On 04/23/2018 05:00 PM, Olivier Sallou wrote: > I had a look to fix latest picard-tools and found there are missing deps: > > > Could not resolve com.intel.gkl:gkl:0.8.2. > Required by: > project : > > No cached version of com.intel.gkl:gkl:0.8.2 available for > offline mode. > > No cached version of com.intel.gkl:gkl:0.8.2 available for > offline mode. > > Could not resolve org.broadinstitute:barclay:2.0.0. > Required by: > project : > > No cached version of org.broadinstitute:barclay:2.0.0 > available for offline mode. > > No cached version of org.broadinstitute:barclay:2.0.0 > available for offline mode. > > > > those libs don't seem to be in debian. after quick and dirty packaging of missing deps (locally), there are still other issues. Jar packaging needs other deps (may try *simple* jar like was done before) but more annoying needs a specific jar patched from an other source:
org.broadinstitute:google-cloud-nio-GATK4-custom-patch:0.20.4-alpha-GCS-RETRY-FIX can't find related sources, only generated jar (and rebuilding it seems we will again need additional deps... :-( ) i have contacted picard team to get more info on this dependency [0] [0] https://github.com/broadinstitute/picard/issues/1164 > > To avoid javadoc errors I found at first when building package, I > locally updated build.gradle to remove all refs to javadocJDKFiles. > This may not be valid when going to doc task, but wanted at least test > to see if compilation etc was ok.... > > Olivier -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
