Comments (1)
kasperdanielhansen
commented on June 30, 2024
This was caused by a switch from scan() to data.table::fread(). The later function is much faster but does not support gzipped files. Pete has just committed a fix yesterday (which only support gzip I think), and we might switch from data.table::fread() to readr::read_tsv() even though it is slower because this other function has full support for compressed files.
from bsseq.
Related Issues (20)
- read.bismark() too slow - input format issue? HOT 8
- BSmooth - Error in env[[as.character(i)]] <- value : wrong args for environment subassignment HOT 2
- Error: C stack usage 10847362 is too close to the limit HOT 3
- Is it possible to append metadata to the GRanges within BSseq objects? HOT 3
- Normalization of the WGBS smooth data HOT 5
- bsseq incompatible with tictoc library HOT 1
- Error BSmooth HOT 3
- read.bismark: option to change tmpdir in fread? HOT 4
- BSmooth with HDF5 realization backend error: Stop worker failed with the error: wrong args for environment subassignment HOT 5
- combineList: BACKEND Argument not working as intended HOT 1
- BSmooth.tstat issue HOT 11
- Updating beachmat to tatami HOT 1
- combine(sample1.smooth, sample2.smooth) gives in unsmooth results? HOT 4
- bsmooth() fails - Error in `h()`: ! error in evaluating the argument 'seed' in selecting a method for function 'DelayedArray': HDF5. File accessibility. Unable to open file. HOT 3
- Reading H5 files directly HOT 3
- error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark. HOT 26
- Represent a CpG with single row during import HOT 11
- exclude "Y" chromosome from bsseq object HOT 3
- Upcoming change to DelayedArray::realize() HOT 2
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