[R] RSQLite slowness

Jeff Newmiller jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Wed Oct 6 21:11:00 CEST 2021

Since the sqlite package is contributed, it is NOT related to "core R", and is in fact technically off-topic on this list.

FWIW all SQL implementations work better with indexes, but AFAIK the R data frame support does nothing with indexes. This may be related to your question, or not. I am not a regular sqlite user.

As for fast reading of tsv files, I think arrow, readr, and data.table packages all offer high-performance import functions that could be relevant.

On October 6, 2021 11:49:55 AM PDT, Rasmus Liland <jral using posteo.no> wrote:
>Thank you Bert, I set up a new thread on 
>BioStars [1].  So far, I'm a bit 
>unfamilliar with Bioconductor (but will 
>hopefully attend a course about it in 
>November, which I'm kinda hyped about), 
>other than installing and updating R 
>packages using BiocManager ....  Did you 
>think of something else than 
>BioStars.org when saying «Bioconductor?»
>The question could be viewed as gene 
>related, but I think it is really about 
>how can one easier than with sqlite 
>handle large tsv files, and why is that 
>parser thing so slow ...  I think this 
>is more like a core R thing than gene 
>related question ...  
>[1] https://www.biostars.org/p/9492486/

Sent from my phone. Please excuse my brevity.

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