Michael L Heuer

Sorry for all the trouble with Jenkins, I have seen something similar recently on another project https://amplab.cs.berkeley.edu/jenkins/job/mango-prb/1002/HADOOP_VERSION=2.7.5,SCALAVER=2.12,SPARK_VERSION=2.4.7,label=amp-jenkins-staging-worker-02/console That Apache mirror download link 404s, not sure what the actual issue is....

And a note from our admin staff: > i'm going to be upgrading jenkins to something more reasonable, and there will definitely be > some downtime as i get things...

re: Jenkins, might want to follow these threads http://apache-spark-developers-list.1001551.n3.nabble.com/jenkins-downtime-tomorrow-evening-weekend-td30405.html http://apache-spark-developers-list.1001551.n3.nabble.com/build-system-IMPORTANT-UPDATE-td30430.html

Re ``` The JAVA_HOME environment variable is not defined correctly This environment variable is needed to run this program NB: JAVA_HOME should point to a JDK not a JRE Build...

See also #2150

Hello @Hoeze! Thank you for submitting this issue. I assume this is recent, with the most recent release version 0.29.0 of `bdgenomics.adam` ? @akmorrow13 Could you also take a look?

I still need to look into this further, which may be difficult as campus is without power at the moment. Meanwhile, one of the following might work Try the most...

Sorry, I personally don't have that much experience packaging python, and to be honest I get quite confused with regards to conda and pip and virtualenv and such. I created...

After a bit of experimenting, removing the egg-related lines from `pyadam` may work with the `pip`-installed version ``` $ diff pyadam pyadam2 25d24 < ADAM_EGG=$(${SOURCE_DIR}/find-adam-egg.sh) 36d34 < --py-files ${ADAM_EGG} \...

Hello @akmorrow13, might you be able to weigh in on this issue?