Category Archives: R

Line starting ‘ …’ is malformed! error

Posted on November 10, 2013 by Thomas Cokelaer

Playing with a Python wrapper of an R package, I suddenly got this error after a trivial change of the code: Line starting ‘<!DOCTYPE html> …’ is malformed!Line starting ‘<!DOCTYPE html> …’ is malformed! Wondering for a couple of minutes … Continue reading →

Posted in R | Tagged , , | Leave a comment

R package dependencies: difference between imports, depends, suggests, enhances

Posted on July 31, 2013 by Thomas Cokelaer

When you want to assemble R codes into a package, you will need to write a file called DESCRIPTION. This file contains some metadata and keywords to be used and some keywords are definitely confusing (at least to me). Here … Continue reading →

Posted in R, Uncategorized | Tagged | 1 Comment

Using valgrind to debug R programs

Posted on March 14, 2013 by Thomas Cokelaer

If you want to debug your R program because of a segmentation fault or memory leak, you can use valgrind as follows in a shell: R -d "valgrind –leak-check=full –show-reachable=yes" -f your_script.RR -d "valgrind –leak-check=full –show-reachable=yes" -f your_script.R

Posted in R | Tagged , | Leave a comment

How use R to build permutation or combination

Posted on November 23, 2012 by Thomas Cokelaer

In a previous post, I used itertools in Python to create combination and permutation using the standard module itertools. What about using R language to perform the same task. The permutation function allows you to get permutation of N values … Continue reading →

Posted in Python, R | Tagged , | Leave a comment

Bioconductor: first installation

Posted on October 28, 2012 by Thomas Cokelaer

Bioconductor is a website that gathers open source software for bioinformatics in the R language. You can install a Bioconductor package using their interface. As an example, let us install the RBGL package. First, start a R session, and then … Continue reading →

Posted in R | Leave a comment