* Package:    sci-biology/gatk-1.5
 * Repository: gentoo
 * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
 * USE:        amd64 elibc_glibc kernel_linux multilib userland_GNU
 * FEATURES:   nostrip sandbox splitdebug
 * Using: icedtea-bin-7
>>> Unpacking source...
>>> Unpacking gatk-1.5.tar.gz to /var/tmp/portage/sci-biology/gatk-1.5/work
>>> Source unpacked in /var/tmp/portage/sci-biology/gatk-1.5/work
>>> Preparing source in /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
Rewriting attributes
Rewriting ./build.xml
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
 * Disabling all optional ANT_TASKS
Buildfile: /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build.xml

git.describe:
     [exec] Result: 128

tagged.build.version:

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

untagged.build.version:

generate.build.version:

init:
     [echo] GATK build      : core
     [echo] Scala build     : none
     [echo] source revision : exported
     [echo] build time      : 2012/06/01 11:09:20
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/lib
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build/java/classes
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build/java/contracts

init.resolve:
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-1.5/work/.ant/lib
      [get] Getting: http://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar
      [get] To: /var/tmp/portage/sci-biology/gatk-1.5/work/.ant/lib/ivy-2.2.0.jar

resolve:
[ivy:retrieve] :: Ivy 2.2.0 - 20100923230623 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: file = /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: org.broadinstitute#Sting;working@vostro.doma
[ivy:retrieve] 	confs: [default]
[ivy:retrieve] 	found net.sf#sam;1.59.1066 in projects
[ivy:retrieve] 	[1.59.1066] net.sf#sam;latest.integration
[ivy:retrieve] 	found net.sf#picard;1.59.1066 in projects
[ivy:retrieve] 	[1.59.1066] net.sf#picard;latest.integration
[ivy:retrieve] 	found edu.mit.broad#picard-private-parts;2181 in projects
[ivy:retrieve] 	[2181] edu.mit.broad#picard-private-parts;latest.integration
[ivy:retrieve] 	found org.broad#tribble;53 in projects
[ivy:retrieve] 	[53] org.broad#tribble;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;0.9.5-RC2 in reflections-repo
[ivy:retrieve] 	found com.google.collections#google-collections;1.0 in maven
[ivy:retrieve] 	found javassist#javassist;3.8.0.GA in maven
[ivy:retrieve] 	found org.slf4j#slf4j-api;1.5.6 in maven
[ivy:retrieve] 	found dom4j#dom4j;1.6 in maven
[ivy:retrieve] 	found xml-apis#xml-apis;1.0.b2 in maven
[ivy:retrieve] 	found com.google.code.gson#gson;1.4 in maven
[ivy:retrieve] 	found ch.qos.logback#logback-classic;0.9.9 in maven
[ivy:retrieve] 	found ch.qos.logback#logback-core;0.9.9 in maven
[ivy:retrieve] 	found org.slf4j#slf4j-api;1.5.0 in maven
[ivy:retrieve] 	found gov.nist#Jama;1.0.2 in projects
[ivy:retrieve] 	found org.jgrapht#jgrapht-jdk1.5;0.7.3 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;2.0 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 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;2.8.1 in maven
[ivy:retrieve] 	found org.scala-lang#scala-library;2.8.1 in maven
[ivy:retrieve] 	found com.google.code.cofoja#cofoja;1.0-20110609 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 dom4j#dom4j;1.6.1 in maven
[ivy:retrieve] 	found net.sf.snpeff#snpeff;2.0.5 in projects
[ivy:retrieve] downloading /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf/sam-1.59.1066.jar ...
[ivy:retrieve] .......... (556kB)
[ivy:retrieve] 	[SUCCESSFUL ] net.sf#sam;1.59.1066!sam.jar (3ms)
[ivy:retrieve] downloading /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf/picard-1.59.1066.jar ...
[ivy:retrieve] .................... (1177kB)
[ivy:retrieve] 	[SUCCESSFUL ] net.sf#picard;1.59.1066!picard.jar (3ms)
[ivy:retrieve] downloading /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/edu.mit.broad/picard-private-parts-2181.jar ...
[ivy:retrieve] .. (39kB)
[ivy:retrieve] 	[SUCCESSFUL ] edu.mit.broad#picard-private-parts;2181!picard-private-parts.jar (1ms)
[ivy:retrieve] downloading /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/org.broad/tribble-53.jar ...
[ivy:retrieve] ...... (297kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.broad#tribble;53!tribble.jar (1ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/log4j/log4j/1.2.15/log4j-1.2.15.jar ...
[ivy:retrieve] ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ (382kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] log4j#log4j;1.2.15!log4j.jar (1303ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/javax/mail/mail/1.4.4/mail-1.4.4.jar ...
[ivy:retrieve] ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ (483kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] javax.mail#mail;1.4.4!mail.jar (1458ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/colt/colt/1.2.0/colt-1.2.0.jar ...
[ivy:retrieve] ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... (568kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] colt#colt;1.2.0!colt.jar (1410ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/simpleframework/simple-xml/2.0.4/simple-xml-2.0.4.jar ...
[ivy:retrieve] ........................................................................................................................................................................................................................................................................................................................................................................................................................................................ (216kB)
