fwrite allows sep=""

[ben-schwen]

Closes #4817

[MichaelChirico]

can we benchmark any potential performance impact of those branches added in potentially tight loops?

I guess they could be optimized away, makes sense to test with/without compiler optimization on

[mattdowle]

Yes good thought. I was just about to remove the branches...

[mattdowle]

Yes: I'd be surprised if there was any measurable difference.
The things that might be worth trying are bool instead of int and declaring sep and sepLen locally as const inside that deep loop in the parallel region. That way the const is making it crystal clear to the compiler that each thread doesn't need to check on every iteration to see if the global sep and sepLen has changed. Without const it has to cater for the possibility that another thread changes those globals. As we rely on for the failed global to stop a parallel region early upon error.

[archgen]

Hello, I am getting the below error when trying to set sep='' for fwrite.. I was wondering if you can direct me to how to utilise the added fwrite sep='' functionality?

Thanks very much for your help!
Matthew

Error in fwrite(eigenstrat_file$geno, sep = "", quote = FALSE, row.names = FALSE, :
is.character(sep) && length(sep) == 1L && nchar(sep) == 1L is not TRUE

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

other attached packages:
data.table_1.14.2

[ben-schwen]

@archgen
This feature has not made it to CRAN yet and is only available in the development version.

You can install the development version using data.table::update_dev_pkg()

[archgen]

Hi @ben-schwen thanks for your quick reply! I tried data.table::update_dev_pkg() but got the following error Error: 'update_dev_pkg' is not an exported object from 'namespace:data.table'

[ben-schwen]

@archgen Then data.table:::update_dev_pkg() should work.

[archgen]

Thanks again @ben-schwen , unfortunately, I get the error

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'update_dev_pkg' not found

I'm running on a cluster if that's important to know..

Thanks again for your time and help!

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.7 (Maipo)

Matrix products: default
BLAS/LAPACK: /apps/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib/libopenblas_haswellp-r0.2.18.so

locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] data.table_1.14.2

loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0

[jangorecki]

data.table:::update.dev.pkg()

The "_" function name is in 1.14.3+