Use GATK R Library (gsalib), how to build?

qyu

Hi,

Does anyone use GATK R Library (gsalib)? I follow the guide at this link (http://gatkforums.broadinstitute.org/discussion/1244/what-is-a-gatkreport), when I type "ant gsalib" in my linux system with Java 1.6, the building failed. Here is the error message.

5:00pm qyu@vbronze /bit/data01/projects/prod_scripts/GATK/gatk-master $ ant gsalib Buildfile: build.xml

BUILD FAILED /bit/data01/projects/prod_scripts/GATK/gatk-master/build.xml:184: The type doesn't support the "erroronmissingdir" attribute.

Can anyone know what is wrong here?

Many thanks, Qing

pdexheimer

This sounds like an old version of Ant: http://stackoverflow.com/questions/6491796/fileset-doesnt-support-the-erroronmissingdir-attribute

qyu

Thanks! Now I use ant-1.8, but I get a different error message as below. I have granted full writing permission to the working directory and files.

10:37am qyu@vbronze /bit/data01/projects/prod_scripts/GATK/gatk-master $ ant gsalib Buildfile: /bit/data01/projects/prod_scripts/GATK/gatk-master/build.xml

gsalib: [exec] * installing to library â [exec] Error: ERROR: no permission to install to directory â

BUILD FAILED /bit/data01/projects/prod_scripts/GATK/gatk-master/build.xml:1039: exec returned: 1

Total time: 3 seconds

Can you find what is wrong here?

Many thanks, Qing

pdexheimer

No, I can't help there. I would try to figure out how it got the name of the directory to install to, and why it's such a funny name. It may just be a bad environment variable or something

qyu

Thank you very much!

hong_010

sudo ant gsalib Buildfile: gatk-master/build.xml [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

gsalib: [exec] * installing to library ‘/usr/lib64/R/library’ [exec] * installing source package ‘gsalib’ ... [exec] ERROR: a 'NAMESPACE' file is required [exec] * removing ‘/usr/lib64/R/library/gsalib’

BUILD FAILED

How to reslove?

Thanks!

Geraldine_VdAuwera

Can you try doing a full build (ant clean dist) and see if that works?

Also, what version of the source are you using?

hong_010

ant clean dist->ant gsalib,It's showed the same problem.Download from https://github.com/broadgsa/gatk.This version as follow: Java:1.6._43,Ant:1.8.4,gatk:2.4.9.

Thanks!

Geraldine_VdAuwera

Hi @hong_010, please see this post for a solution contributed by a user who had the same problem: http://gatkforums.broadinstitute.org/discussion/comment/5130#Comment_5130

hong_010

Hi,my problem isnot the same with @ying_sheng_1.Because when I run the ant clean dist ,there was the phenomenon:

Buildfile: gatk-master/build.xml [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

I can not resolve it.Would you give me a help?

Thanks!

Geraldine_VdAuwera

The cloverlib.xml is not a blocking error, it probably has nothing to do with your build failure. Can you post the complete console output that you get when you run ant clean dist?

hong_010

$ ant clean dist

Buildfile: gatk-master/build.xml [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

clean.javadoc:

clean.scaladoc:

clean.gatkdocs:

-check.clover:

clean.clover:

clean: [delete] Deleting directory gatk-master/build [delete] Deleting directory gatk-master/lib [delete] Deleting directory gatk-master/dist

git.describe: [exec] Result: 128

tagged.build.version:

git.rev-parse: [exec] Result: 128

untagged.build.version:

generate.build.version:

init: [echo] BUILD PROPERTIES [echo] Include Scala? : yes [echo] Include Private? : no [echo] Include Protected? : no [echo] Include External? : no [echo] Include Contracts? : no [echo] Source revision : exported [echo] Build time : 2013/04/13 16:42:46 [mkdir] Created dir: gatk-master/build [mkdir] Created dir: gatk-master/lib [mkdir] Created dir: gatk-master/build/java/classes [mkdir] Created dir: gatk-master/build/java/contracts

