch/pipermail/r-help/2008-March/157089.html
This is ubuntu 10.4.

sudo apt-get install libudunits2-0 libudunits2-dev
sudo apt-get install libnetcdf4 libnetcdf-dev

Then in R :
install.packages("RNetCDF",configure.args="--with-netcdf-include=/usr/include")

Note : A regular install is unable to find netcdf.h, giving the error below. Use rather the install.packages command given above.

checking for netcdf.h... no
configure: error: netcdf header netcdf.h not found
ERROR: configuration failed for package ‘ncdf’

ubuntu : installing ubuntugis and R

Add the following lines in /etc/apt/sources.list :

sudo vi /etc/apt/sources.list
deb http://cran.skazkaforyou.com/bin/linux/ubuntu maverick/
deb http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu maverick main
deb-src http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu maverick main

Then add the "canonical partners" software repository from "ubuntu software center-sofware sources" (for sun java jdk/jre)

Get the keys
sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com D67FC6EAE2A11821
sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable


sudo apt-get update
sudo apt-get install r-base-core libgdal1-dev libproj-dev libgdal1-1.7.0-grass qgis grass saga sun-java6-jdk

qmail problem in plesk

Cannot send mail with qmail :

qmail-queue-handlers[xxxxxx]: cannot create temporary file - (13) Permission denied

I searched the web and there seems to be a solution. But it does not work :
http://forum.parallels.com/showthread.php?t=87344
http://forum.parallels.com/showthread.php?t=94593