[ivy:retrieve] ... (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.simpleframework#simple-xml;2.0.4!simple-xml.jar (1177ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/apache/bcel/bcel/5.2/bcel-5.2.jar ...
[ivy:retrieve] ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... (520kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.apache.bcel#bcel;5.2!bcel.jar (1411ms)
[ivy:retrieve] downloading http://reflections.googlecode.com/svn/repo/org/reflections/reflections/0.9.5-RC2/reflections-0.9.5-RC2.jar ...
[ivy:retrieve] ................................................................................................................................................................... (79kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.reflections#reflections;0.9.5-RC2!reflections.jar (1307ms)
[ivy:retrieve] downloading /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/gov.nist/Jama-1.0.2.jar ...
[ivy:retrieve] .. (32kB)
[ivy:retrieve] 	[SUCCESSFUL ] gov.nist#Jama;1.0.2!Jama.jar (1ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/jgrapht/jgrapht-jdk1.5/0.7.3/jgrapht-jdk1.5-0.7.3.jar ...
[ivy:retrieve] ................................................................................................................................................................................................................................................................................................................................................................................... (184kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.jgrapht#jgrapht-jdk1.5;0.7.3!jgrapht-jdk1.5.jar (1049ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/freemarker/freemarker/2.3.18/freemarker-2.3.18.jar ...
[ivy:retrieve] .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... (902kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.freemarker#freemarker;2.3.18!freemarker.jar (1774ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/apache/commons/commons-email/1.2/commons-email-1.2.jar ...
[ivy:retrieve] ..................................................................... (31kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.apache.commons#commons-email;1.2!commons-email.jar (994ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/apache/commons/commons-jexl/2.0/commons-jexl-2.0.jar ...
[ivy:retrieve] .......................................................................................................................................................................................................................................................................................................................................................................................................................................... (205kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.apache.commons#commons-jexl;2.0!commons-jexl.jar (1170ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-lang/commons-lang/2.5/commons-lang-2.5.jar ...
[ivy:retrieve] ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. (272kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] commons-lang#commons-lang;2.5!commons-lang.jar (2350ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar ...
[ivy:retrieve] ............................................................................................................................... (59kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] commons-logging#commons-logging;1.1.1!commons-logging.jar (1068ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.1/commons-io-2.1.jar ...
[ivy:retrieve] ................................................................................................................................................................................................................................................................................................................................................. (159kB)
[ivy:retrieve] ... (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] commons-io#commons-io;2.1!commons-io.jar (1190ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/apache/commons/commons-math/2.2/commons-math-2.2.jar ...
[ivy:retrieve] .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... (965kB)
[ivy:retrieve] ... (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.apache.commons#commons-math;2.2!commons-math.jar (1755ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/net/java/dev/jna/jna/3.2.7/jna-3.2.7.jar ...
[ivy:retrieve] ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ (925kB)
[ivy:retrieve] ... (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] net.java.dev.jna#jna;3.2.7!jna.jar (1879ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/net/java/dev/jets3t/jets3t/0.8.1/jets3t-0.8.1.jar ...
[ivy:retrieve] ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ (488kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] net.java.dev.jets3t#jets3t;0.8.1!jets3t.jar (1457ms)
[ivy:retrieve] downloading /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar ...
[ivy:retrieve] .. (50kB)
[ivy:retrieve] 	[SUCCESSFUL ] net.sf.gridscheduler#drmaa;6.2u5p2!drmaa.jar (1ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/scala-lang/scala-compiler/2.8.1/scala-compiler-2.8.1.jar ...
[ivy:retrieve] ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
[ivy:retrieve] ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
[ivy:retrieve] ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
[ivy:retrieve] ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