init.resolve: [get] Getting: http://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar [get] To: /home/yangch/.ant/lib/ivy-2.2.0.jar [get] Not modified - so not downloaded [get] Getting: http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/2.1.3/maven-ant-tasks-2.1.3.jar [get] To: /home/yangch/.ant/lib/maven-ant-tasks-2.1.3.jar [get] Not modified - so not downloaded

resolve: [ivy:retrieve] :: Ivy 2.2.0 - 20100923230623 :: http://ant.apache.org/ivy/ :: [ivy:retrieve] :: loading settings :: file = gatk-master/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: org.broadinstitute#Sting;working@master [ivy:retrieve] confs: [default] [ivy:retrieve] found net.sf#sam;1.84.1337 in projects [ivy:retrieve] [1.84.1337] net.sf#sam;latest.integration [ivy:retrieve] found net.sf#picard;1.84.1337 in projects [ivy:retrieve] [1.84.1337] net.sf#picard;latest.integration [ivy:retrieve] found edu.mit.broad#picard-private-parts;2662 in projects [ivy:retrieve] [2662] edu.mit.broad#picard-private-parts;latest.integration [ivy:retrieve] found org.broad#tribble;1.84.1337 in projects [ivy:retrieve] [1.84.1337] org.broad#tribble;latest.integration [ivy:retrieve] found org.broadinstitute#variant;1.85.1357 in projects [ivy:retrieve] [1.85.1357] org.broadinstitute#variant;latest.integration [ivy:retrieve] found log4j#log4j;1.2.15 in maven [ivy:retrieve] found javax.mail#mail;1.4.4 in maven [ivy:retrieve] found javax.activation#activation;1.1 in maven [ivy:retrieve] found colt#colt;1.2.0 in maven [ivy:retrieve] found concurrent#concurrent;1.3.4 in maven [ivy:retrieve] found org.simpleframework#simple-xml;2.0.4 in maven [ivy:retrieve] found stax#stax-api;1.0.1 in maven [ivy:retrieve] found stax#stax;1.2.0 in maven [ivy:retrieve] found org.apache.bcel#bcel;5.2 in maven [ivy:retrieve] found jakarta-regexp#jakarta-regexp;1.4 in maven [ivy:retrieve] found org.reflections#reflections;0.9.8 in maven [ivy:retrieve] found com.google.guava#guava;11.0.2 in maven [ivy:retrieve] found com.google.code.findbugs#jsr305;1.3.9 in maven [ivy:retrieve] found javassist#javassist;3.12.1.GA in maven [ivy:retrieve] found dom4j#dom4j;1.6.1 in maven [ivy:retrieve] found xml-apis#xml-apis;1.0.b2 in maven [ivy:retrieve] found org.slf4j#slf4j-log4j12;1.6.1 in maven [ivy:retrieve] found org.slf4j#slf4j-api;1.6.1 in maven [ivy:retrieve] found log4j#log4j;1.2.16 in maven [ivy:retrieve] found gov.nist#Jama;1.0.2 in projects [ivy:retrieve] found net.sf.jgrapht#jgrapht;0.8.3 in maven [ivy:retrieve] found org.freemarker#freemarker;2.3.18 in maven [ivy:retrieve] found org.apache.commons#commons-email;1.2 in maven [ivy:retrieve] found org.apache.commons#commons-jexl;2.1.1 in maven [ivy:retrieve] found commons-logging#commons-logging;1.1.1 in maven [ivy:retrieve] found commons-lang#commons-lang;2.5 in maven [ivy:retrieve] found commons-io#commons-io;2.1 in maven [ivy:retrieve] found commons-collections#commons-collections;3.2.1 in maven [ivy:retrieve] found org.apache.commons#commons-math;2.2 in maven [ivy:retrieve] found net.java.dev.jna#jna;3.2.7 in maven [ivy:retrieve] found net.java.dev.jets3t#jets3t;0.8.1 in maven [ivy:retrieve] found commons-codec#commons-codec;1.3 in maven [ivy:retrieve] found commons-httpclient#commons-httpclient;3.1 in maven [ivy:retrieve] found com.jamesmurty.utils#java-xmlbuilder;0.4 in maven [ivy:retrieve] found net.sf.gridscheduler#drmaa;6.2u5p2 in projects [ivy:retrieve] [6.2u5p2] net.sf.gridscheduler#drmaa;latest.integration [ivy:retrieve] found org.scala-lang#scala-compiler;2.9.2 