On Tue, Apr 14, 2020 at 06:52:56PM +0200, Florian Weimer wrote: > * Andreas Tille: > > 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.
This is a good hint. So I tried: $ git diff diff --git a/debian/rules b/debian/rules index 529c38a..bde1d1b 100755 --- a/debian/rules +++ b/debian/rules @@ -1,5 +1,6 @@ #!/usr/bin/make -f +export CLASSPATH=/usr/share/java/cdk-interfaces.jar:/usr/share/java/cdk-silent.jar + %: dh $@ --buildsystem R and while the first error vanished that way I get the next one: *** installing help indices ** building package indices ** 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: .jcall("org/openscience/cdk/silent/SilentChemObjectBuilder", error: RcallMethod: cannot determine object class 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:6: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 root:/# grep SilentChemObjectBuilder /usr/share/java/* Binary file /usr/share/java/cdk-silent-2.3.jar matches Binary file /usr/share/java/cdk-silent.jar matches Seems I did not really understood the trick to set CLASSPATH. :-( Kind regards and thanks so far Andreas. -- http://fam-tille.de