Entering edit mode
4.7 years ago
joyk2a
▴
30
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!
This link might help:
https://stackoverflow.com/questions/26296288/how-to-avoid-sink-stack-is-full-error-when-sink-is-used-to-capture-messages
Fatima, I did check the site but sadly I can't edit it. Hm..
Do you suggest advice about 2nd question?
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
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?
I haven't used it sorry :(
Have you checked their forum?
https://software.broadinstitute.org/cancer/cga/forum/5