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[INFO] Including org.bdgenomics.mango:mango-cli-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.12:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.6 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.12.6 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark3_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.12:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.12:jar:1.0.6 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.12.8 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.9.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:4.2.2 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.9.0 in the shaded jar.
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar, adam-cli-spark3_2.12-0.32.0.jar define 3 overlapping classes:
[WARNING] - org.bdgenomics.adam.cli.CommandGroup
[WARNING] - org.bdgenomics.adam.cli.InitArgs
[WARNING] - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes:
[WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING] - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with /tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-shaded.jar
[INFO]
[INFO] --------< org.bdgenomics.mango:mango-distribution-spark3_2.12 >---------
[INFO] Building mango_2.12: Distribution 0.0.6-SNAPSHOT [4/5]
[INFO] --------------------------------[ pom ]---------------------------------
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[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution-spark3_2.12 >>>
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution-spark3_2.12 <<<
[INFO]
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution-spark3_2.12 ---
[INFO] No source files found
[INFO]
[INFO] --- maven-assembly-plugin:2.2-beta-5:single (default) @ mango-distribution-spark3_2.12 ---
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Progress (2): 217/222 kB | 80 kB
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0.4/maven-artifact-2.0.4.jar (80 kB at 692 kB/s)
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[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building tar : /tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.bz2
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.zip
[INFO]
[INFO] -----------< org.bdgenomics.mango:mango-parent-spark3_2.12 >------------
[INFO] Building mango_2.12 0.0.6-SNAPSHOT [5/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent-spark3_2.12 ---
[INFO] Modified 0 of 41 .scala files
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.12 >>>
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.12 <<<
[INFO]
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.12 0.0.6-SNAPSHOT:
[INFO]
[INFO] mango_2.12: CORE ................................... SUCCESS [ 31.195 s]
[INFO] mango_2.12: CLI .................................... SUCCESS [ 33.718 s]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 27.484 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [01:03 min]
[INFO] mango_2.12 ......................................... SUCCESS [ 0.859 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:36 min
[INFO] Finished at: 2020-08-19T12:51:28Z
[INFO] ------------------------------------------------------------------------
# make sure that the distribution package contains an assembly jar
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzf mango-distribution/target/mango-distribution*-bin.tar.gz | \
grep mango-assembly | \
grep jar | \
grep -v -e sources -e javadoc
+ grep mango-assembly
+ grep jar
+ tar tzf mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
+ grep -v -e sources -e javadoc
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar
# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvn2D2tFce
/tmp/mangoTestMvn2D2tFce
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/referenceName=1
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/referenceName=1/positionBin=0/.part-00000-db654ec6-76da-4aac-899b-142a475decba.c000.snappy.parquet.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/referenceName=1/positionBin=0/part-00000-db654ec6-76da-4aac-899b-142a475decba.c000.snappy.parquet
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/._samples.avro.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/._SUCCESS.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/_SUCCESS
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/_references.avro
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/_samples.avro
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/._header.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/_partitionedByStartPos
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/_header
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163.adam/._references.avro.crc
/tmp/mangoTestMvn2D2tFce/fake-2630894692860056456.sh
/tmp/mangoTestMvn2D2tFce/TempSuite6534471808675552163
/tmp/mangoTestMvn2D2tFce/invalidBuild.genome3507082582675920664
/tmp/mangoTestMvn2D2tFce/invalidBuild.genome3507082582675920664/properties.txt
/tmp/mangoTestMvn2D2tFce/2468417409789316905
/tmp/mangoTestMvn2D2tFce/fake-4767614896597976493.txt
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113
/tmp/mangoTestMvn2D2tFce/5297073243029049384
/tmp/mangoTestMvn2D2tFce/5297073243029049384/anoGam1.genome
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/._readGroups.avro.crc
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/_readGroups.avro
