Comments (6)
Thanks for the report.
I've investigated, and found that the bug is also present in R-2.15.1. It was fixed in R-3.1.1, which reported it as affecting formulas with exactly 32 variables (PR 15735). I've incorporated the R-3.1.1 fix in the development version of pqR. I may put out a minor update with this and other fixes, or it may wait until the new version with automatic differentiation is ready.
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Thank you Radford for investigating and fixing this bug. I would say it is better to publish a minor update, which includes this and other bug fixes. That is the purpose of minor updates. And it would allow more people to use pqR as a drop-in replacement for GNU-R.
I came across this project while trying out Oracle's FastR (a JVM-based R implementation) to speed up the performance of the oSCR package. In my only benchmark pqR turned out to be twice as fast as GNU-R and 1.5 times as fast as FastR. Now a friend of mine is using pqR for his research.
I read in the Issues that your enhancements to R are unlikely to be accepted by the R Core Team, which is a pity (to say the least). I suggested to the main FastR developer to incorporate some of your optimizations. It would be great for your hard work to get more recognition and make a wider impact now that R is so fashionable for Big Data and ML. I would also like to note that FastR can be coupled with GraalVM's visual profiler, which makes it pretty easy to detect hot spots in an R package.
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@mardukbp If you still wanna try out this fix in a Dockerfile: Clone https://github.com/nuest/pqr-docker an then run
$ REF=cbc944dabe0818875f99afe298f09430ecb450a2; docker build --tag pqr:$(echo $REF) --build-arg REF=$REF --file dev/Dockerfile .
$ docker run --rm -it pqr:cbc944dabe0818875f99afe298f09430ecb450a2
pqR version 2.15.1 (2019-00-00), based on R 2.15.0 (2012-03-30)
R 2.15.0 is Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Modifications to R in pqR are Copyright (C) 2013-2019 Radford M. Neal
Some modules are from R-2.15.1 or later versions distributed by the R Core Team
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Used CRAN mirror: ftp://price.utstat.utoronto.ca/2019-02-19
No helper threads, task merging enabled, uncompressed pointers.
> sessionInfo()
R version 2.15.1 (2019-00-00)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
> update(~1, ~. - y)
~1
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Comparison to the commit before the fix:
$ REF=21b7226f26524933ff88ea6335bf807e9c768630; docker build --tag pqr:$(echo $REF) --build-arg REF=$REF --file dev/Dockerfile .
$ docker run --rm -it pqr:21b7226f26524933ff88ea6335bf807e9c768630 Rscript -e 'update(~1, ~. - y)'
Used CRAN mirror: ftp://price.utstat.utoronto.ca/2019-02-19
~1 - 1
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Thank you Daniel! I already tried the fix on my laptop and on an AWS EC2 instance. Your Docker file would make it easy for people to deploy pqR on AWS. I think this use case should be advertised on the project's website.
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I have no experience with AWS, so if you have a small code chunk or example configuration, I'd be very happy about a PR to the README :-).
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Related Issues (20)
- What is preventing the merge of pqR into R? HOT 1
- pqR side by side with GNU-R HOT 8
- T and F don't work with mat_mult_with_BLAS configuration argument
- Docker image for pqR HOT 3
- No window version available HOT 1
- Incompatible library version HOT 3
- Will pqR code be merged to R? HOT 9
- Missing <R_ext/sggc-app.h> HOT 11
- Proposal of new feature: native 64 bit integers support HOT 2
- R/time.R - filename restricted? HOT 5
- make error: multiple definitions HOT 6
- segfault when using attributes HOT 1
- buffer overflow when using attributes on a recursive function HOT 2
- floating point exception
- pqR aborted when using plot
- Problems with installation ubuntu 20.04 HOT 5
- Pqr and running Rstudio on mac
- Installation fails on Slackware 15.0 HOT 13
- Slow pqR loops vs R (CRAN)
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