R module RHmm for ibd2.r script

[AJERYC]

I'm trying to run the R script ibd2.R in order to perform IBD=2 analysis on exome sequences (Bioinformatics. 2011 Mar 15;27(6):829-36. 2011 Jan 28. Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders), but having big troubles in installing the RHmm module into R, under Ubuntu. I first thought it was the old R version that comes with Ubuntu 12, but after I have upgraded R to the last version 2.15, I am still having the same troubles with different message of error,

In getDependencies(pkgs, dependencies, available, lib) : package ‘RHmm’ is not available

or
Warning: invalid package ‘RHmm_2.0.2.tar.gz’

can someone give me some hint to carry on?
Thanks,

[GenoMax]

Do you have the two dependencies installed (MASS, nlme)? Are you trying to install RHmm from the source?

[AJERYC]

Yes, both are already installed.

[GenoMax]

Can you post the complete error message(s) or are you just getting that one line? Have you tried to re-download the source package in case the copy you have is corrupt.

[AJERYC]

This is what the paper recommends:
> install.packages("RHmm", repos="http://R-Forge.R-project.org")
Alternatively, the package can be downloaded from homepage of the RHmm project at R-Forge1 It can be installed from the linux command line by the following command:
$ R CMD INSTALL RHmm_1.4.2.tar.gz

This is what I get with one or the other solution:
Warning message:
package ‘RHmm’ is not available (for R version 2.15.3)

or

Warning: invalid package ‘RHmm_2.0.2.tar.gz’

Thanks,

[GenoMax]

I just installed it using the "R CMD INSTALL" option on a RHEL system (with R v.2.14.0) using the source tarball that I downloaded from here (http://cran.r-project.org/src/contrib/RHmm_2.0.2.tar.gz).

Have you installed packages using the command line on the server you are using before?

[AJERYC]

(SOLVED) Thanks for backup. This is what worked for me: in R:
install.packages("RHmm")

Installing package(s) into ‘~/R/x86_64-pc-linux-gnu-library/2.15’ (as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.at.r-project.org/src/contrib/RHmm_2.0.2.tar.gz'
Content type 'application/x-gzip' length 127791 bytes (124 Kb) opened URL
==================================================
downloaded 124 Kb

* installing *source* package ‘RHmm’ ...
.....
g++ -I/usr/share/R/include -DNDEBUG -w -D_RDLL_ -fpic -O3 -pipe -g -c cUnivariateNormal.cpp -o cUnivariateNormal.o
g++ -I/usr/share/R/include -DNDEBUG -w -D_RDLL_ -fpic -O3 -pipe -g -c cViterbi.cpp -o cViterbi.o
g++ -shared -o RHmm.so Kmeans.o LogProb.o Main.o MultivariateNormalUtil.o RHmm.o SamplesUtil.o StatUtil.o StdAfxRHmm.o cBaumWelch.o cBaumWelchInParam.o cDMatrix.o cDVector.o cDerivative.o cDiscrete.o cHmm.o cHmmFit.o cInParam.o cLogBaumWelch.o cMixtMultivariateNormal.o cMixtUnivariateNormal.o cMultivariateNormal.o cOTError.o cRUtils.o cUnivariateNormal.o cViterbi.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to ~/R/x86_64-pc-linux-gnu-library/2.15/RHmm/libs
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (RHmm)