Comments (20)
jeremydouglass
commented on May 29, 2024
1
I've posted a question about listings of available test-passing renjin packages here: https://groups.google.com/forum/#!topic/renjin-dev/rrLM4wo3by8
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jeremydouglass
commented on May 29, 2024
1
From the dependency list, tcltk in particular jumps out at me as probably huge and possibly not necessary. Interesting that plyr passed automatic testing on the renjin package site -- looking at these dependencies I would have guessed that it wouldn't.
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jeremydouglass
commented on May 29, 2024
1
Maarten on the renjin-dev list has responded with a very useful list of suggested renjin R packages for testing.
https://groups.google.com/d/msg/renjin-dev/rrLM4wo3by8/O7cDR6V8AAAJ
These entries from his suggestion list look like good starting points:
plyr-- we were already looking at thisregexr-- http://packages.renjin.org/package/org.renjin.cran/regexrforeach-- http://packages.renjin.org/package/org.renjin.cran/foreachmagrittr-- http://packages.renjin.org/package/org.renjin.cran/magrittr
regexr, foreach, and magrittr are all syntax / control structure packages, and they look light on dependencies. Perhaps one would work better for a quick test?
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jeremydouglass
commented on May 29, 2024
@gaocegege --
What are some top CRAN / BioConductor R packages that you would be interested in testing (or in having someone test for you)? Ideally these would be popular packages, low level (not a lot of dependencies), not have their own graphical outputs (for simplicity, and not to overlap with Processing), and be something that Processing users might want to use .
For example, I might be interested in:
- Bioconductor -- see: Download stats for Bioconductor software packages:
- CRAN -- see: The most popular R packages or Top 20 R packages by popularity:
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jeremydouglass
commented on May 29, 2024
A preliminary look at Renjin package listings shows that they automatically test -- however they don't provide a single listing of packages that pass, and the packages that I chose above didn't pass testing (possibly because they are dependency-heavy or C/++ optimized), so we need to be systematic about searching or pick well-documented examples.
- graph: This package can be loaded by Renjin but there was an error compiling C/FORTRAN sources and 38 out 51 tests failed.
- pcaMethods: This package can be loaded by Renjin but there was an error compiling C/FORTRAN sources and 18 out 28 tests failed.
- dplyr: This package can be loaded by Renjin but there was an error compiling C/FORTRAN sources and 35 out 62 tests failed.
- stringi: This package can be loaded by Renjin but there was an error compiling C/FORTRAN sources and 48 out 49 tests failed.
- stringr: This package can be loaded by Renjin but all tests failed.
- lubridate: This package can be loaded by Renjin but all tests failed.
By contrast, here is a package in a Renjin-specific version that passes all tests. We might use it for our preliminary testing of whether importing works:
- org.renjin.cran:plyr. Use it with
library('org.renjin.cran:plyr')
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gaocegege
commented on May 29, 2024
Yeah, there are some packages which pass all the tests. And I agree that we could use them to test whether it works.
As for those packages which fails some test cases, I think we should dive into the packages and have a try. And if there are some important libraries, maybe we could help renjin to implement them in JVM. Then we could use it in our mode.
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gaocegege
commented on May 29, 2024
ref https://github.com/bedatadriven/renjin/tree/master/cli/src/main/java/org/renjin/cli
Renjin CLI will download the package at runtime, we could take a look at it.
from processing.r.
gaocegege
commented on May 29, 2024
Take plyr as an example, it has a lot of dependencies, put them into lib/mode manually is not what we want. I will take a look further.
<dependencies>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>methods</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>parallel</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>datasets</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>stats</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>splines</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>grDevices</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>tcltk</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>stats4</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>Rcpp</artifactId>
<version>0.12.5-renjin-7</version>
</dependency>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>Rcpp</artifactId>
<version>0.12.5-renjin-7</version>
<classifier>headers</classifier>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>tools</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>utils</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>grid</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>graphics</artifactId>
<version>0.8.2343</version>
</dependency>
<dependency>
<groupId>org.renjin</groupId>
<artifactId>compiler</artifactId>
<version>0.8.2343</version>
<scope>provided</scope>
</dependency>
</dependencies>from processing.r.
jeremydouglass
commented on May 29, 2024
Strange -- I just noticed that renjin's CRAN listing for plyr only lists a single dependency -- RCPP.
http://packages.renjin.org/package/org.renjin.cran/plyr/1.8.4
...which doesn't list any dependencies. So the web listings aren't matching up with that dependencies report.
