Hi,

I am trying to set up"ABSOLUTE" in R.

My reference site is "https://software.broadinstitute.org/cancer/cga/absolute_run".

To test it, I copied and run the R code with the example data in the above site

1) First error shows..

foreach (scan=scans, .combine=c) %dopar% {DoAbsolute(scan, sif)}

Error in { : task 1 failed - "sink stack is full"
Error in sink(file, type = type, split = split) : sink stack is full

2) My second concern is "HAPSEG" package should be installed before it runs.

If then, I downloaded HAPSEG_1.1.1.tar.gz and tried to install.

(Because I thought the below command line has "hapseg".

seg.dat.fn <- file.path("output", scan, "hapseg",
                          pasteplate.name, "_", scan, "_segdat.RData", sep=""))

However it showed an error again.

* installing *source* package 'HAPSEG' ...
** using staged installation
** libs

*** arch - i386
Warning in system(cmd) :  'make' not found
ERROR: compilation failed for package 'HAPSEG'

If you can help me, it will be great help for my setting.

Thanks in advance!