in maven [ivy:retrieve] found org.scala-lang#scala-library;2.9.2 in maven [ivy:retrieve] found org.testng#testng;6.8 in maven [ivy:retrieve] found junit#junit;4.10 in maven [ivy:retrieve] found org.hamcrest#hamcrest-core;1.1 in maven [ivy:retrieve] found org.beanshell#bsh;2.0b4 in maven [ivy:retrieve] found com.beust#jcommander;1.27 in maven [ivy:retrieve] found org.yaml#snakeyaml;1.6 in maven [ivy:retrieve] found org.uncommons#reportng;1.1.2 in maven [ivy:retrieve] found velocity#velocity;1.4 in maven [ivy:retrieve] found velocity#velocity-dep;1.4 in maven [ivy:retrieve] found com.google.caliper#caliper;0.5-rc1 in maven [ivy:retrieve] found com.google.code.java-allocation-instrumenter#java-allocation-instrumenter;2.0 in maven [ivy:retrieve] found asm#asm;3.3.1 in maven [ivy:retrieve] found asm#asm-analysis;3.3.1 in maven [ivy:retrieve] found asm#asm-tree;3.3.1 in maven [ivy:retrieve] found asm#asm-commons;3.3.1 in maven [ivy:retrieve] found asm#asm-util;3.3.1 in maven [ivy:retrieve] found asm#asm-xml;3.3.1 in maven [ivy:retrieve] found com.google.inject#guice;3.0 in maven [ivy:retrieve] found javax.inject#javax.inject;1 in maven [ivy:retrieve] found aopalliance#aopalliance;1.0 in maven [ivy:retrieve] found org.sonatype.sisu.inject#cglib;2.2.1-v20090111 in maven [ivy:retrieve] found com.google.code.cofoja#cofoja;1.0-r139 in projects [ivy:retrieve] found asm#asm-all;3.3.1 in maven [ivy:retrieve] found org.apache.poi#poi;3.8-beta3 in maven [ivy:retrieve] found commons-codec#commons-codec;1.5 in maven [ivy:retrieve] found org.apache.poi#poi-ooxml;3.8-beta3 in maven [ivy:retrieve] found org.apache.poi#poi-ooxml-schemas;3.8-beta3 in maven [ivy:retrieve] found org.apache.xmlbeans#xmlbeans;2.3.0 in maven [ivy:retrieve] found net.sf.snpeff#snpeff;2.0.5 in projects [ivy:retrieve] found org.mongodb#mongo-java-driver;2.7.3 in maven [ivy:retrieve] found com.google.code.gson#gson;2.2.2 in maven [ivy:retrieve] found org.apache.httpcomponents#httpclient;4.1.1 in maven [ivy:retrieve] found org.apache.httpcomponents#httpcore;4.1 in maven [ivy:retrieve] :: resolution report :: resolve 6413ms :: artifacts dl 51ms [ivy:retrieve] :: evicted modules: [ivy:retrieve] log4j#log4j;1.2.15 by [log4j#log4j;1.2.16] in [default] [ivy:retrieve] javax.mail#mail;1.4 by [javax.mail#mail;1.4.4] in [default] [ivy:retrieve] javax.mail#mail;1.4.1 by [javax.mail#mail;1.4.4] in [default] [ivy:retrieve] commons-codec#commons-codec;1.3 by [commons-codec#commons-codec;1.5] in [default] [ivy:retrieve] org.testng#testng;5.0 by [org.testng#testng;6.8] in [default] [ivy:retrieve] com.google.code.gson#gson;1.7.1 by [com.google.code.gson#gson;2.2.2] in [default] [ivy:retrieve] com.google.guava#guava;11.0.1 by [com.google.guava#guava;11.0.2] in [default] [ivy:retrieve] com.google.guava#guava;r08 by [com.google.guava#guava;11.0.2] in [default] [ivy:retrieve] asm#asm;3.1 by [asm#asm;3.3.1] in [default] [ivy:retrieve] commons-codec#commons-codec;1.4 by [commons-codec#commons-codec;1.5] in [default] --------------------------------------------------------------------- | | modules || artifacts | | conf | number| search|dwnlded|evicted|| number|dwnlded| --------------------------------------------------------------------- | default | 83 | 6 | 0 | 10 || 73 | 0 | --------------------------------------------------------------------- [ivy:retrieve] :: retrieving :: org.broadinstitute#Sting [ivy:retrieve] confs: [default] [ivy:retrieve] 73 artifacts copied, 0 already retrieved (52083kB/378ms)

