Need to Update for Java 11

[zachcp]

@rajarshi ,

I received an email from CRAN about fixing an rcdk version check before the release to Java 11. I didn't update a fix in time and noticed that as of this morning I have been booted from Maintainership as of rcdk (see https://cran.r-project.org/web/packages/rcdk/rcdk.pdf)

I will look into a fix of the Java version test to patch an updated version, but I don't know if I will be able to submit the patch. Build error and and correction updated below. A fix will need to either:

1. Fix the Java11 issue but avoid your recent updates which require a more recent CDK
2. Update the rCDKlibs with a new release and then add the Java 11 Patch to master.

Any preferences on which route to take?

zach cp

* testing if installed package can be loaded
Warning in fun(libname, pkgname) : NAs introduced by coercion
Error: package or namespace load failed for ‘rcdk’:
  .onLoad failed in loadNamespace() for 'rcdk', details:
   call: if (isjavagood == FALSE) {
   error: missing value where TRUE/FALSE needed

jversion evaluates as 11-ea+22" .

The code in 'Writing R Extensions' does work portably,

Please correct ASAP and before Sep 25 (the currently expected release
date for Java 11).

[rajarshi]

It's probably a good idea to make a new release of rcdklibs and patch master.

[rajarshi]

Just submitted the latest rcdklibs (2.2.1)

[zachcp]

ok. i'll take a look at applying the batch and building/submitting.

zcp

[zachcp]

@rajarshi

I am running into the following vignette error when building.

library(rcdk)
sp <- get.smiles.parser()
molecule <- parse.smiles('N')[[1]]
convert.implicit.to.explicit(molecule)
formula <- get.mol2formula(molecule, charge=0)

Error in .jcall(ch, "D", "doubleValue") : RcallMethod: invalid object parameter

3. .jcall(ch, "D", "doubleValue")

2. .cdkFormula.createObject(.jcast(moleculaJT, .IMolecularFormula))

1. get.mol2formula(molecule, charge = 0)

[zachcp]

fixed. there were two errors - some "mol" vs "molecule" typos and a new error deu to the addition of a new molecular descriptor