Help needed for calling Java class from R

[Andreas Tille <andreas@an3as.eu>]

Hi,

in the COVID-19 packaging effort I need r-cran-rcdk as a predependency.
I have injected it into r-pkg-team Git[1].  It is using the rjava interface
and depends from r-cran-rcdklibs (which has a dependency from libcdk-java).
When I try to build I get:


** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'rcdk':
 .onLoad failed in loadNamespace() for 'rcdk', details:
  call: .jnew("org/openscience/cdk/formula/rules/NitrogenRule")
  error: java.lang.NoClassDefFoundError: org/openscience/cdk/exception/CDKException
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/build/r-cran-rcdk-3.5.0/debian/r-cran-rcdk/usr/lib/R/site-library/rcdk'
dh_auto_install: error: R CMD INSTALL -l /build/r-cran-rcdk-3.5.0/debian/r-cran-rcdk/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 23 Mar 2020 21:27:30 +0100'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package


I verified in the pbuilder chroot that the missing class exists in CLASSPATH:

root:/# grep NitrogenRule /usr/share/java/*
Binary file /usr/share/java/cdk-formula-2.3.jar matches
Binary file /usr/share/java/cdk-formula.jar matches


Any idea how I can make sure that this class can be really found?

Kind regards

       Andreas.


[1] https://salsa.debian.org/r-pkg-team/r-cran-rcdk

-- 
http://fam-tille.de