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/_partitionedByStartPos
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=2
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=2/positionBin=189/part-00000-7e18b784-7b2e-486d-ade0-c8b2bd00a540.c000.snappy.parquet
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=2/positionBin=189/.part-00000-7e18b784-7b2e-486d-ade0-c8b2bd00a540.c000.snappy.parquet.crc
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/_SUCCESS
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/_processingSteps.avro
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/._SUCCESS.crc
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/._references.avro.crc
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/_references.avro
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=1
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=1/positionBin=240/part-00000-7e18b784-7b2e-486d-ade0-c8b2bd00a540.c000.snappy.parquet
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=1/positionBin=240/.part-00000-7e18b784-7b2e-486d-ade0-c8b2bd00a540.c000.snappy.parquet.crc
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=1/positionBin=26/.part-00000-7e18b784-7b2e-486d-ade0-c8b2bd00a540.c000.snappy.parquet.crc
/tmp/mangoTestMvn2D2tFce/TempSuite329222605091541234.adam/referenceName=1/positionBin=26/part-00000-7e18b784-7b2e-486d-ade0-c8b2bd00a540.c000.snappy.parquet
/tmp/mangoTestMvn2D2tFce/invalidBuild.genome8691923836469450005
/tmp/mangoTestMvn2D2tFce/invalidBuild.genome8691923836469450005/properties.txt
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/_samples.avro
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/_partitionedByStartPos
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/_references.avro
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/_SUCCESS
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/._samples.avro.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/._SUCCESS.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/referenceName=1
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/referenceName=1/positionBin=0/part-00000-ac7c932b-23a3-421c-9a00-0d7e5c447fa8.c000.snappy.parquet
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/referenceName=1/positionBin=0/.part-00000-ac7c932b-23a3-421c-9a00-0d7e5c447fa8.c000.snappy.parquet.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/._header.crc
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/_header
/tmp/mangoTestMvn2D2tFce/TempSuite6056494253379944113.adam/._references.avro.crc
/tmp/mangoTestMvn2D2tFce/genomes7775382685571521918
/tmp/mangoTestMvn2D2tFce/genomes7775382685571521918/hg19.genome
/tmp/mangoTestMvn2D2tFce/mmbroken17958119421521919.genome
/tmp/mangoTestMvn2D2tFce/8979627547056962237
/tmp/mangoTestMvn2D2tFce/8979627547056962237/anoGam1.genome
/tmp/mangoTestMvn2D2tFce/fake-4454351471997664475.sh
/tmp/mangoTestMvn2D2tFce/fake-3245015587612098303.txt
/tmp/mangoTestMvn2D2tFce/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvn2D2tFce/mmbroken2737345172761428112.genome
/tmp/mangoTestMvn2D2tFce/genomes5432946135877482551
/tmp/mangoTestMvn2D2tFce/genomes5432946135877482551/hg19.genome
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/_references.avro
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/_processingSteps.avro
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/._references.avro.crc
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/_SUCCESS
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=2
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=2/positionBin=189/part-00000-6425c5ca-c29f-4c40-a4c6-6f263f362a14.c000.snappy.parquet
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=2/positionBin=189/.part-00000-6425c5ca-c29f-4c40-a4c6-6f263f362a14.c000.snappy.parquet.crc
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/._readGroups.avro.crc
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/_readGroups.avro
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=1
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=1/positionBin=26/.part-00000-6425c5ca-c29f-4c40-a4c6-6f263f362a14.c000.snappy.parquet.crc
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=1/positionBin=26/part-00000-6425c5ca-c29f-4c40-a4c6-6f263f362a14.c000.snappy.parquet
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=1/positionBin=240/part-00000-6425c5ca-c29f-4c40-a4c6-6f263f362a14.c000.snappy.parquet
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/referenceName=1/positionBin=240/.part-00000-6425c5ca-c29f-4c40-a4c6-6f263f362a14.c000.snappy.parquet.crc
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/._SUCCESS.crc
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502.adam/_partitionedByStartPos
/tmp/mangoTestMvn2D2tFce/2747392694290971399
/tmp/mangoTestMvn2D2tFce/TempSuite224744081065043502
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvn2D2tFce
find . -name pom.xml \
-exec sed -i.bak \
-e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${MANGO_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
{} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/mangoTestMvn2D2tFce:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'
# set spark artifact string for downloading assembly
SPARK=spark-${SPARK_VERSION}
+ SPARK=spark-3.0.0
# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
HADOOP=hadoop2.7
else
echo "Unknown Hadoop version."
