dada2 is taciturn

[rec3141]

even with verbose=T, dada2 is very quiet. sometimes this is good but it would be nice to have more feedback at times, especially on long running commands. one example is with removeBimeraDenovo, it would be useful to output some kind of progress when verbose=T. same with the other commands. thanks

[spholmes]

It is true, that like its creator dada2 likes to be very discrete, maybe
every 1K iterations/sequences
it could output a dot
................
would show that the process is still alive.

On Thu, Mar 23, 2017 at 6:11 PM, rec3141 [e-mail] wrote:

even with verbose=T, dada2 is very quiet. sometimes this is good but it
would be nice to have more feedback at times, especially on long running
commands. one example is with removeBimeraDenovo, it would be useful to
output some kind of progress when verbose=T. same with the other commands.
thanks

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[benjjneb]

Progress dots would be a nice feature. There is a complication in that output from multithreaded commands can cause problems in R Guis (like Rstudio) as R itself is single-threaded.

Will look into that a bit more though.

[benjjneb]

@cdiener from #318

Some of the dada2 functions like learnErrors and dada always print output to the terminal and this behavior can not be controlled with any argument as far as I can see. This makes it hard to use those functions in code using progress bars (for instance pbapply) and also clutters Rmarkdown documents a bit. Also a lot of the output does not indicate a problem or warning so it might be nice to be able to switch it off. Maybe a real logging solution would be nice where I can set the level of info I want to see across the current environment or log everything into a log file.

[benjjneb]

@cdiener The non-error output of dada and learnErrors can now be silenced with dada(..., verbose=0) and learnErrors(..., verbose=0). The regular verbose=TRUE or FALSE values still work as before (see help text): b937e42fa37149ab6f78e71ac7973c5aae2e223b

Unfortunately progress-reporting while multithreading remains unsolved for this (1.6) release.

[cdiener]

Thanks that's all I wanted!