Hi,
I keep getting this error when calling
DMRs <- dmrseq(bs=bs, testCovariate="group", cutoff = 0.05, BPPARAM = MulticoreParam(1))
After running through chr1 and chr2, it suddenly causes:
Error in asin.gls.cov(ix = ind[Index], design = design, coeff = coeff) :promise already under evaluation: recursive default argument reference or earlier problems?
the pData(bs)
looks like:
DataFrame with 6 rows and 2 columns
group patient
<factor> <integer>
B02_22093.CRC non 1
B02_22093.NORMAL NORMAL.non 1
B02_2911.CRC non 2
B02_2911.NORMAL NORMAL.non 2
B03_501.CRC non 3
B03_501.NORMAL NORMAL.non 3
I ran the test dataset data(BS.chr21)
, and it ran fine, so I wonder if it has to do with running one chromosome after the other?
Any ideas are appreciated!
Hi,
Thank you for reporting this issue.
Can you verify which version of dmrseq you are using, and check that all other packages are up to date (using BiocManager::valid())?
If you are using a current version with updated dependencies and the error still persists, would you be able to send along a subset of the BSseq object you are using as an .rds file (either linked here or via email to keegan at jimmy.harvard.edu). The subset including just the chromosome that throws the error should be sufficient. That will help me to diagnose the error message.
Thank you!
Best, Keegan
Hi, thanks for answering!
So
BiocManager::valid()
is TRUE, and dmrseq version is 1.4.5.I was making a subset for you with 2 chromosomes, and tested it and worked (???). Now that I'm testing the full first two chromosomes, it complains again. I will send you this last one by email (if it's not too big), otherwise I'll test with other subsets, and see where it fails.
Thanks for checking on the version and dependencies.
If a single chromosome runs fine, this might be an out of memory issue.
If the file is too large, shoot me an email and I'll send you back a link where you can upload it.
Best, Keegan