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Different Exit code 1

Different Exit code 1
Answer
7/22/13 4:31 PM
Hi,
Have been using the RobiNA program with a number of data sets with great success. Ran one today and got the following error:

Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object(s) are masked from 'package:stats':

xtabs

The following object(s) are masked from 'package:base':

Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocInstaller
BiocInstaller version 1.4.7, ?biocLite for help
R(1019,0xac82ba28) malloc: *** mmap(size=838864896) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(1019,0xac82ba28) malloc: *** mmap(size=838864896) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error: cannot allocate vector of size 800.0 Mb
Execution halted

what does this mean? I dont think i changed anything compared to what I had been doing before

RE: Different Exit code 1
Answer
7/22/13 4:42 PM as a reply to mark howard.
Hi Mark,

thanks for your feedback. Good to hear that you find RobiNA useful. The problem
you've encountered this time is, according to the error message you've attached,
memory related. The R engine embedded in RobiNA complains that it can't allocate
data vector of 800MB. This is most likely happening because there is not enough
free memory left in the computer. Reasons for this could, for example, be other
programs running at the same time or a machine with insufficient memory.

How much RAM does your computer have and which operating system does it
run?

Please try closing all other applications and try rerunning the analysis with RobiNA
being the only active program.

Hope this helps,
best greetings,
Marc

RE: Different Exit code 1
Answer
7/22/13 4:52 PM as a reply to Marc Lohse.
Thanks for the swift response. I actually just got a brand new mac here at work with 8GB of memory running OS X so I'm not sure how I could be running out? I tried with no other programs running and got the same error message

RE: Different Exit code 1
Answer
7/22/13 5:10 PM as a reply to mark howard.
That, indeed, sounds strange. Most probably this is related to the Mac OS X version. I presume
your old machine was a mac too (?) and ran an older version of Mac OS X (e.g. 10.6.x ?) while your
new machine is running 10.8.x ?

RE: Different Exit code 1
Answer
7/22/13 5:18 PM as a reply to Marc Lohse.
I have been running datasets successfully both on this new computer as well as my previous one. The only other things I can think of is that this one is slightly larger than previous datasets with 16 total CEL files. Don't know if that is relevant

I can try the analysis on my home computer with an earlier OS X version once I get home tonight, see if it is the operating system

RE: Different Exit code 1
Answer
7/29/13 12:27 PM as a reply to mark howard.
Hi, sorry for the delay, I have tried the dataset on my other computer with an older version of OS X with the same result. The computer is a couple of years old so I dont know if it is an OS X problem or something else?