Question: I can't run on example data of ABSOLUTE....
1
gravatar for joyk2a
10 months ago by
joyk2a30
joyk2a30 wrote:

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!

R • 408 views
ADD COMMENTlink modified 10 months ago by zx87549.9k • written 10 months ago by joyk2a30

This link might help:

https://stackoverflow.com/questions/26296288/how-to-avoid-sink-stack-is-full-error-when-sink-is-used-to-capture-messages

ADD REPLYlink written 10 months ago by Fatima890

Fatima, I did check the site but sadly I can't edit it. Hm..

Do you suggest advice about 2nd question?

ADD REPLYlink written 10 months ago by joyk2a30

Hi :) There are several ways to install a package in R, so you might need to try another method:

https://software.broadinstitute.org/cancer/cga/hapseg_run

ADD REPLYlink written 10 months ago by Fatima890

Fatima, Yep. I started to install it from the same site. hm.... Have you used ABSOLUTE before? If you had, can I have your example R.code?

ADD REPLYlink written 10 months ago by joyk2a30

I haven't used it sorry :(

Have you checked their forum?

https://software.broadinstitute.org/cancer/cga/forum/5

ADD REPLYlink modified 10 months ago • written 10 months ago by Fatima890
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