exit 1
fi
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7
# Spark 2.4.3+ and less than 3.0.0 needs special case for Scala 2.12
if [ ${SCALAVER} == 2.12 ] && [ ${SPARK_VERSION} == 2.4.6 ]
then
curl \
-L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-without-hadoop-scala-2.12.tgz" \
-o ${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12.tgz
tar xzf ${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12.tgz --directory ${MANGO_TMP_DIR}
export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12
curl \
-L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=hadoop/core/hadoop-2.7.7/hadoop-2.7.7.tar.gz" \
-o ${MANGO_TMP_DIR}/hadoop-2.7.7.tar.gz
tar xzf ${MANGO_TMP_DIR}/hadoop-2.7.7.tar.gz --directory ${MANGO_TMP_DIR}
# remove references to avro 1.7.x
find ${MANGO_TMP_DIR}/hadoop-2.7.7 -name *.jar | grep avro | xargs rm
export SPARK_DIST_CLASSPATH=$(${MANGO_TMP_DIR}/hadoop-2.7.7/bin/hadoop classpath)
else
curl \
-v \
-L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
-o ${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}.tgz
tar xzf ${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}.tgz --directory ${MANGO_TMP_DIR}
export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}
fi
+ '[' 2.12 == 2.12 ']'
+ '[' 3.0.0 == 2.4.6 ']'
+ curl -v -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz' -o /tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7.tgz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying 40.79.78.1...
* TCP_NODELAY set
* Connected to www.apache.org (40.79.78.1) port 443 (#0)
* ALPN, offering h2
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [113 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4639 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [333 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server accepted to use http/1.1
* Server certificate:
* subject: OU=Domain Control Validated; OU=PositiveSSL Wildcard; CN=*.apache.org
* start date: Jul 1 00:00:00 2019 GMT
* expire date: Jun 30 23:59:59 2021 GMT
* subjectAltName: host "www.apache.org" matched cert's "*.apache.org"
* issuer: C=GB; ST=Greater Manchester; L=Salford; O=Sectigo Limited; CN=Sectigo RSA Domain Validation Secure Server CA
* SSL certificate verify ok.
} [5 bytes data]
> GET /dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz HTTP/1.1
> Host: www.apache.org
> User-Agent: curl/7.52.1
> Accept: */*
>
{ [5 bytes data]
< HTTP/1.1 302 Found
< Date: Wed, 19 Aug 2020 12:51:30 GMT
< Server: Apache/2.4.18 (Ubuntu)
< Location: https://apache.claz.org/spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz
< Cache-Control: max-age=3600
< Expires: Wed, 19 Aug 2020 13:51:30 GMT
< Content-Length: 0
<
* Curl_http_done: called premature == 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
* Connection #0 to host www.apache.org left intact
* Issue another request to this URL: 'https://apache.claz.org/spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz'
* Trying 69.162.86.134...
* TCP_NODELAY set
* Connected to apache.claz.org (69.162.86.134) port 443 (#1)
* ALPN, offering h2
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [102 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [3930 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [333 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server accepted to use h2
* Server certificate:
* subject: CN=claz.org
* start date: Jul 31 21:02:49 2020 GMT
* expire date: Oct 29 21:02:49 2020 GMT
* subjectAltName: host "apache.claz.org" matched cert's "*.claz.org"
* issuer: C=US; O=Let's Encrypt; CN=Let's Encrypt Authority X3
* SSL certificate verify ok.
* Using HTTP2, server supports multi-use
* Connection state changed (HTTP/2 confirmed)
* Copying HTTP/2 data in stream buffer to connection buffer after upgrade: len=0
} [5 bytes data]
* Using Stream ID: 1 (easy handle 0x55c99e291e80)
} [5 bytes data]
> GET /spark/spark-3.0.0/spark-3.0.0-bin-hadoop2.7.tgz HTTP/1.1
> Host: apache.claz.org
> User-Agent: curl/7.52.1
> Accept: */*
>
{ [5 bytes data]
* Connection state changed (MAX_CONCURRENT_STREAMS updated)!
