I've been trying to figure where the error could show up and I have
some "poor" guesses. In order to figure it out better, please install
the developer's version of R.utils, which I just updated:
source('http://callr.org/install#HenrikBengtsson/R.utils@develop')
If the error occurs anywhere r
>
> Hmm... assuming you're on a *nix-like system, see if there are any
> empty (zero-size) RDS files is:
>
> ls -la
> cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/*.rds
>
>
>
> The original error message suggests that there could exist such a file.
>
Indeed, I
Hmm... assuming you're on a *nix-like system, see if there are any
empty (zero-size) RDS files is:
ls -la
cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/*.rds
The original error message suggests that there could exist such a file.
Also, you wrote "it systematically c
Hi Henrik,
does the error occur when you run:
>
> fit(cbs, verbose=verbose)
>
Yes, because I never got the "print(cbs)" output
> or did that complete successfully and you get the error while running:
>
> pathname <- writeRegions(cbs, verbose=verbose)
>
> If you run interactively, what
Hi,
does the error occur when you run:
fit(cbs, verbose=verbose)
or did that complete successfully and you get the error while running:
pathname <- writeRegions(cbs, verbose=verbose)
If you run interactively, what does traceback() output if called
immediately after the error occurs?
Also,
Hi all,
I'm processing a large set of SNP6 samples (1020) and performing CBS
segmentations afterwards. It's a very lengthy process and the annoying part
is that it systematically crashes on the last sample, see code and output
below:
# Run CBS paired segmentation with pooled normal samples
cbs