gatk.compile.internal.source: [javac] Compiling 659 source files to gatk-master/build/java/classes [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/refdata/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/commandline/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/walkers/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/filters/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/queue/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/providers/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/alignment/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/utils/threading/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reference/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/executive/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/utils/sam/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/utils/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/traversals/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/rmd/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reads/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/iterators/package-info.class [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/utils/fasta/package-info.class

gatk.compile.external.source:

gatk.compile.source:

gatk.contracts:

gatk.compile:

init.extracthelp: [loadfile] gatk-master/build/java/classes/StingText.properties doesn't exist

extracthelp: [javadoc] Generating Javadoc [javadoc] Javadoc execution

init.queue-extensions.generate:

queue-extensions.generate: [mkdir] Created dir: gatk-master/build/queue-extensions/src [echo] Generating Queue GATK extensions...

init.scala.compile:

scala.compile: [mkdir] Created dir: gatk-master/build/scala/classes [echo] Building Scala... [scalac] Compiling 101 source files to gatk-master/build/scala/classes [scalac] Compiling 90 source files to gatk-master/build/scala/classes

sting.compile:

init.jar: [mkdir] Created dir: gatk-master/dist [copy] Copying 73 files to gatk-master/dist

R.public.tar: [mkdir] Created dir: gatk-master/build/R/src/org/broadinstitute/sting/utils/R [tar] Nothing to do: gatk-master/build/R/src/org/broadinstitute/sting/utils/R/gsalib.tar.gz is up to date.

R.script.stage: [mkdir] Created dir: gatk-master/build/R/stage [copy] Copying 3 files to gatk-master/build/R/stage

sting-utils.jar: [jar] Building jar: gatk-master/dist/StingUtils.jar

gatk.jar: [jar] Building jar: gatk-master/dist/GenomeAnalysisTK.jar [jar] Building jar: gatk-master/dist/Aligner.jar [subant] No sub-builds to iterate on

queue.jar: [jar] Building jar: gatk-master/dist/Queue.jar

sting.jar:

init.manifests:

sting-utils.manifests: [jar] Updating jar: gatk-master/dist/StingUtils.jar

gatk.manifests: [jar] Updating jar: gatk-master/dist/GenomeAnalysisTK.jar

queue.manifests: [jar] Updating jar: gatk-master/dist/Queue.jar

sting.manifests:

dist:

BUILD SUCCESSFUL Total time: 1 minute 17 seconds

Geraldine_VdAuwera

Great, your build is successful! Then you just need to do the same steps as Ying Sheng, either install gsalib manually or fix the namespace issue as Ying Sheng described.

hong_010

Hi！ My build was successful,but it pointed out:

[taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

When I installed gaslib,it pointed out:

$ ls -l public/R/src/org/broadinstitute/sting/utils/R/ total 128 drwxr-xr-x 5 yang bio 131072 Mar 19 13:09 gsalib

$ R CMD INSTALL public/R/src/org/broadinstitute/sting/utils/R/ Warning: invalid package ‘public/R/src/org/broadinstitute/sting/utils/R/’ Error: ERROR: no packages specified

Why?

Would you give me a help?

Thanks!

Geraldine_VdAuwera

Hi Hong,

The cloverlib error is not important, don't worry about it.

For the install command, you have to add "gsalib" to the package path. You're passing the actual package, not the enclosing directory that it is in.

hong_010

Thank you very much!

I have done the following modifications：

1.cd public/R/src/org/broadinstitute/sting/utils/R/gsalib --> create the NAMESPACE file

2.R CMD INSTALL -l R_library gatk-master/public/R/src/org/broadinstitute/sting/utils/R/gsalib

It works now!

