Posts Tagged ‘ linux ’

Music file graphs with R

May 22, 2011
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Music file graphs with R

Today we will use R to extract some interesting summary statistics regarding the music files stored in the computer. For all mp3 files I keep certain metadata in their ID3 tag. We will use this information to explore the distribution of music files with respect to the year of release. All the following are done

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R 2.12 to 2.13 package upgrade

April 14, 2011
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R 2.12 to 2.13 package upgrade

If you: use Linux have just upgraded your R installation from 2.12 to 2.13 installed some/all of your packages in your home area (e.g. ~/R/i486-pc-linux-gnu-library/2.12) and… …are wondering why R can’t see them any more just do this: # at a shell prompt cp ~/R/i486-pc-linux-gnu-library/2.12 ~/R/i486-pc-linux-gnu-library/2.13 # in R console update.packages(checkBuilt=TRUE, ask=FALSE) # back to

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Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

April 11, 2011
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Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

Lately I haven't written as many full length posts as usual, but here's a quick roundup of a few links I've shared on Twitter (@genetics_blog) over the last week:First, 23andMe is having a big DNA Day Sale ($108) for the kit + 1 year of their personal ...

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A new series of mishaps

March 12, 2011
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A new series of mishaps

Following the slight difficulties of last week, I had a hard week on the computer front: indeed, on Monday, I received my 2007 macbook from the repair shop, with a new video card, courtesy of Apple. Unfortunately, this started a series of problems. First, the old macbook stopped recognizing the NVIDIA video and, while it

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Disas-tea-R at dawn

December 16, 2010
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Disas-tea-R at dawn

This was bound to happen sooner or later, given my addiction to tea and sleepless nights, so I eventually managed to spill a cup of tea over my Mac… I had been working for a few hours in my hotel room in Philadelphia, completing an ABC paper with Jean-Michel Marin and Robin Ryder. We had

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upgrade R – F77 cause compilation error

October 20, 2010
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I try to compile the source code of R 2.12 on CentOS, but it throw an error when trying to install *cluster*. * installing *source* package ‘cluster’ ... Read More: 3800 Words Totally

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The wonderful world of vim

July 20, 2010
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The wonderful world of vim

When searching for a way to recover control carriage return symbols ^M into genuine ones (under vim), I found this handy page of vim tips. And then saw that the enthusiastic author had even a blog about vim! Obviously, this post will be meaningless for all readers not aware of the joys of the vim

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Shrinking R’s PDF output

June 17, 2010
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Shrinking R’s PDF output

R is great for graphics, but I've found that the PDF's R produces when drawing large plots can be extremely large. This is especially common when using spplot() to plot a large raster. I've made a 15 page PDF full of rasters that was hundreds of MB in ...

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General steps to compile JAGS in a Linux based OS system and install rjags in R

June 6, 2010
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I have an entry here about how to install JAGS and rjags in Fedora.  However, I have exchanged emails with Robert Dorazio and Dr. Martyn Plummer.  Here are the easier steps to compile JAGS and install rjags in R. 1. After you extract the source code...

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JAGS, rjags, and coda packages for Fedora

June 6, 2010
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Christopher has the RPMs (for Fedora users) for JAGS, coda, and rjags on his blog. The specific blog entry is here: http://cddesjardins.wordpress.com/2010/06/04/jags-package-for-fedora-13-64-bit/ If you have trouble installing JAGS or rjags in Fedora,...

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