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rCDK Maintainer Wanted. #154
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Activity
I'd be open to that
I think that's a great idea. What do you need? And thank you
What do you need?
I would suggest:
- move this repo to github.com/cdk or github.com/blueobelisk
- check/set up write credentials for everyone
- get me up to speed with making CRAN releases (been a while)
@egonw that sounds like a plan. I would probably move all of the following repos:
- rcdklibs - basically just provides the CDK uberjar
- rcdk - functionality on top of the jar
- rinchi - maybe obsolete with new CDK code?
- fingerprint - i would recommend re-wrapping CDK fingerprints
- depict - fns to wrap the DepictionGenerator
I've invited you as the Owner of this organization. You can move the repos and give me Contributor access on the new repos. We can bump a release to add you as the Primary maintainer on each of those packages - I THINK thats all that will be needed for CRAN. On the release side - the jar stuff is straighforward but the build step for CDKR can be a pain.
Egon let's hold on moving these repos until I'm finished with the releases
So the current status is:
- RCDK: 20250910 vbump #156 minor fixes to keep up with CRAN standards.
- RCDKLIBS: 20250910 vbump rcdklibs#6 we will not be able to use the standard CRAN release mechanism to host JARs. The size has become a problem and a new way of getting the JARs would be required.
@zachcp, can you give an update? It seems we have a regression, and I am getting rJava errors:
> huhn <- "CC(=O)Nc1ccccc1" > mol <- parse.smiles(huhn) > get.smiles(mol) Error in .jcall(smigen, "S", "create", molecule) : method create with signature ()Ljava/lang/String; not found > view.molecule.2d(mol) Error in view.molecule.2d(mol) : java.lang.NoSuchMethodError: <init>Specifically, can I move and take over the packages?
Hi @egonw,
The issue is that CRAN denied us this time. The JAR files have long been well over the size limit of 5MB and for years we have been granted an exception.
To distribute rCDK as a CRAN package we would need an alternative method by which to retrieve and install the JAR files and add them to the rJava class path. The last time I investigated this possibility I couldn't identify a clean way to do this that didn't violate CRANs security policies which limit what a package can do once installed. There are of course direct GitHub installs that can be used but you lose the guarantees, discoverability, testing, and reverse dependency support that CRAN provides.
So current status is that we need an alternate install mechanism and I haven't identified one.
Zach cp
( cc: @rajarshi )