} [5 bytes data]
< HTTP/2 200
< date: Wed, 19 Aug 2020 12:51:30 GMT
< server: Apache/2.4.29 (Ubuntu)
< last-modified: Sat, 06 Jun 2020 13:35:40 GMT
< etag: "d2116ec-5a76a742b962c"
< accept-ranges: bytes
< content-length: 220272364
< content-type: application/x-gzip
<
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99 210M 99 209M 0 0 518k 0 0:06:54 0:06:54 --:--:-- 509k* Curl_http_done: called premature == 0
100 210M 100 210M 0 0 518k 0 0:06:54 0:06:54 --:--:-- 528k
* Connection #1 to host apache.claz.org left intact
+ tar xzf /tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7.tgz --directory /tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded
+ export SPARK_HOME=/tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7
+ SPARK_HOME=/tmp/mangoTestWhpBZle/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7
# create a conda environment for python build, if necessary
pythons=( 3.6 )
+ pythons=(3.6)
for python in ${pythons[*]}
do
conda create -y -q -c conda-forge -n mango-build-${PYTHON_UUID} python=${python} pip=19.3.1 jupyterlab=2.0.1
conda activate mango-build-${PYTHON_UUID}
# install npm and node in the venv for mango-pileup
conda install -y nodejs
# prepare mango python
pushd mango-python
make prepare
popd
# we can run the python build, now that we have a spark executable
# requires SPARK_HOME to be set
mvn -U \
-P python,distribution \
package \
-DskipTests \
-Dhadoop.version=${HADOOP_VERSION} \
-Dspark.version=${SPARK_VERSION}
# clean mango python
pushd mango-python
make clean
popd
# prepare mango viz
pushd mango-pileup
make prepare
popd
# run the widgets tests (mango-pileup)
mvn -P widgets test
# clean mango viz
pushd mango-pileup
make clean
popd
# make sure that the distribution package contains an egg
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzf mango-distribution/target/mango-distribution*-bin.tar.gz | \
grep bdgenomics.mango | \
grep egg
# test mango notebook, output to temporary log file
MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log
# notebook args --ip=0.0.0.0 --no-browser --allow-root required for docker
bash -xv ${PROJECT_ROOT}/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root &> ${MANGO_NOTEBOOK_LOGS} &
# sleep for 2 seconds to let mango-notebook start up
sleep 2
# if mango-notebook fails, then trying to kill the process will fail
if kill $! ; then
echo "Mango Notebook Succeeded"
else
echo "Mango Notebook failed with logs:"
cat ${MANGO_NOTEBOOK_LOGS}
exit 1
fi
# deactivate and remove the conda env
set +e +x
source deactivate
conda remove -y --name mango-build-${PYTHON_UUID} --all
set -e -x
done
+ for python in ${pythons[*]}
+ conda create -y -q -c conda-forge -n mango-build-436288f8-dfdd-428d-b2e3-d5ca9e744a29 python=3.6 pip=19.3.1 jupyterlab=2.0.1
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/jenkins/.conda/envs/mango-build-436288f8-dfdd-428d-b2e3-d5ca9e744a29
added / updated specs:
- jupyterlab=2.0.1
- pip=19.3.1
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 1_gnu 22 KB conda-forge
argon2-cffi-20.1.0 | py36h8c4c3a4_1 47 KB conda-forge
attrs-19.3.0 | py_0 35 KB conda-forge
backcall-0.2.0 | pyh9f0ad1d_0 13 KB conda-forge
backports-1.0 | py_2 4 KB conda-forge
backports.functools_lru_cache-1.6.1| py_0 8 KB conda-forge
bleach-3.1.5 | pyh9f0ad1d_0 112 KB conda-forge
brotlipy-0.7.0 |py36h8c4c3a4_1000 346 KB conda-forge
ca-certificates-2020.6.20 | hecda079_0 145 KB conda-forge
certifi-2020.6.20 | py36h9f0ad1d_0 151 KB conda-forge
cffi-1.14.1 | py36h0ff685e_0 223 KB conda-forge
chardet-3.0.4 |py36h9f0ad1d_1006 188 KB conda-forge
cryptography-3.0 | py36h45558ae_0 640 KB conda-forge
decorator-4.4.2 | py_0 11 KB conda-forge
defusedxml-0.6.0 | py_0 22 KB conda-forge
entrypoints-0.3 |py36h9f0ad1d_1001 12 KB conda-forge
idna-2.10 | pyh9f0ad1d_0 52 KB conda-forge
importlib-metadata-1.7.0 | py36h9f0ad1d_0 44 KB conda-forge
importlib_metadata-1.7.0 | 0 3 KB conda-forge
ipykernel-5.3.4 | py36h95af2a2_0 165 KB conda-forge
ipython-7.16.1 | py36h95af2a2_0 1.1 MB conda-forge
ipython_genutils-0.2.0 | py_1 21 KB conda-forge
jedi-0.17.2 | py36h9f0ad1d_0 950 KB conda-forge
jinja2-2.11.2 | pyh9f0ad1d_0 93 KB conda-forge
json5-0.9.4 | pyh9f0ad1d_0 20 KB conda-forge
jsonschema-3.2.0 | py36h9f0ad1d_1 89 KB conda-forge
jupyter_client-6.1.6 | py_0 75 KB conda-forge
jupyter_core-4.6.3 | py36h9f0ad1d_1 71 KB conda-forge
jupyterlab-2.0.1 | py_0 5.7 MB conda-forge
jupyterlab_server-1.2.0 | py_0 25 KB conda-forge
ld_impl_linux-64-2.34 | hc38a660_9 612 KB conda-forge
libffi-3.2.1 | he1b5a44_1007 47 KB conda-forge
libgcc-ng-9.3.0 | h24d8f2e_15 7.8 MB conda-forge
libgomp-9.3.0 | h24d8f2e_15 378 KB conda-forge
libsodium-1.0.18 | h516909a_0 339 KB conda-forge
libstdcxx-ng-9.3.0 | hdf63c60_15 4.0 MB conda-forge
markupsafe-1.1.1 | py36h8c4c3a4_1 26 KB conda-forge
mistune-0.8.4 |py36h8c4c3a4_1001 53 KB conda-forge
nbconvert-5.6.1 | py36h9f0ad1d_1 487 KB conda-forge
nbformat-5.0.7 | py_0 99 KB conda-forge
ncurses-6.2 | he1b5a44_1 993 KB conda-forge
notebook-6.1.3 | py36h9f0ad1d_0 6.2 MB conda-forge
openssl-1.1.1g | h516909a_1 2.1 MB conda-forge
packaging-20.4 | pyh9f0ad1d_0 32 KB conda-forge
pandoc-2.10.1 | h516909a_0 19.3 MB conda-forge
pandocfilters-1.4.2 | py_1 9 KB conda-forge
parso-0.7.1 | pyh9f0ad1d_0 70 KB conda-forge
pexpect-4.8.0 | py36h9f0ad1d_1 79 KB conda-forge
pickleshare-0.7.5 |py36h9f0ad1d_1001 13 KB conda-forge
pip-19.3.1 | py36_0 1.9 MB conda-forge
prometheus_client-0.8.0 | pyh9f0ad1d_0 44 KB conda-forge
prompt-toolkit-3.0.6 | py_0 235 KB conda-forge
ptyprocess-0.6.0 | py_1001 15 KB conda-forge
pycparser-2.20 | pyh9f0ad1d_2 94 KB conda-forge
pygments-2.6.1 | py_0 683 KB conda-forge
pyopenssl-19.1.0 | py_1 47 KB conda-forge
pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge
pyrsistent-0.16.0 | py36h8c4c3a4_0 89 KB conda-forge
