* Andreas Tille: > 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
Please check if /usr/share/java/cdk-interfaces.jar is on the classpath. The missing class is org.openscience.cdk.exception.CDKException (apparently a superinterface of org.openscience.cdk.formula.rules.NitrogenRule), and it's contained in that JAR file.