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@tferr
Last active November 12, 2018 14:57
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n5-viewer NPE
ferreirat@ferreirat-ws1:~/code/n5-utils$ _JAVA_OPTIONS=-Djdk.net.URLClassPath.disableClassPathURLCheck=true ./install $HOME/bin
Installing into /groups/mousebrainmicro/home/ferreirat/bin
Assuming operating system linux
Picked up _JAVA_OPTIONS: -Djdk.net.URLClassPath.disableClassPathURLCheck=true
[INFO] Scanning for projects...
Downloading from saalfeld-lab-maven-repo: https://saalfeldlab.github.io/maven/org/scijava/pom-scijava/22.3.0/pom-scijava-22.3.0.pom
Downloading from imagej.public: https://maven.imagej.net/content/groups/public/org/scijava/pom-scijava/22.3.0/pom-scijava-22.3.0.pom
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Downloading from saalfeld-lab-maven-repo: https://saalfeldlab.github.io/maven/org/scijava/pom-scijava-base/3.5.2/pom-scijava-base-3.5.2.pom
Downloading from imagej.public: https://maven.imagej.net/content/groups/public/org/scijava/pom-scijava-base/3.5.2/pom-scijava-base-3.5.2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-webdav-jackrabbit/1.0/wagon-webdav-jackrabbit-1.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-http-shared/1.0/wagon-http-shared-1.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/jsoup/jsoup/1.6.1/jsoup-1.6.1.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-nop/1.5.3/slf4j-nop-1.5.3.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/1.0/wagon-provider-api-1.0.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/jsoup/jsoup/1.6.1/jsoup-1.6.1.jar (282 kB at 2.5 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.2/plexus-utils-1.4.2.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-api/1.5.3/slf4j-api-1.5.3.jar (20 kB at 180 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/jackrabbit/jackrabbit-webdav/1.5.0/jackrabbit-webdav-1.5.0.jar (303 kB at 2.6 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-nop/1.5.3/slf4j-nop-1.5.3.jar (5.2 kB at 43 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/1.0/wagon-provider-api-1.0.jar (53 kB at 385 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.2/plexus-utils-1.4.2.jar (190 kB at 1.3 MB/s)
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building n5-utils 0.0.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-enforcer-plugin/1.4.1/maven-enforcer-plugin-1.4.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-enforcer-plugin/1.4.1/maven-enforcer-plugin-1.4.1.pom (7.3 kB at 93 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/enforcer/enforcer/1.4.1/enforcer-1.4.1.pom
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[INFO] Skipping Rule Enforcement.
[INFO]
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[INFO]
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[INFO] Executing: /bin/sh -c cd '/groups/mousebrainmicro/home/ferreirat/code/n5-utils' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] Working directory: /groups/mousebrainmicro/home/ferreirat/code/n5-utils
[INFO] Storing buildNumber: 08ede8446c98f04cb321c170f919e22291918940 at timestamp: 1542033438219
[INFO] Storing buildScmBranch: master
[INFO]
[INFO] --- scijava-maven-plugin:1.0.0:set-rootdir (set-rootdir) @ n5-utils ---
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[INFO] Compiling 3 source files to /groups/mousebrainmicro/home/ferreirat/code/n5-utils/target/classes
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[INFO] Building jar: /groups/mousebrainmicro/home/ferreirat/code/n5-utils/target/n5-utils-0.0.2-SNAPSHOT.jar
[INFO]
[INFO] >>> maven-source-plugin:3.0.1:jar (attach-sources) > generate-sources @ n5-utils >>>
[INFO]
[INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-rules) @ n5-utils ---
[INFO] Skipping Rule Enforcement.
[INFO]
[INFO] --- build-helper-maven-plugin:1.12:regex-property (sanitize-version) @ n5-utils ---
[INFO]
[INFO] --- buildnumber-maven-plugin:1.4:create (default) @ n5-utils ---
[INFO]
[INFO] --- scijava-maven-plugin:1.0.0:set-rootdir (set-rootdir) @ n5-utils ---
[INFO]
[INFO] <<< maven-source-plugin:3.0.1:jar (attach-sources) < generate-sources @ n5-utils <<<
[INFO]
[INFO]
[INFO] --- maven-source-plugin:3.0.1:jar (attach-sources) @ n5-utils ---
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[INFO] Building jar: /groups/mousebrainmicro/home/ferreirat/code/n5-utils/target/n5-utils-0.0.2-SNAPSHOT-sources.jar
[INFO]
[INFO] --- maven-shade-plugin:1.6:shade (default) @ n5-utils ---
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[INFO] Including args4j:args4j:jar:2.0.29 in the shaded jar.
[INFO] Including net.imglib2:imglib2:jar:5.3.0 in the shaded jar.
[INFO] Including org.janelia.saalfeldlab:n5:jar:2.0.2 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.6 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.14 in the shaded jar.
[INFO] Including net.jpountz.lz4:lz4:jar:1.3.0 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.8.5 in the shaded jar.
[INFO] Including org.scijava:scijava-common:jar:2.74.1 in the shaded jar.
[INFO] Including org.scijava:parsington:jar:1.0.1 in the shaded jar.
[INFO] Including org.bushe:eventbus:jar:1.4 in the shaded jar.
[INFO] Including org.janelia.saalfeldlab:n5-imglib2:jar:3.0.0 in the shaded jar.
[INFO] Including sc.fiji:bigdataviewer-vistools:jar:1.0.0-beta-11 in the shaded jar.
[INFO] Including net.imglib2:imglib2-realtransform:jar:2.0.0 in the shaded jar.
[INFO] Including gov.nist.math:jama:jar:1.0.3 in the shaded jar.
[INFO] Including jitk:jitk-tps:jar:3.0.0 in the shaded jar.
[INFO] Including com.googlecode.efficient-java-matrix-library:ejml:jar:0.24 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including net.imglib2:imglib2-ui:jar:2.0.0 in the shaded jar.
[INFO] Including org.scijava:ui-behaviour:jar:1.7.3 in the shaded jar.
[INFO] Including net.sf.trove4j:trove4j:jar:3.0.3 in the shaded jar.
[INFO] Including org.yaml:snakeyaml:jar:1.13 in the shaded jar.
[INFO] Including net.imglib2:imglib2-cache:jar:1.0.0-beta-9 in the shaded jar.
[INFO] Including com.github.ben-manes.caffeine:caffeine:jar:2.4.0 in the shaded jar.
[INFO] Including org.janelia.saalfeldlab:n5-hdf5:jar:1.0.2 in the shaded jar.
[INFO] Including cisd:jhdf5:jar:14.12.6 in the shaded jar.
[INFO] Including commons-lang:commons-lang:jar:2.6 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.janelia.saalfeldlab:n5-aws-s3:jar:2.0.2 in the shaded jar.
[INFO] Including com.amazonaws:aws-java-sdk-s3:jar:1.11.294 in the shaded jar.
[INFO] Including com.amazonaws:aws-java-sdk-kms:jar:1.11.294 in the shaded jar.
[INFO] Including com.amazonaws:aws-java-sdk-core:jar:1.11.294 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.5 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.9 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including software.amazon.ion:ion-java:jar:1.0.2 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.dataformat:jackson-dataformat-cbor:jar:2.6.7 in the shaded jar.
[INFO] Including joda-time:joda-time:jar:2.9.9 in the shaded jar.
[INFO] Including com.amazonaws:jmespath-java:jar:1.11.294 in the shaded jar.
[INFO] Including org.janelia.saalfeldlab:n5-google-cloud:jar:2.1.0 in the shaded jar.
[INFO] Including com.google.cloud:google-cloud-storage:jar:1.20.0 in the shaded jar.
[INFO] Including com.google.cloud:google-cloud-core:jar:1.20.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:21.0 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:3.0.1 in the shaded jar.
[INFO] Including com.google.api:api-common:jar:1.4.0 in the shaded jar.
[INFO] Including com.google.api:gax:jar:1.19.0 in the shaded jar.
[INFO] Including org.threeten:threetenbp:jar:1.3.3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.5.1 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.5.1 in the shaded jar.
[INFO] Including com.google.api.grpc:proto-google-common-protos:jar:1.2.0 in the shaded jar.
[INFO] Including com.google.api.grpc:proto-google-iam-v1:jar:0.3.0 in the shaded jar.
[INFO] Including com.google.cloud:google-cloud-core-http:jar:1.20.0 in the shaded jar.
[INFO] Including com.google.auth:google-auth-library-credentials:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.auth:google-auth-library-oauth2-http:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.oauth-client:google-oauth-client:jar:1.23.0 in the shaded jar.
[INFO] Including com.google.http-client:google-http-client-appengine:jar:1.23.0 in the shaded jar.
[INFO] Including com.google.http-client:google-http-client-jackson:jar:1.23.0 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.11 in the shaded jar.
[INFO] Including com.google.api:gax-httpjson:jar:0.36.0 in the shaded jar.
[INFO] Including io.opencensus:opencensus-api:jar:0.11.1 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including io.grpc:grpc-context:jar:1.9.0 in the shaded jar.
[INFO] Including io.opencensus:opencensus-contrib-http-util:jar:0.11.1 in the shaded jar.
[INFO] Including com.google.apis:google-api-services-storage:jar:v1-rev114-1.23.0 in the shaded jar.
[INFO] Including com.google.cloud:google-cloud-resourcemanager:jar:0.38.0-alpha in the shaded jar.
[INFO] Including com.google.apis:google-api-services-cloudresourcemanager:jar:v1-rev470-1.23.0 in the shaded jar.
[INFO] Including com.google.apis:google-api-services-oauth2:jar:v2-rev134-1.23.0 in the shaded jar.
[INFO] Including com.google.api-client:google-api-client:jar:1.23.0 in the shaded jar.
[INFO] Including com.google.http-client:google-http-client-jackson2:jar:1.23.0 in the shaded jar.
[INFO] Including com.google.http-client:google-http-client:jar:1.23.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.1.3 in the shaded jar.
[INFO] Including com.google.oauth-client:google-oauth-client-jetty:jar:1.23.0 in the shaded jar.
[INFO] Including com.google.oauth-client:google-oauth-client-java6:jar:1.23.0 in the shaded jar.
[INFO] Including org.mortbay.jetty:jetty:jar:6.1.26 in the shaded jar.
[INFO] Including org.mortbay.jetty:jetty-util:jar:6.1.26 in the shaded jar.
[INFO] Including org.mortbay.jetty:servlet-api:jar:2.5-20081211 in the shaded jar.
[INFO] Including sc.fiji:bigdataviewer-core:jar:5.0.0 in the shaded jar.
[INFO] Including net.imglib2:imglib2-algorithm:jar:0.9.0 in the shaded jar.
[INFO] Including net.imglib2:imglib2-roi:jar:0.5.1 in the shaded jar.
[INFO] Including org.ojalgo:ojalgo:jar:45.1.0 in the shaded jar.
[INFO] Including sc.fiji:spim_data:jar:2.2.1 in the shaded jar.
[INFO] Including org.jdom:jdom2:jar:2.0.6 in the shaded jar.
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /groups/mousebrainmicro/home/ferreirat/code/n5-utils/target/n5-utils-0.0.2-SNAPSHOT.jar with /groups/mousebrainmicro/home/ferreirat/code/n5-utils/target/n5-utils-0.0.2-SNAPSHOT-shaded.jar
[INFO]
[INFO] --- maven-jar-plugin:2.6:test-jar (default) @ n5-utils ---
[INFO] Skipping packaging of the test-jar
[INFO]
[INFO] --- maven-failsafe-plugin:2.21.0:integration-test (default) @ n5-utils ---
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/2.21.0/maven-surefire-common-2.21.0.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/0.9.3/plexus-java-0.9.3.pom
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[INFO] No tests to run.
[INFO]
[INFO] --- maven-failsafe-plugin:2.21.0:verify (default) @ n5-utils ---
[INFO]
[INFO] --- maven-install-plugin:2.5.2:install (default-install) @ n5-utils ---
Downloading from central: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/1.6/commons-codec-1.6.pom
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[INFO] Installing /groups/mousebrainmicro/home/ferreirat/code/n5-utils/target/n5-utils-0.0.2-SNAPSHOT.jar to /groups/mousebrainmicro/home/ferreirat/.m2/repository/org/saalfeldlab/n5-utils/0.0.2-SNAPSHOT/n5-utils-0.0.2-SNAPSHOT.jar
[INFO] Installing /groups/mousebrainmicro/home/ferreirat/code/n5-utils/dependency-reduced-pom.xml to /groups/mousebrainmicro/home/ferreirat/.m2/repository/org/saalfeldlab/n5-utils/0.0.2-SNAPSHOT/n5-utils-0.0.2-SNAPSHOT.pom
[INFO] Installing /groups/mousebrainmicro/home/ferreirat/code/n5-utils/target/n5-utils-0.0.2-SNAPSHOT-sources.jar to /groups/mousebrainmicro/home/ferreirat/.m2/repository/org/saalfeldlab/n5-utils/0.0.2-SNAPSHOT/n5-utils-0.0.2-SNAPSHOT-sources.jar
[INFO]
[INFO] --- imagej-maven-plugin:0.7.0:copy-jars (copy-jars) @ n5-utils ---
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-artifact-transfer/0.9.1/maven-artifact-transfer-0.9.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-artifact-transfer/0.9.1/maven-artifact-transfer-0.9.1.pom (7.6 kB at 293 kB/s)
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-containers/1.7.1/plexus-containers-1.7.1.pom
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Downloading from central: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/1.10/commons-codec-1.10.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-parent/1.7.25/slf4j-parent-1.7.25.pom
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[INFO] Total time: 01:09 min
[INFO] Finished at: 2018-11-12T09:37:36-05:00
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[INFO]
[INFO] --- maven-dependency-plugin:3.0.0:build-classpath (default-cli) @ n5-utils ---
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[INFO] Wrote classpath file '/groups/mousebrainmicro/home/ferreirat/code/n5-utils/cp.txt'.
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 9.214 s
[INFO] Finished at: 2018-11-12T09:37:47-05:00
[INFO] Final Memory: 32M/766M
[INFO] ------------------------------------------------------------------------
ferreirat@ferreirat-ws1:~/code/n5-utils$ ~/bin/n5-view -i /groups/mousebrainmicro/mousebrainmicro/n5/SAMPLES.n5 -d /2018-08-15/c0,/2018-08-15/c0 -c 0,65535 -r 1,1,2
Exception in thread "main" java.lang.NullPointerException
at org.saalfeldlab.View$Options.<init>(View.java:271)
at org.saalfeldlab.View.main(View.java:370)
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