pysocks-1.7.1 | py36h9f0ad1d_1 27 KB conda-forge
python-3.6.11 |h4d41432_2_cpython 34.2 MB conda-forge
python-dateutil-2.8.1 | py_0 220 KB conda-forge
python_abi-3.6 | 1_cp36m 4 KB conda-forge
pyzmq-19.0.2 | py36h9947dbf_0 465 KB conda-forge
readline-8.0 | he28a2e2_2 281 KB conda-forge
requests-2.24.0 | pyh9f0ad1d_0 47 KB conda-forge
send2trash-1.5.0 | py_0 12 KB conda-forge
setuptools-49.6.0 | py36h9f0ad1d_0 935 KB conda-forge
six-1.15.0 | pyh9f0ad1d_0 14 KB conda-forge
sqlite-3.33.0 | h4cf870e_0 1.4 MB conda-forge
terminado-0.8.3 | py36h9f0ad1d_1 23 KB conda-forge
testpath-0.4.4 | py_0 85 KB conda-forge
tk-8.6.10 | hed695b0_0 3.2 MB conda-forge
tornado-6.0.4 | py36h8c4c3a4_1 639 KB conda-forge
traitlets-4.3.3 | py36h9f0ad1d_1 133 KB conda-forge
urllib3-1.25.10 | py_0 92 KB conda-forge
wcwidth-0.2.5 | pyh9f0ad1d_1 33 KB conda-forge
webencodings-0.5.1 | py_1 12 KB conda-forge
wheel-0.35.1 | pyh9f0ad1d_0 29 KB conda-forge
xz-5.2.5 | h516909a_1 343 KB conda-forge
zeromq-4.3.2 | he1b5a44_3 326 KB conda-forge
zipp-3.1.0 | py_0 10 KB conda-forge
zlib-1.2.11 | h516909a_1007 106 KB conda-forge
------------------------------------------------------------
Total: 98.7 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
argon2-cffi conda-forge/linux-64::argon2-cffi-20.1.0-py36h8c4c3a4_1
attrs conda-forge/noarch::attrs-19.3.0-py_0
backcall conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
backports conda-forge/noarch::backports-1.0-py_2
backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.1-py_0
bleach conda-forge/noarch::bleach-3.1.5-pyh9f0ad1d_0
brotlipy conda-forge/linux-64::brotlipy-0.7.0-py36h8c4c3a4_1000
ca-certificates conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
certifi conda-forge/linux-64::certifi-2020.6.20-py36h9f0ad1d_0
cffi conda-forge/linux-64::cffi-1.14.1-py36h0ff685e_0
chardet conda-forge/linux-64::chardet-3.0.4-py36h9f0ad1d_1006
cryptography conda-forge/linux-64::cryptography-3.0-py36h45558ae_0
decorator conda-forge/noarch::decorator-4.4.2-py_0
defusedxml conda-forge/noarch::defusedxml-0.6.0-py_0
entrypoints conda-forge/linux-64::entrypoints-0.3-py36h9f0ad1d_1001
idna conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
importlib-metadata conda-forge/linux-64::importlib-metadata-1.7.0-py36h9f0ad1d_0
importlib_metadata conda-forge/noarch::importlib_metadata-1.7.0-0
ipykernel conda-forge/linux-64::ipykernel-5.3.4-py36h95af2a2_0
ipython conda-forge/linux-64::ipython-7.16.1-py36h95af2a2_0
ipython_genutils conda-forge/noarch::ipython_genutils-0.2.0-py_1
jedi conda-forge/linux-64::jedi-0.17.2-py36h9f0ad1d_0
jinja2 conda-forge/noarch::jinja2-2.11.2-pyh9f0ad1d_0
json5 conda-forge/noarch::json5-0.9.4-pyh9f0ad1d_0
jsonschema conda-forge/linux-64::jsonschema-3.2.0-py36h9f0ad1d_1
jupyter_client conda-forge/noarch::jupyter_client-6.1.6-py_0
jupyter_core conda-forge/linux-64::jupyter_core-4.6.3-py36h9f0ad1d_1
jupyterlab conda-forge/noarch::jupyterlab-2.0.1-py_0
jupyterlab_server conda-forge/noarch::jupyterlab_server-1.2.0-py_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_15
libgomp conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_15
libsodium conda-forge/linux-64::libsodium-1.0.18-h516909a_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_15
markupsafe conda-forge/linux-64::markupsafe-1.1.1-py36h8c4c3a4_1
mistune conda-forge/linux-64::mistune-0.8.4-py36h8c4c3a4_1001
nbconvert conda-forge/linux-64::nbconvert-5.6.1-py36h9f0ad1d_1
nbformat conda-forge/noarch::nbformat-5.0.7-py_0
ncurses conda-forge/linux-64::ncurses-6.2-he1b5a44_1
notebook conda-forge/linux-64::notebook-6.1.3-py36h9f0ad1d_0
openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_1
packaging conda-forge/noarch::packaging-20.4-pyh9f0ad1d_0
pandoc conda-forge/linux-64::pandoc-2.10.1-h516909a_0
pandocfilters conda-forge/noarch::pandocfilters-1.4.2-py_1
parso conda-forge/noarch::parso-0.7.1-pyh9f0ad1d_0
pexpect conda-forge/linux-64::pexpect-4.8.0-py36h9f0ad1d_1
pickleshare conda-forge/linux-64::pickleshare-0.7.5-py36h9f0ad1d_1001
pip conda-forge/linux-64::pip-19.3.1-py36_0
prometheus_client conda-forge/noarch::prometheus_client-0.8.0-pyh9f0ad1d_0
prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.6-py_0
ptyprocess conda-forge/noarch::ptyprocess-0.6.0-py_1001
pycparser conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
pygments conda-forge/noarch::pygments-2.6.1-py_0
pyopenssl conda-forge/noarch::pyopenssl-19.1.0-py_1
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
pyrsistent conda-forge/linux-64::pyrsistent-0.16.0-py36h8c4c3a4_0
pysocks conda-forge/linux-64::pysocks-1.7.1-py36h9f0ad1d_1
python conda-forge/linux-64::python-3.6.11-h4d41432_2_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-64::python_abi-3.6-1_cp36m
pyzmq conda-forge/linux-64::pyzmq-19.0.2-py36h9947dbf_0
readline conda-forge/linux-64::readline-8.0-he28a2e2_2
requests conda-forge/noarch::requests-2.24.0-pyh9f0ad1d_0
send2trash conda-forge/noarch::send2trash-1.5.0-py_0
setuptools conda-forge/linux-64::setuptools-49.6.0-py36h9f0ad1d_0
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
sqlite conda-forge/linux-64::sqlite-3.33.0-h4cf870e_0
terminado conda-forge/linux-64::terminado-0.8.3-py36h9f0ad1d_1
testpath conda-forge/noarch::testpath-0.4.4-py_0
tk conda-forge/linux-64::tk-8.6.10-hed695b0_0
tornado conda-forge/linux-64::tornado-6.0.4-py36h8c4c3a4_1
traitlets conda-forge/linux-64::traitlets-4.3.3-py36h9f0ad1d_1
urllib3 conda-forge/noarch::urllib3-1.25.10-py_0
wcwidth conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_1
webencodings conda-forge/noarch::webencodings-0.5.1-py_1
wheel conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zeromq conda-forge/linux-64::zeromq-4.3.2-he1b5a44_3
zipp conda-forge/noarch::zipp-3.1.0-py_0
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1007
