Question: Please help with workspace error in R
gravatar for Sara
12 months ago by
Sara0 wrote:

Hi all,

I'm running a Fisher exact test with a large amount of data (2 columns and about 3000 rows) on the cluster (Rocks 6.2) with R 3.3.2 , but I got the below workspace error with 1e9 value as workspace:

 FEXACT error 7.
LDSTP is too small for this problem.
Try increasing the size of the workspace.
Calls: [ -> [.data.table -> fisher.test
Execution halted

With increasing workspace, I got another error:

cannot allocate memory block of size 134217728 Tb
Calls: [ -> [.data.table -> fisher.test
In addition: Warning message:
In fisher.test(matrix(c(a1, a2, b1, b2), ncol = 2),  :
  NAs introduced by coercion to integer range
Execution halted


I used "subR -input=file.R -mem=200G" for submitting and running R on the cluster. I played a lot with workspace value, but one of the two above-mentioned errors appeared. Also, "ulimit" returned me "unlimited" , so sounds that there is no limitation from system admin. Surprisingly, I before run the Fisher test on the same dataset with the same workspace value (1e9) on another server successfully during just 10 minutes. Although I didn't remember its RMA, the RAM and other properties were not higher the current server I'm working on it. Could you please kindly help me out to solve this problem?


Many thanks in advance

R test fisher exact workspace • 310 views
ADD COMMENTlink modified 12 months ago by Aaron Lun25k • written 12 months ago by Sara0
Answer: Please help with workspace error in R
gravatar for Aaron Lun
12 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:
  1. This is not a Bioconductor question, you should ask this on a general R programming forum like Stack Overflow, or on the R-help mailing list.
  2. This is already a well-encountered "problem" that has much commentary online (just google "fisher exact test workspace", for example). The error is also described in ?fisher.test.
  3. Make your life easier and just use a chi-squared test.
ADD COMMENTlink written 12 months ago by Aaron Lun25k

Thanks Aaron for your response. Yes, it's not specific to Bioconductor, but it may be a basic question for this forum so I asked here, sorry. I searched a lot before the posting question, however, none of them was helpful, and I'm not sure how accurate is the test using the simulate p-value as one of the suggested solutions? Also, as there are some values smaller than 5 (actually, they are 0), in my dataset so I cannot use the chi-squared test.

ADD REPLYlink modified 12 months ago • written 12 months ago by Sara0
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