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jeremydouglass
commented on May 29, 2024
Perhaps for future research we could instead try something like stringi, which is a renjin-specific version and lists (?) no dependencies.
http://packages.renjin.org/package/org.renjin.cran/stringi
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gaocegege
commented on May 29, 2024
I will take a look
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jeremydouglass
commented on May 29, 2024
Strange. For plyr I looked at the renjin build log and test results, and I don't see any of those dependencies (like tcltk) -- unless I'm misunderstanding.
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gaocegege
commented on May 29, 2024
Take plyr-1.8.4 as an example, the deps are defined in https://nexus.bedatadriven.com/content/groups/public/org/renjin/cran/plyr/1.8.4-b17/plyr-1.8.4-b17.pom. They are maven dependencies.
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jeremydouglass
commented on May 29, 2024
Hmm, something is off about that this. Those aren't true dependencies, that is an expanded copy of the "Suggests" list from plyr 1.8.4 on CRAN:
https://cran.r-project.org/web/packages/plyr/index.html
Depends: R (≥ 3.1.0)
Imports: Rcpp (≥ 0.11.0)
LinkingTo: Rcpp
Suggests: abind, testthat, tcltk, foreach, doParallel, itertools, iterators, covr
tcltk is definitely not a dependency.
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gaocegege
commented on May 29, 2024
🤔 I have tried to run without them and it returns an error, I will have a try again and get some details
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jeremydouglass
commented on May 29, 2024
Hmm. "Suggests" means that plyr "uses some functions from these packages in examples or in its vignettes."
So if a build is running tests against examples or vignettes that make calls to the "suggests" packages then those tests would fail if the "suggests" are not installed -- but plyr will still work, it just can't run those examples. What kind of error are you getting?
For discussion see:
- https://cran.r-project.org/web/packages/miniCRAN/vignettes/miniCRAN-dependency-graph.html
- ...and more on dependency analysis in R: http://blog.revolutionanalytics.com/2014/07/dependencies-of-popular-r-packages.html
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gaocegege
commented on May 29, 2024
When I runs without Rcpp, it raises:
org.renjin.eval.EvalException: IOException while loading package org.renjin.cran:plyr: Could not load package Rcpp; tried org.renjin.bioconductor:Rcpp, org.renjin.cran:Rcpp
at org.renjin.primitives.packaging.NamespaceRegistry.tryLoad(NamespaceRegistry.java:234)
at org.renjin.primitives.packaging.NamespaceRegistry.tryGetNamespace(NamespaceRegistry.java:191)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:153)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:115)
at org.renjin.primitives.packaging.Packages.library(Packages.java:41)
at org.renjin.primitives.R$primitive$library.doApply(R$primitive$library.java:73)
at org.renjin.primitives.R$primitive$library.apply(R$primitive$library.java:34)
at org.renjin.primitives.special.InternalFunction.apply(InternalFunction.java:45)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.primitives.special.BeginFunction.apply(BeginFunction.java:38)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.eval.Context.evaluate(Context.java:197)
at org.renjin.sexp.Closure.doApply(Closure.java:84)
at org.renjin.eval.ClosureDispatcher.apply(ClosureDispatcher.java:76)
at org.renjin.eval.ClosureDispatcher.applyClosure(ClosureDispatcher.java:58)
at org.renjin.sexp.Closure.apply(Closure.java:79)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.eval.Context.evaluateExpressionVector(Context.java:351)
at org.renjin.eval.Context.evaluate(Context.java:254)
at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:168)
at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:127)
at rprocessing.RLangPApplet.setup(Unknown Source)
at processing.core.PApplet.handleDraw(PApplet.java:2414)
at processing.awt.PSurfaceAWT$12.callDraw(PSurfaceAWT.java:1547)
at processing.core.PSurfaceNone$AnimationThread.run(PSurfaceNone.java:316)
Caused by: org.renjin.eval.EvalException: Could not load package Rcpp; tried org.renjin.bioconductor:Rcpp, org.renjin.cran:Rcpp
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:160)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:115)
