Support packages (libraries) in R #17
Comments
|
@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:
|
jeremydouglass
changed the title
|
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.
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:
|
|
I've posted a question about listings of available test-passing renjin packages here: https://groups.google.com/forum/#!topic/renjin-dev/rrLM4wo3by8 |
|
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. |
|
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. |
|
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 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. |
|
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. |
|
Perhaps for future research we could instead try something like stringi, which is a renjin-specific version and lists (?) no dependencies. |
|
I will take a look |
|
Strange. For |
|
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. |
|
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
tcltk is definitely not a dependency. |
|
🤔 I have tried to run without them and it returns an error, I will have a try again and get some details |
|
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: |
|
When I runs without Rcpp, it raises: When I run with plyr and Rcpp: |
|
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:
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? |
|
Yeah, I will have a look. Thanks for your information :) |
|
Great! Should we add an example sketch that demonstrates using an R library to the example set? |
|
Yeah, I will try to write an example. |
Renjin supports some of CRAN and BioConductor R libraries, Processing.R could benefit from it.
ref the post in forum
The text was updated successfully, but these errors were encountered: