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statgenetics / seqspark

SEQSpark documentation
https://statgenetics.github.io/seqspark/
Apache License 2.0
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Cannot find target/scala-2.11/SeqSpark.jar, compiling failed? #8

Closed jasminebro closed 4 months ago

jasminebro commented 4 years ago

Hi,

I am trying to install SeqSpark on Ubuntu( a single user workspace). I am not sure if that is the best option ;however, I do not currently have access to a server. I received the following error and was hoping you could help me figure out the problem. I also included the entire print out from my screen during installation until the error.

Best,

Jasmine

Error:

Cannot find target/scala-2.11/SeqSpark.jar, compiling failed? at ./install line 84, <$fh> line 48.

Will install into /home/jnbaker/bin, database files will be downloaded to /user/jnbaker/seqspark Building seqspark ... Copying runtime jar. [info] [launcher] getting org.scala-sbt sbt 0.13.16 (this may take some time)... downloading https://repo1.maven.org/maven2/org/scala-lang/scala-library/2.10.6/scala-library-2.10.6.jar ... :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/main/0.13.16/jars/main.jar ... :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/sbt/0.13.16/jars/sbt.jar ... :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/process/0.13.16/jars/process.jar ... :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/main-settings/0.13.16/jars/main-settings.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/actions/0.13.16/jars/actions.jar ... :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/logging/0.13.16/jars/logging.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/interface/0.13.16/jars/interface.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/logic/0.13.16/jars/logic.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/compiler-interface/0.13.16/jars/compiler-interface.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/io/0.13.16/jars/io.jar ... :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/ivy/0.13.16/jars/ivy.jar ... :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml :: loading settings :: url = jar:file:/home/jnbaker/.sdkman/candidates/sbt/1.3.2/bin/sbt-launch.jar!/org/apache/ivy/core/settings/ivysettings.xml [SUCCESSFUL ] org.scala-lang#scala-library;2.10.6!scala-library.jar (485ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/run/0.13.16/jars/run.jar ... [SUCCESSFUL ] org.scala-sbt#sbt;0.13.16!sbt.jar (1196ms) [SUCCESSFUL ] org.scala-sbt#process;0.13.16!process.jar (1280ms) downloading https://repo1.maven.org/maven2/org/scala-sbt/launcher-interface/1.0.1/launcher-interface-1.0.1.jar ... [SUCCESSFUL ] org.scala-sbt#launcher-interface;1.0.1!launcher-interface.jar (26ms) [SUCCESSFUL ] org.scala-sbt#interface;0.13.16!interface.jar (1331ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/command/0.13.16/jars/command.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/classpath/0.13.16/jars/classpath.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/completion/0.13.16/jars/completion.jar ... [SUCCESSFUL ] org.scala-sbt#compiler-interface;0.13.16!compiler-interface.jar (1525ms) [SUCCESSFUL ] org.scala-sbt#logic;0.13.16!logic.jar (1531ms) [SUCCESSFUL ] org.scala-sbt#io;0.13.16!io.jar (1545ms) [SUCCESSFUL ] org.scala-sbt#ivy;0.13.16!ivy.jar (1612ms) [SUCCESSFUL ] org.scala-sbt#logging;0.13.16!logging.jar (1614ms) [SUCCESSFUL ] org.scala-sbt#run;0.13.16!run.jar (1161ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/api/0.13.16/jars/api.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/compiler-integration/0.13.16/jars/compiler-integration.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/compiler-ivy-integration/0.13.16/jars/compiler-ivy-integration.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/relation/0.13.16/jars/relation.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/tasks/0.13.16/jars/tasks.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/task-system/0.13.16/jars/task-system.jar ... [SUCCESSFUL ] org.scala-sbt#main-settings;0.13.16!main-settings.jar (2107ms) [SUCCESSFUL ] org.scala-sbt#classpath;0.13.16!classpath.jar (870ms) [SUCCESSFUL ] org.scala-sbt#actions;0.13.16!actions.jar (2219ms) downloading https://repo1.maven.org/maven2/org/scala-lang/scala-compiler/2.10.6/scala-compiler-2.10.6.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/tracking/0.13.16/jars/tracking.jar ... [SUCCESSFUL ] org.scala-sbt#completion;0.13.16!completion.jar (959ms) downloading https://repo1.maven.org/maven2/org/scala-lang/scala-reflect/2.10.6/scala-reflect-2.10.6.jar ... [SUCCESSFUL ] org.scala-sbt#command;0.13.16!command.jar (1181ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/testing/0.13.16/jars/testing.jar ... [SUCCESSFUL ] org.scala-sbt#compiler-ivy-integration;0.13.16!compiler-ivy-integration.jar (962ms) [SUCCESSFUL ] org.scala-sbt#api;0.13.16!api.jar (987ms) downloading https://repo1.maven.org/maven2/jline/jline/2.14.4/jline-2.14.4.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/control/0.13.16/jars/control.jar ... [SUCCESSFUL ] jline#jline;2.14.4!jline.jar (94ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/collections/0.13.16/jars/collections.jar ... [SUCCESSFUL ] org.scala-sbt#compiler-integration;0.13.16!compiler-integration.jar (1203ms) [SUCCESSFUL ] org.scala-lang#scala-reflect;2.10.6!scala-reflect.jar (469ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/classfile/0.13.16/jars/classfile.jar ... [SUCCESSFUL ] org.scala-sbt#relation;0.13.16!relation.jar (1262ms) [SUCCESSFUL ] org.scala-sbt#task-system;0.13.16!task-system.jar (1261ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/incremental-compiler/0.13.16/jars/incremental-compiler.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/compile/0.13.16/jars/compile.jar ... [SUCCESSFUL ] org.scala-sbt#tasks;0.13.16!tasks.jar (1362ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/persist/0.13.16/jars/persist.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-tools.sbinary/sbinary_2.10/0.4.2/jars/sbinary_2.10.jar ... [SUCCESSFUL ] org.scala-sbt#tracking;0.13.16!tracking.jar (1065ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/cross/0.13.16/jars/cross.jar ... downloading https://repo1.maven.org/maven2/org/scala-sbt/ivy/ivy/2.3.0-sbt-48dd0744422128446aee9ac31aa356ee203cc9f4/ivy-2.3.0-sbt-48dd0744422128446aee9ac31aa356ee203cc9f4.jar ... [SUCCESSFUL ] org.scala-sbt.ivy#ivy;2.3.0-sbt-48dd0744422128446aee9ac31aa356ee203cc9f4!ivy.jar (80ms) downloading https://repo1.maven.org/maven2/com/jcraft/jsch/0.1.50/jsch-0.1.50.jar ... [SUCCESSFUL ] com.jcraft#jsch;0.1.50!jsch.jar (34ms) downloading https://repo1.maven.org/maven2/org/scala-sbt/serialization_2.10/0.1.2/serialization_2.10-0.1.2.jar ... [SUCCESSFUL ] org.scala-sbt#testing;0.13.16!testing.jar (1126ms) downloading https://repo1.maven.org/maven2/org/scala-lang/modules/scala-pickling_2.10/0.10.1/scala-pickling_2.10-0.10.1.jar ... [SUCCESSFUL ] org.scala-sbt#serialization_2.10;0.1.2!serialization_2.10.jar (40ms) downloading https://repo1.maven.org/maven2/org/json4s/json4s-core_2.10/3.2.10/json4s-core_2.10-3.2.10.jar ... [SUCCESSFUL ] org.scala-lang.modules#scala-pickling_2.10;0.10.1!scala-pickling_2.10.jar (65ms) downloading https://repo1.maven.org/maven2/org/spire-math/jawn-parser_2.10/0.6.0/jawn-parser_2.10-0.6.0.jar ... [SUCCESSFUL ] org.json4s#json4s-core_2.10;3.2.10!json4s-core_2.10.jar (54ms) downloading https://repo1.maven.org/maven2/org/spire-math/json4s-support_2.10/0.6.0/json4s-support_2.10-0.6.0.jar ... [SUCCESSFUL ] org.spire-math#jawn-parser_2.10;0.6.0!jawn-parser_2.10.jar (28ms) downloading https://repo1.maven.org/maven2/org/scalamacros/quasiquotes_2.10/2.0.1/quasiquotes_2.10-2.0.1.jar ... [SUCCESSFUL ] org.spire-math#json4s-support_2.10;0.6.0!json4s-support_2.10.jar (25ms) downloading https://repo1.maven.org/maven2/org/json4s/json4s-ast_2.10/3.2.10/json4s-ast_2.10-3.2.10.jar ... [SUCCESSFUL ] org.json4s#json4s-ast_2.10;3.2.10!json4s-ast_2.10.jar (27ms) downloading https://repo1.maven.org/maven2/com/thoughtworks/paranamer/paranamer/2.6/paranamer-2.6.jar ... [SUCCESSFUL ] org.scalamacros#quasiquotes_2.10;2.0.1!quasiquotes_2.10.jar (50ms) [SUCCESSFUL ] com.thoughtworks.paranamer#paranamer;2.6!paranamer.jar (26ms) [SUCCESSFUL ] org.scala-sbt#control;0.13.16!control.jar (1095ms) downloading file:////home/jnbaker/.sbt/preloaded/org/scala-sbt/test-interface/1.0/test-interface-1.0.jar ... [SUCCESSFUL ] org.scala-sbt#test-interface;1.0!test-interface.jar (11ms) [SUCCESSFUL ] org.scala-sbt#main;0.13.16!main.jar (3592ms) downloading file:////home/jnbaker/.sbt/preloaded/org/scala-sbt/template-resolver/0.1/template-resolver-0.1.jar ... [SUCCESSFUL ] org.scala-sbt#template-resolver;0.1!template-resolver.jar (10ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/cache/0.13.16/jars/cache.jar ... downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/test-agent/0.13.16/jars/test-agent.jar ... [SUCCESSFUL ] org.scala-sbt#collections;0.13.16!collections.jar (1125ms) [SUCCESSFUL ] org.scala-sbt#incremental-compiler;0.13.16!incremental-compiler.jar (894ms) downloading https://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/apply-macro/0.13.16/jars/apply-macro.jar ... [SUCCESSFUL ] org.scala-sbt#classfile;0.13.16!classfile.jar (1141ms) [SUCCESSFUL ] org.scala-sbt#compile;0.13.16!compile.jar (1139ms) [SUCCESSFUL ] org.scala-sbt#persist;0.13.16!persist.jar (1055ms) [SUCCESSFUL ] org.scala-sbt#cross;0.13.16!cross.jar (1067ms) [SUCCESSFUL ] org.scala-tools.sbinary#sbinary_2.10;0.4.2!sbinary_2.10.jar (1301ms) [SUCCESSFUL ] org.scala-lang#scala-compiler;2.10.6!scala-compiler.jar (2085ms) [SUCCESSFUL ] org.scala-sbt#test-agent;0.13.16!test-agent.jar (927ms) [SUCCESSFUL ] org.scala-sbt#apply-macro;0.13.16!apply-macro.jar (990ms) [SUCCESSFUL ] org.scala-sbt#cache;0.13.16!cache.jar (1075ms) :: retrieving :: org.scala-sbt#boot-app confs: [default] 49 artifacts copied, 0 already retrieved [info] [launcher] getting Scala 2.10.6 (for sbt)... downloading https://repo1.maven.org/maven2/org/fusesource/jansi/jansi/1.4/jansi-1.4.jar ... downloading https://repo1.maven.org/maven2/org/scala-lang/jline/2.10.6/jline-2.10.6.jar ... [SUCCESSFUL ] org.fusesource.jansi#jansi;1.4!jansi.jar (30ms) [SUCCESSFUL ] org.scala-lang#jline;2.10.6!jline.jar (30ms) :: retrieving :: org.scala-sbt#boot-scala confs: [default] 5 artifacts copied, 0 already retrieved [info] Updated file /home/jnbaker/bin/seqspark/project/build.properties: set sbt.version to 0.13.16 [info] Loading project definition from /home/jnbaker/bin/seqspark/project [info] Updating {file:/home/jnbaker/bin/seqspark/project/}seqspark-build... WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by sbt.ivyint.ErrorMessageAuthenticator$ (file:/home/jnbaker/.sbt/boot/scala-2.10.6/org.scala-sbt/sbt/0.13.16/ivy-0.13.16.jar) to field java.net.Authenticator.theAuthenticator WARNING: Please consider reporting this to the maintainers of sbt.ivyint.ErrorMessageAuthenticator$ WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release [info] Resolving org.fusesource.jansi#jansi;1.4 ... [info] downloading https://repo.scala-sbt.org/scalasbt/sbt-plugin-releases/com.eed3si9n/sbt-assembly/scala_2.10/sbt_0.13/0.14.6/jars/sbt-assembly.jar ... [info] [SUCCESSFUL ] com.eed3si9n#sbt-assembly;0.14.6!sbt-assembly.jar (1575ms) [info] downloading https://repo1.maven.org/maven2/org/scalactic/scalactic_2.10/3.0.1/scalactic_2.10-3.0.1.jar ... [info] [SUCCESSFUL ] org.scalactic#scalactic_2.10;3.0.1!scalactic_2.10.jar(bundle) (75ms) [info] downloading https://repo1.maven.org/maven2/org/pantsbuild/jarjar/1.6.5/jarjar-1.6.5.jar ... [info] [SUCCESSFUL ] org.pantsbuild#jarjar;1.6.5!jarjar.jar (64ms) [info] downloading https://repo1.maven.org/maven2/org/apache/ant/ant/1.9.9/ant-1.9.9.jar ... [info] [SUCCESSFUL ] org.apache.ant#ant;1.9.9!ant.jar (115ms) [info] downloading https://repo1.maven.org/maven2/org/ow2/asm/asm/6.0/asm-6.0.jar ... [info] [SUCCESSFUL ] org.ow2.asm#asm;6.0!asm.jar (37ms) [info] downloading https://repo1.maven.org/maven2/org/ow2/asm/asm-commons/6.0/asm-commons-6.0.jar ... [info] [SUCCESSFUL ] org.ow2.asm#asm-commons;6.0!asm-commons.jar (27ms) [info] downloading https://repo1.maven.org/maven2/org/apache/maven/maven-plugin-api/3.3.9/maven-plugin-api-3.3.9.jar ... [info] [SUCCESSFUL ] org.apache.maven#maven-plugin-api;3.3.9!maven-plugin-api.jar (31ms) [info] downloading https://repo1.maven.org/maven2/org/apache/ant/ant-launcher/1.9.9/ant-launcher-1.9.9.jar ... [info] [SUCCESSFUL ] org.apache.ant#ant-launcher;1.9.9!ant-launcher.jar (33ms) [info] downloading https://repo1.maven.org/maven2/org/ow2/asm/asm-tree/6.0/asm-tree-6.0.jar ... [info] [SUCCESSFUL ] org.ow2.asm#asm-tree;6.0!asm-tree.jar (38ms) [info] downloading https://repo1.maven.org/maven2/org/apache/maven/maven-model/3.3.9/maven-model-3.3.9.jar ... [info] [SUCCESSFUL ] org.apache.maven#maven-model;3.3.9!maven-model.jar (42ms) [info] downloading https://repo1.maven.org/maven2/org/apache/maven/maven-artifact/3.3.9/maven-artifact-3.3.9.jar ... [info] [SUCCESSFUL ] org.apache.maven#maven-artifact;3.3.9!maven-artifact.jar (27ms) [info] downloading https://repo1.maven.org/maven2/org/eclipse/sisu/org.eclipse.sisu.plexus/0.3.2/org.eclipse.sisu.plexus-0.3.2.jar ... [info] [SUCCESSFUL ] org.eclipse.sisu#org.eclipse.sisu.plexus;0.3.2!org.eclipse.sisu.plexus.jar(eclipse-plugin) (35ms) [info] downloading https://repo1.maven.org/maven2/org/codehaus/plexus/plexus-utils/3.0.22/plexus-utils-3.0.22.jar ... [info] [SUCCESSFUL ] org.codehaus.plexus#plexus-utils;3.0.22!plexus-utils.jar (35ms) [info] downloading https://repo1.maven.org/maven2/org/apache/commons/commons-lang3/3.4/commons-lang3-3.4.jar ... [info] [SUCCESSFUL ] org.apache.commons#commons-lang3;3.4!commons-lang3.jar (47ms) [info] downloading https://repo1.maven.org/maven2/javax/enterprise/cdi-api/1.0/cdi-api-1.0.jar ... [info] [SUCCESSFUL ] javax.enterprise#cdi-api;1.0!cdi-api.jar (27ms) [info] downloading https://repo1.maven.org/maven2/org/eclipse/sisu/org.eclipse.sisu.inject/0.3.2/org.eclipse.sisu.inject-0.3.2.jar ... [info] [SUCCESSFUL ] org.eclipse.sisu#org.eclipse.sisu.inject;0.3.2!org.eclipse.sisu.inject.jar(eclipse-plugin) (41ms) [info] downloading https://repo1.maven.org/maven2/org/codehaus/plexus/plexus-component-annotations/1.5.5/plexus-component-annotations-1.5.5.jar ... [info] [SUCCESSFUL ] org.codehaus.plexus#plexus-component-annotations;1.5.5!plexus-component-annotations.jar (26ms) [info] downloading https://repo1.maven.org/maven2/org/codehaus/plexus/plexus-classworlds/2.5.2/plexus-classworlds-2.5.2.jar ... [info] [SUCCESSFUL ] org.codehaus.plexus#plexus-classworlds;2.5.2!plexus-classworlds.jar(bundle) (27ms) [info] downloading https://repo1.maven.org/maven2/javax/annotation/jsr250-api/1.0/jsr250-api-1.0.jar ... [info] [SUCCESSFUL ] javax.annotation#jsr250-api;1.0!jsr250-api.jar (27ms) [info] downloading https://repo1.maven.org/maven2/javax/inject/javax.inject/1/javax.inject-1.jar ... [info] [SUCCESSFUL ] javax.inject#javax.inject;1!javax.inject.jar (26ms) [info] Done updating. [info] Set current project to seqspark (in build file:/home/jnbaker/bin/seqspark/) [info] Updating {file:/home/jnbaker/bin/seqspark/}seqspark... [info] Resolving org.sonatype.oss#oss-parent;9 ... [info] downloading https://repo1.maven.org/maven2/org/scala-lang/scala-library/2.11.12/scala-library-2.11.12.jar ... [info] [SUCCESSFUL ] org.scala-lang#scala-library;2.11.12!scala-library.jar (230ms) [info] downloading https://repo1.maven.org/maven2/com/typesafe/config/1.2.1/config-1.2.1.jar ... [info] [SUCCESSFUL ] com.typesafe#config;1.2.1!config.jar(bundle) (31ms) [info] downloading https://repo1.maven.org/maven2/org/scalaz/scalaz-core_2.11/7.2.4/scalaz-core_2.11-7.2.4.jar ... [info] [SUCCESSFUL ] org.scalaz#scalaz-core_2.11;7.2.4!scalaz-core_2.11.jar(bundle) (488ms) [info] downloading https://repo1.maven.org/maven2/org/scalatest/scalatest_2.11/2.2.4/scalatest_2.11-2.2.4.jar ... 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[info] [SUCCESSFUL ] com.github.fommil.netlib#netlib-native_system-linux-armhf;1.1!netlib-native_system-linux-armhf.jar (46ms) [info] downloading https://repo1.maven.org/maven2/com/github/fommil/netlib/netlib-native_system-win-x86_64/1.1/netlib-native_system-win-x86_64-1.1-natives.jar ... [info] [SUCCESSFUL ] com.github.fommil.netlib#netlib-native_system-win-x86_64;1.1!netlib-native_system-win-x86_64.jar (53ms) [info] downloading https://repo1.maven.org/maven2/com/github/fommil/netlib/netlib-native_system-win-i686/1.1/netlib-native_system-win-i686-1.1-natives.jar ... [info] [SUCCESSFUL ] com.github.fommil.netlib#netlib-native_system-win-i686;1.1!netlib-native_system-win-i686.jar (59ms) [info] downloading https://repo1.maven.org/maven2/com/github/fommil/netlib/native_ref-java/1.1/native_ref-java-1.1.jar ... [info] [SUCCESSFUL ] com.github.fommil.netlib#native_ref-java;1.1!native_ref-java.jar (30ms) [info] downloading https://repo1.maven.org/maven2/com/github/fommil/jniloader/1.1/jniloader-1.1.jar ... [info] [SUCCESSFUL ] com.github.fommil#jniloader;1.1!jniloader.jar (26ms) [info] downloading https://repo1.maven.org/maven2/com/github/fommil/netlib/native_system-java/1.1/native_system-java-1.1.jar ... [info] [SUCCESSFUL ] com.github.fommil.netlib#native_system-java;1.1!nativesystem-java.jar (34ms) [info] downloading https://repo1.maven.org/maven2/jline/jline/2.14.3/jline-2.14.3.jar ... [info] [SUCCESSFUL ] jline#jline;2.14.3!jline.jar (35ms) [info] Done updating. [info] Compiling 76 Scala sources to /home/jnbaker/bin/seqspark/target/scala-2.11/classes... [info] 'compiler-interface' not yet compiled for Scala 2.11.12. Compiling... [info] Compilation completed in 9.047 s [warn] /home/jnbaker/bin/seqspark/src/main/scala/org/dizhang/seqspark/util/LogicalParser.scala:91: Exhaustivity analysis reached max recursion depth, not all missing cases are reported. [warn] (Please try with scalac -Ypatmat-exhaust-depth 40 or -Ypatmat-exhaust-depth off.) [warn] logExpr match { [warn] ^ [warn] /home/jnbaker/bin/seqspark/src/main/scala/org/dizhang/seqspark/util/LogicalParser.scala:112: Exhaustivity analysis reached max recursion depth, not all missing cases are reported. [warn] (Please try with scalac -Ypatmat-exhaust-depth 40 or -Ypatmat-exhaust-depth off.) [warn] logExpr match { [warn] ^ [warn] /home/jnbaker/bin/seqspark/src/main/scala/org/dizhang/seqspark/util/LogicalParser.scala:133: match may not be exhaustive. [warn] It would fail on the following input: Error() [warn] logExpr match { [warn] ^ [warn] /home/jnbaker/bin/seqspark/src/main/scala/org/dizhang/seqspark/util/LogicalParser.scala:152: match may not be exhaustive. [warn] It would fail on the following input: Error(_) [warn] logExpr match { [warn] ^ [warn] four warnings found java.lang.ExceptionInInitializerError at scala.collection.parallel.ParIterableLike$class.$init$(ParIterableLike.scala:166) at scala.collection.parallel.immutable.ParVector.(ParVector.scala:43) at scala.collection.immutable.Vector.par(Vector.scala:88) at sbtassembly.Assembly$.assembleMappings(Assembly.scala:181) at sbtassembly.Assembly$$anonfun$assembledMappingsTask$1.apply(Assembly.scala:252) at sbtassembly.Assembly$$anonfun$assembledMappingsTask$1.apply(Assembly.scala:250) at scala.Function1$$anonfun$compose$1.apply(Function1.scala:47) at sbt.$tilde$greater$$anonfun$$u2219$1.apply(TypeFunctions.scala:40) at sbt.std.Transform$$anon$4.work(System.scala:63) at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:228) at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:228) at sbt.ErrorHandling$.wideConvert(ErrorHandling.scala:17) at sbt.Execute.work(Execute.scala:237) at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:228) at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:228) at sbt.ConcurrentRestrictions$$anon$4$$anonfun$1.apply(ConcurrentRestrictions.scala:159) at sbt.CompletionService$$anon$2.call(CompletionService.scala:28) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) Caused by: java.lang.NumberFormatException: Not a version: 11 at scala.util.PropertiesTrait$class.parts$1(Properties.scala:176) at scala.util.PropertiesTrait$class.isJavaAtLeast(Properties.scala:180) at scala.util.Properties$.isJavaAtLeast(Properties.scala:16) at scala.collection.parallel.package$.getTaskSupport(package.scala:45) at scala.collection.parallel.package$.(package.scala:48) at scala.collection.parallel.package$.(package.scala) at scala.collection.parallel.ParIterableLike$class.$init$(ParIterableLike.scala:166) at scala.collection.parallel.immutable.ParVector.(ParVector.scala:43) at scala.collection.immutable.Vector.par(Vector.scala:88) at sbtassembly.Assembly$.assembleMappings(Assembly.scala:181) at sbtassembly.Assembly$$anonfun$assembledMappingsTask$1.apply(Assembly.scala:252) at sbtassembly.Assembly$$anonfun$assembledMappingsTask$1.apply(Assembly.scala:250) at scala.Function1$$anonfun$compose$1.apply(Function1.scala:47) at sbt.$tilde$greater$$anonfun$$u2219$1.apply(TypeFunctions.scala:40) at sbt.std.Transform$$anon$4.work(System.scala:63) at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:228) at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:228) at sbt.ErrorHandling$.wideConvert(ErrorHandling.scala:17) at sbt.Execute.work(Execute.scala:237) at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:228) at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:228) at sbt.ConcurrentRestrictions$$anon$4$$anonfun$1.apply(ConcurrentRestrictions.scala:159) at sbt.CompletionService$$anon$2.call(CompletionService.scala:28) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) [error] (*:assembly::assembledMappings) java.lang.ExceptionInInitializerError [error] Total time: 112 s, completed Oct 10, 2019, 9:10:36 PM Finished building seqspark. Cannot find target/scala-2.11/SeqSpark.jar, compiling failed? at ./install line 84, <$fh> line 48.

zhangdi-devel commented 4 years ago

Hi, I haven't encountered this error before. Might have something to do with sbt/java versions. If you could wait a few days, I'll create a Dockerfile for local/single-server development. It won't be the best way to run SeqSpark in a production environment but hopefully would help the single server test.

jasminebro commented 4 years ago

Hi, thank you for offering to create a Dockerfile. Fingers crossed the Dockerfile helps.

zhangdi-devel commented 4 years ago

Hello @jasminebro, I've created a Dockerfile/image and updated the README on how to use it. Please let me know if you have any questions.

jasminebro commented 4 years ago

Hi, I was able to download the Docker image via option 2 (When I tried to use Option 1 I got the following error-- Error response from daemon: Dockerfile parse error line 7: unknown instruction: <!DOCTYPE).

Next, when I tried to run docker I got the following error: Unable to find image 'seqspark:latest' locally. docker: Error response from daemon: pull access denied for seqspark, repository does not exist or may require 'docker login': denied: requested access to the resource is denied. See 'docker run --help'.

zhangdi-devel commented 4 years ago

Hi @jasminebro ,

I had a typo in README. Please run this command: docker tag zhangdbio/seqspark:test seqspark:latest.

I accidentally typed lastest instead of latest in the doc, and that's why it complained "Unable to find image" when you tried to run it later.

Thank you for letting me know about this error. I'll update the doc accordingly.

zhangdi-devel commented 4 years ago

The error with Option 1 is odd to me though. Did you get the Dockerfile by running git pull (This is the right way to do it)?
If you directly download the file from GitHub, it will become an HTML file and "<!DOCTYPE" looks like part of a header line of an HTML file.

And even if you manage to download the Dockerfile to the old source code of seqspark, it might not work because I had to change some other files to make it work with the Dockefile.

jasminebro commented 4 years ago

I did not get the Dockerfile by running git pull. I believe it downloaded why I tried option 1 even though Option 1 did not fully work. The Dockerfile I have is an HTML file.

Also,when I tried to run seqspark this time using the following command: docker run -v ${PWD}/db:/opt/seqspark/ref -v ${PWD}:/home/seqspark seqspark JasmineScd_project.conf

I got this error: docker: Error response from daemon: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:319: getting the final child's pid from pipe caused \"EOF\"": unknown. ERRO[0003] error waiting for container: context canceled

jasminebro commented 4 years ago

I wonder if the issue is with attaching the volume to the container.

zhangdi-devel commented 4 years ago

What is the version of your docker engine? It might help if you could upgrade it to the latest stable version (as of now 19.03.4).

jasminebro commented 4 years ago

I am using Docker version 19.03.3, build a872fc2f86.

zhangdi-devel commented 4 years ago

Hi @jasminebro , Can you try to remove the image and re-download or re-build? You can also try to run the container or log into it without mounting the volumes.

jasminebro commented 4 years ago

Hi,

I tried to remove the image and re-download it and rebuild multiple times. I am not sure if this is a system specific problem on my end. I also tried without mounting the volumes. Very strange. Thanks for your help. I may have to try another software.