The most important thing is to set the installation directory。

I hope to be useful to others。

ref:http://stackoverflow.com/questions/8012596/error-with-asreml-d-package-in-r-2-14-0/8014357#8014357

Geraldine_VdAuwera

Thanks for reporting your full solution! I'm sure this will be helpful for other users.

Innsbrucker

hi, i have the following problem. I have download the gatk-master.zip file from Github. Using the ant clean dist command produces an error -> Build failed.

Here are the console output:

[root@radjedef gatk-master]# ant clean dist Buildfile: build.xml [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

clean.javadoc:

clean.scaladoc:

clean.gatkdocs:

-check.clover:

clean.clover:

clean: [delete] Deleting directory /export/vols/meritites_v2/programs/GATK/gatk-master/build [delete] Deleting directory /export/vols/meritites_v2/programs/GATK/gatk-master/lib [delete] Deleting directory /export/vols/meritites_v2/programs/GATK/gatk-master/dist

git.describe: [exec] Result: 128

tagged.build.version:

git.rev-parse: [exec] Result: 128

untagged.build.version:

generate.build.version:

init: [echo] BUILD PROPERTIES [echo] Include Scala? : yes [echo] Include Private? : no [echo] Include Protected? : no [echo] Include External? : no [echo] Include Contracts? : no [echo] Source revision : exported [echo] Build time : 2013/04/18 13:40:33 [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/lib [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/contracts

init.resolve: [get] Getting: http://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar [get] To: /root/.ant/lib/ivy-2.2.0.jar [get] Not modified - so not downloaded [get] Getting: http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/2.1.3/maven-ant-tasks-2.1.3.jar [get] To: /root/.ant/lib/maven-ant-tasks-2.1.3.jar [get] Not modified - so not downloaded