at org.renjin.primitives.packaging.Namespace.initImports(Namespace.java:181)
at org.renjin.primitives.packaging.NamespaceRegistry.tryLoad(NamespaceRegistry.java:214)
When I run with plyr and Rcpp:
org.renjin.eval.EvalException: IOException while loading package org.renjin.cran:plyr: IOException while loading package org.renjin.cran:Rcpp: Expected object of class 'NativeSymbolInfo'
at org.renjin.primitives.packaging.NamespaceRegistry.tryLoad(NamespaceRegistry.java:234)
at org.renjin.primitives.packaging.NamespaceRegistry.tryGetNamespace(NamespaceRegistry.java:191)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:153)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:115)
at org.renjin.primitives.packaging.Packages.library(Packages.java:41)
at org.renjin.primitives.R$primitive$library.doApply(R$primitive$library.java:73)
at org.renjin.primitives.R$primitive$library.apply(R$primitive$library.java:34)
at org.renjin.primitives.special.InternalFunction.apply(InternalFunction.java:45)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.primitives.special.BeginFunction.apply(BeginFunction.java:38)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.eval.Context.evaluate(Context.java:197)
at org.renjin.sexp.Closure.doApply(Closure.java:84)
at org.renjin.eval.ClosureDispatcher.apply(ClosureDispatcher.java:76)
at org.renjin.eval.ClosureDispatcher.applyClosure(ClosureDispatcher.java:58)
at org.renjin.sexp.Closure.apply(Closure.java:79)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.eval.Context.evaluateExpressionVector(Context.java:351)
at org.renjin.eval.Context.evaluate(Context.java:254)
at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:168)
at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:127)
at rprocessing.RLangPApplet.setup(Unknown Source)
at processing.core.PApplet.handleDraw(PApplet.java:2414)
at processing.awt.PSurfaceAWT$12.callDraw(PSurfaceAWT.java:1547)
at processing.core.PSurfaceNone$AnimationThread.run(PSurfaceNone.java:316)
Caused by: org.renjin.eval.EvalException: IOException while loading package org.renjin.cran:Rcpp: Expected object of class 'NativeSymbolInfo'
at org.renjin.primitives.packaging.NamespaceRegistry.tryLoad(NamespaceRegistry.java:234)
at org.renjin.primitives.packaging.NamespaceRegistry.tryGetNamespace(NamespaceRegistry.java:191)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:153)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:115)
at org.renjin.primitives.packaging.Namespace.initImports(Namespace.java:181)
at org.renjin.primitives.packaging.NamespaceRegistry.tryLoad(NamespaceRegistry.java:214)
... 27 more
Caused by: org.renjin.eval.EvalException: Expected object of class 'NativeSymbolInfo'
at org.renjin.primitives.Native.external(Native.java:452)
at org.renjin.primitives.R$primitive$$External.apply(R$primitive$$External.java:63)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.eval.Context.evaluate(Context.java:197)
at org.renjin.sexp.Closure.doApply(Closure.java:84)
at org.renjin.eval.ClosureDispatcher.apply(ClosureDispatcher.java:76)
at org.renjin.eval.ClosureDispatcher.applyClosure(ClosureDispatcher.java:58)
at org.renjin.sexp.Closure.apply(Closure.java:79)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.primitives.special.BeginFunction.apply(BeginFunction.java:38)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.eval.Context.evaluate(Context.java:197)
at org.renjin.sexp.Closure.doApply(Closure.java:84)
at org.renjin.eval.ClosureDispatcher.apply(ClosureDispatcher.java:76)
at org.renjin.eval.ClosureDispatcher.applyClosure(ClosureDispatcher.java:58)
at org.renjin.sexp.Closure.apply(Closure.java:79)
at org.renjin.eval.Context.evaluateCall(Context.java:368)
at org.renjin.eval.Context.evaluate(Context.java:256)
at org.renjin.primitives.packaging.NamespaceRegistry.tryLoad(NamespaceRegistry.java:220)
... 32 more
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gaocegege
commented on May 29, 2024
Yeah, I will have a look. Thanks for your information :)
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jeremydouglass
commented on May 29, 2024
Great!
Should we add an example sketch that demonstrates using an R library to the example set?
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gaocegege
commented on May 29, 2024
Yeah, I will try to write an example.
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