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ conda activate mango-build-436288f8-dfdd-428d-b2e3-d5ca9e744a29
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
## Package Plan ##
environment location: /home/jenkins/.conda/envs/mango-build-436288f8-dfdd-428d-b2e3-d5ca9e744a29
The following packages will be REMOVED:
_libgcc_mutex-0.1-conda_forge
_openmp_mutex-4.5-1_gnu
argon2-cffi-20.1.0-py36h8c4c3a4_1
attrs-19.3.0-py_0
backcall-0.2.0-pyh9f0ad1d_0
backports-1.0-py_2
backports.functools_lru_cache-1.6.1-py_0
bleach-3.1.5-pyh9f0ad1d_0
brotlipy-0.7.0-py36h8c4c3a4_1000
ca-certificates-2020.6.20-hecda079_0
certifi-2020.6.20-py36h9f0ad1d_0
cffi-1.14.1-py36h0ff685e_0
chardet-3.0.4-py36h9f0ad1d_1006
cryptography-3.0-py36h45558ae_0
decorator-4.4.2-py_0
defusedxml-0.6.0-py_0
entrypoints-0.3-py36h9f0ad1d_1001
idna-2.10-pyh9f0ad1d_0
importlib-metadata-1.7.0-py36h9f0ad1d_0
importlib_metadata-1.7.0-0
ipykernel-5.3.4-py36h95af2a2_0
ipython-7.16.1-py36h95af2a2_0
ipython_genutils-0.2.0-py_1
jedi-0.17.2-py36h9f0ad1d_0
jinja2-2.11.2-pyh9f0ad1d_0
json5-0.9.4-pyh9f0ad1d_0
jsonschema-3.2.0-py36h9f0ad1d_1
jupyter_client-6.1.6-py_0
jupyter_core-4.6.3-py36h9f0ad1d_1
jupyterlab-2.0.1-py_0
jupyterlab_server-1.2.0-py_0
ld_impl_linux-64-2.34-hc38a660_9
libffi-3.2.1-he1b5a44_1007
libgcc-ng-9.3.0-h24d8f2e_15
libgomp-9.3.0-h24d8f2e_15
libsodium-1.0.18-h516909a_0
libstdcxx-ng-9.3.0-hdf63c60_15
markupsafe-1.1.1-py36h8c4c3a4_1
mistune-0.8.4-py36h8c4c3a4_1001
nbconvert-5.6.1-py36h9f0ad1d_1
nbformat-5.0.7-py_0
ncurses-6.2-he1b5a44_1
notebook-6.1.3-py36h9f0ad1d_0
openssl-1.1.1g-h516909a_1
packaging-20.4-pyh9f0ad1d_0
pandoc-2.10.1-h516909a_0
pandocfilters-1.4.2-py_1
parso-0.7.1-pyh9f0ad1d_0
pexpect-4.8.0-py36h9f0ad1d_1
pickleshare-0.7.5-py36h9f0ad1d_1001
pip-19.3.1-py36_0
prometheus_client-0.8.0-pyh9f0ad1d_0
prompt-toolkit-3.0.6-py_0
ptyprocess-0.6.0-py_1001
pycparser-2.20-pyh9f0ad1d_2
pygments-2.6.1-py_0
pyopenssl-19.1.0-py_1
pyparsing-2.4.7-pyh9f0ad1d_0
pyrsistent-0.16.0-py36h8c4c3a4_0
pysocks-1.7.1-py36h9f0ad1d_1
python-3.6.11-h4d41432_2_cpython
python-dateutil-2.8.1-py_0
python_abi-3.6-1_cp36m
pyzmq-19.0.2-py36h9947dbf_0
readline-8.0-he28a2e2_2
requests-2.24.0-pyh9f0ad1d_0
send2trash-1.5.0-py_0
setuptools-49.6.0-py36h9f0ad1d_0
six-1.15.0-pyh9f0ad1d_0
sqlite-3.33.0-h4cf870e_0
terminado-0.8.3-py36h9f0ad1d_1
testpath-0.4.4-py_0
tk-8.6.10-hed695b0_0
tornado-6.0.4-py36h8c4c3a4_1
traitlets-4.3.3-py36h9f0ad1d_1
urllib3-1.25.10-py_0
wcwidth-0.2.5-pyh9f0ad1d_1
webencodings-0.5.1-py_1
wheel-0.35.1-pyh9f0ad1d_0
xz-5.2.5-h516909a_1
zeromq-4.3.2-he1b5a44_3
zipp-3.1.0-py_0
zlib-1.2.11-h516909a_1007
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Remove all packages in environment /home/jenkins/.conda/envs/mango-build-436288f8-dfdd-428d-b2e3-d5ca9e744a29:
Build step 'Execute shell' marked build as failure
Finished: FAILURE
![[Jenkins]](/jenkins/static/7165055c/images/jenkins-header-logo-v2.svg){kind=logo}