resolve: [ivy:retrieve] :: Ivy 2.2.0 - 20100923230623 :: http://ant.apache.org/ivy/ :: [ivy:retrieve] :: loading settings :: file = /export/vols/meritites_v2/programs/GATK/gatk-master/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: org.broadinstitute#Sting;working@localhost [ivy:retrieve] confs: [default] [ivy:retrieve] found net.sf#sam;1.84.1337 in projects [ivy:retrieve] [1.84.1337] net.sf#sam;latest.integration [ivy:retrieve] found net.sf#picard;1.84.1337 in projects [ivy:retrieve] [1.84.1337] net.sf#picard;latest.integration [ivy:retrieve] found edu.mit.broad#picard-private-parts;2662 in projects [ivy:retrieve] [2662] edu.mit.broad#picard-private-parts;latest.integration [ivy:retrieve] found org.broad#tribble;1.84.1337 in projects [ivy:retrieve] [1.84.1337] org.broad#tribble;latest.integration [ivy:retrieve] found org.broadinstitute#variant;1.85.1357 in projects [ivy:retrieve] [1.85.1357] org.broadinstitute#variant;latest.integration [ivy:retrieve] found log4j#log4j;1.2.15 in maven [ivy:retrieve] found javax.mail#mail;1.4.4 in maven [ivy:retrieve] found javax.activation#activation;1.1 in maven [ivy:retrieve] found colt#colt;1.2.0 in maven [ivy:retrieve] found concurrent#concurrent;1.3.4 in maven [ivy:retrieve] found org.simpleframework#simple-xml;2.0.4 in maven [ivy:retrieve] found stax#stax-api;1.0.1 in maven [ivy:retrieve] found stax#stax;1.2.0 in maven [ivy:retrieve] found org.apache.bcel#bcel;5.2 in maven [ivy:retrieve] found jakarta-regexp#jakarta-regexp;1.4 in maven [ivy:retrieve] found org.reflections#reflections;0.9.8 in maven [ivy:retrieve] found com.google.guava#guava;11.0.2 in maven [ivy:retrieve] found com.google.code.findbugs#jsr305;1.3.9 in maven [ivy:retrieve] found javassist#javassist;3.12.1.GA in maven [ivy:retrieve] found dom4j#dom4j;1.6.1 in maven [ivy:retrieve] found xml-apis#xml-apis;1.0.b2 in maven [ivy:retrieve] found org.slf4j#slf4j-log4j12;1.6.1 in maven [ivy:retrieve] found org.slf4j#slf4j-api;1.6.1 in maven [ivy:retrieve] found log4j#log4j;1.2.16 in maven [ivy:retrieve] found gov.nist#Jama;1.0.2 in projects [ivy:retrieve] found net.sf.jgrapht#jgrapht;0.8.3 in maven [ivy:retrieve] found org.freemarker#freemarker;2.3.18 in maven [ivy:retrieve] found org.apache.commons#commons-email;1.2 in maven [ivy:retrieve] found org.apache.commons#commons-jexl;2.1.1 in maven [ivy:retrieve] found commons-logging#commons-logging;1.1.1 in maven [ivy:retrieve] found commons-lang#commons-lang;2.5 in maven [ivy:retrieve] found commons-io#commons-io;2.1 in maven [ivy:retrieve] found commons-collections#commons-collections;3.2.1 in maven [ivy:retrieve] found org.apache.commons#commons-math;2.2 in maven [ivy:retrieve] found net.java.dev.jna#jna;3.2.7 in maven [ivy:retrieve] found net.java.dev.jets3t#jets3t;0.8.1 in maven [ivy:retrieve] found commons-codec#commons-codec;1.3 in maven [ivy:retrieve] found commons-httpclient#commons-httpclient;3.1 in maven [ivy:retrieve] found com.jamesmurty.utils#java-xmlbuilder;0.4 in maven [ivy:retrieve] found net.sf.gridscheduler#drmaa;6.2u5p2 in projects [ivy:retrieve] [6.2u5p2] net.sf.gridscheduler#drmaa;latest.integration [ivy:retrieve] found org.scala-lang#scala-compiler;2.9.2 in maven [ivy:retrieve] found org.scala-lang#scala-library;2.9.2 in maven [ivy:retrieve] found org.testng#testng;6.8 in maven [ivy:retrieve] found junit#junit;4.10 in maven [ivy:retrieve] found org.hamcrest#hamcrest-core;1.1 in maven [ivy:retrieve] found org.beanshell#bsh;2.0b4 in maven [ivy:retrieve] found com.beust#jcommander;1.27 in maven [ivy:retrieve] found org.yaml#snakeyaml;1.6 in maven [ivy:retrieve] found org.uncommons#reportng;1.1.2 in maven [ivy:retrieve] found velocity#velocity;1.4 in maven [ivy:retrieve] found velocity#velocity-dep;1.4 in maven [ivy:retrieve] found com.google.caliper#caliper;0.5-rc1 in maven [ivy:retrieve] found com.google.code.java-allocation-instrumenter#java-allocation-instrumenter;2.0 in maven [ivy:retrieve] found asm#asm;3.3.1 in maven [ivy:retrieve] found asm#asm-analysis;3.3.1 in maven [ivy:retrieve] found asm#asm-tree;3.3.1 in maven [ivy:retrieve] found asm#asm-commons;3.3.1 in maven [ivy:retrieve] found asm#asm-util;3.3.1 in maven [ivy:retrieve] found asm#asm-xml;3.3.1 in maven [ivy:retrieve] found com.google.inject#guice;3.0 in maven [ivy:retrieve] found javax.inject#javax.inject;1 in maven [ivy:retrieve] found aopalliance#aopalliance;1.0 in maven [ivy:retrieve] found org.sonatype.sisu.inject#cglib;2.2.1-v20090111 in maven [ivy:retrieve] found com.google.code.cofoja#cofoja;1.0-r139 in projects [ivy:retrieve] found asm#asm-all;3.3.1 in maven [ivy:retrieve] found org.apache.poi#poi;3.8-beta3 in maven [ivy:retrieve] found commons-codec#commons-codec;1.5 in maven [ivy:retrieve] found org.apache.poi#poi-ooxml;3.8-beta3 in maven [ivy:retrieve] found org.apache.poi#poi-ooxml-schemas;3.8-beta3 in maven [ivy:retrieve] found org.apache.xmlbeans#xmlbeans;2.3.0 in maven [ivy:retrieve] found net.sf.snpeff#snpeff;2.0.5 in projects [ivy:retrieve] found org.mongodb#mongo-java-driver;2.7.3 in maven [ivy:retrieve] found com.google.code.gson#gson;2.2.2 in maven [ivy:retrieve] found org.apache.httpcomponents#httpclient;4.1.1 in maven [ivy:retrieve] found org.apache.httpcomponents#httpcore;4.1 in maven [ivy:retrieve] :: resolution report :: resolve 5507ms :: artifacts dl 80ms [ivy:retrieve] :: evicted modules: [ivy:retrieve] log4j#log4j;1.2.15 by [log4j#log4j;1.2.16] in [default] [ivy:retrieve] javax.mail#mail;1.4 by [javax.mail#mail;1.4.4] in [default] [ivy:retrieve] javax.mail#mail;1.4.1 by [javax.mail#mail;1.4.4] in [default] [ivy:retrieve] commons-codec#commons-codec;1.3 by [commons-codec#commons-codec;1.5] in [default] [ivy:retrieve] org.testng#testng;5.0 by [org.testng#testng;6.8] in [default] [ivy:retrieve] com.google.code.gson#gson;1.7.1 by [com.google.code.gson#gson;2.2.2] in [default] [ivy:retrieve] com.google.guava#guava;11.0.1 by [com.google.guava#guava;11.0.2] in [default] [ivy:retrieve] com.google.guava#guava;r08 by [com.google.guava#guava;11.0.2] in [default] [ivy:retrieve] asm#asm;3.1 by [asm#asm;3.3.1] in [default] [ivy:retrieve] commons-codec#commons-codec;1.4 by [commons-codec#commons-codec;1.5] in [default] --------------------------------------------------------------------- | | modules || artifacts | | conf | number| search|dwnlded|evicted|| number|dwnlded| --------------------------------------------------------------------- | default | 83 | 6 | 0 | 10 || 73 | 0 | --------------------------------------------------------------------- [ivy:retrieve] :: retrieving :: org.broadinstitute#Sting [ivy:retrieve] confs: [default] [ivy:retrieve] 73 artifacts copied, 0 already retrieved (52083kB/513ms)