[ivy:retrieve] ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... (8774kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.scala-lang#scala-compiler;2.8.1!scala-compiler.jar (7397ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/scala-lang/scala-library/2.8.1/scala-library-2.8.1.jar ...
[ivy:retrieve] ..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
[ivy:retrieve] ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
[ivy:retrieve] ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
[ivy:retrieve] ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... (6343kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.scala-lang#scala-library;2.8.1!scala-library.jar (6251ms)
[ivy:retrieve] downloading /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar ...
[ivy:retrieve] ....... (368kB)
[ivy:retrieve] 	[SUCCESSFUL ] com.google.code.cofoja#cofoja;1.0-20110609!cofoja.jar (2ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/asm/asm-all/3.3.1/asm-all-3.3.1.jar ...
[ivy:retrieve] .......................................................................................................................................................................................................................................................................................................................................................................................................................................... (202kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] asm#asm-all;3.3.1!asm-all.jar (1147ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/apache/poi/poi/3.8-beta3/poi-3.8-beta3.jar ...
[ivy:retrieve] ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. (1692kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.apache.poi#poi;3.8-beta3!poi.jar (2287ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/org/apache/poi/poi-ooxml/3.8-beta3/poi-ooxml-3.8-beta3.jar ...
[ivy:retrieve] ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. (555kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] org.apache.poi#poi-ooxml;3.8-beta3!poi-ooxml.jar (1452ms)
[ivy:retrieve] downloading /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf.snpeff/snpeff-2.0.5.jar ...
[ivy:retrieve] ................................................................. (4080kB)
[ivy:retrieve] 	[SUCCESSFUL ] net.sf.snpeff#snpeff;2.0.5!snpeff.jar (4ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/javax/activation/activation/1.1/activation-1.1.jar ...
[ivy:retrieve] ...................................................................................................................................... (61kB)
[ivy:retrieve] ... (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] javax.activation#activation;1.1!activation.jar (1021ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/concurrent/concurrent/1.3.4/concurrent-1.3.4.jar ...
[ivy:retrieve] .................................................................................................................................................................................................................................................................................................................................................................... (184kB)
[ivy:retrieve] ... (0kB)
[ivy:retrieve] 	[SUCCESSFUL ] concurrent#concurrent;1.3.4!concurrent.jar (1158ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/stax/stax-api/1.0.1/stax-api-1.0.1.jar ...
[ivy:retrieve] ................................................ (25kB)
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[ivy:retrieve] 	[SUCCESSFUL ] stax#stax-api;1.0.1!stax-api.jar (997ms)
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[ivy:retrieve] :: resolution report :: resolve 177799ms :: artifacts dl 90947ms
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[ivy:retrieve] :: retrieving :: org.broadinstitute#Sting
[ivy:retrieve] 	confs: [default]
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gatk.compile.public.source:
    [javac] Compiling 738 source files to /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build/java/classes
    [javac] /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/public/java/src/org/broadinstitute/sting/utils/MathUtils.java:1103: error: name clash: sum(Collection<Integer>) and sum(Collection<Number>) have the same erasure
    [javac]     public static long sum(Collection<Integer> x) {
    [javac]                        ^
    [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] 1 error

BUILD FAILED
/var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build.xml:292: Compile failed; see the compiler error output for details.

Total time: 4 minutes 41 seconds
 * ERROR: sci-biology/gatk-1.5 failed (compile phase):
 *   eant failed
 * 
 * Call stack:
 *     ebuild.sh, line   85:  Called src_compile
 *   environment, line 3860:  Called java-pkg-2_src_compile
 *   environment, line 1911:  Called eant 'dist' '-f' 'build.xml'
 *   environment, line  523:  Called die
 * The specific snippet of code:
 *       ant ${antflags} "${@}" || die "eant failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/gatk-1.5'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/gatk-1.5'`.
!!! When you file a bug report, please include the following information:
GENTOO_VM=icedtea-bin-7  CLASSPATH="" JAVA_HOME="/opt/icedtea-bin-7.2.1"
JAVACFLAGS="-source 1.6 -target 1.6" COMPILER="javac"
and of course, the output of emerge --info
 * The complete build log is located at '/var/tmp/portage/sci-biology/gatk-1.5/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/gatk-1.5/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24'
 * S: '/var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24'