gatk.compile.internal.source: [javac] Compiling 659 source files to /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/refdata/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/commandline/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/walkers/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/filters/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/queue/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/providers/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/alignment/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/utils/threading/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reference/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/executive/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/utils/sam/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/utils/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/traversals/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/rmd/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reads/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/iterators/package-info.class [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/utils/fasta/package-info.class

gatk.compile.external.source:

gatk.compile.source:

gatk.contracts:

gatk.compile:

init.extracthelp: [loadfile] /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/StingText.properties doesn't exist

extracthelp: [javadoc] Generating Javadoc [javadoc] Javadoc execution

init.queue-extensions.generate:

queue-extensions.generate: [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/queue-extensions/src [echo] Generating Queue GATK extensions...

init.scala.compile:

scala.compile: [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/scala/classes [echo] Building Scala... [scalac] Compiling 101 source files to /export/vols/meritites_v2/programs/GATK/gatk-master/build/scala/classes [scalac] Compiling 90 source files to /export/vols/meritites_v2/programs/GATK/gatk-master/build/scala/classes

sting.compile:

init.jar: [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/dist [copy] Copying 73 files to /export/vols/meritites_v2/programs/GATK/gatk-master/dist

R.public.tar: [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/R/src/org/broadinstitute/sting/utils/R [tar] Building tar: /export/vols/meritites_v2/programs/GATK/gatk-master/build/R/src/org/broadinstitute/sting/utils/R/gsalib.tar.gz

R.script.stage: [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/R/stage

BUILD FAILED /export/vols/meritites_v2/programs/GATK/gatk-master/build.xml:643: No supported regular expression matcher found: java.lang.ClassNotFoundException: org.apache.tools.ant.util.regexp.Jdk14RegexpMatcher

Total time: 1 minute 29 seconds

Thanks for help!

Geraldine_VdAuwera

Hi there,

This looks like an environment issue. What is your platform and java / JDK version?

droazen

It's probably your ant version -- you should be using ant 1.7 or 1.8.