sci-biology:gatk-2.4:20160213-121713.log

sci-biology:gatk-2.4:20160213-121713.log (text/plain), 4.63 KB, created by Toralf Förster on 2016-02-13 14:24:34 UTC

 * Package:    sci-biology/gatk-2.4
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
 * Using: oracle-jdk-bin-1.8
>>> Unpacking source...
>>> Source unpacked in /var/tmp/portage/sci-biology/gatk-2.4/work
>>> Preparing source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ...
Rewriting attributes
Rewriting ./build.xml
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ...
 * Disabling all optional ANT_TASKS
Buildfile: /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build.xml
  [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

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         : 2016/02/13 13:17:22
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/lib
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build/java/classes
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build/java/contracts

init.resolve:
    [mkdir] Created dir: /var/tmp/portage/sci-biology/gatk-2.4/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-2.4/work/.ant/lib/ivy-2.2.0.jar
      [get] Error getting http://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar to /var/tmp/portage/sci-biology/gatk-2.4/work/.ant/lib/ivy-2.2.0.jar

BUILD FAILED
/var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build.xml:249: java.net.UnknownHostException: repo1.maven.org
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:589)
	at java.net.Socket.connect(Socket.java:538)
	at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)
	at sun.net.www.http.HttpClient.<init>(HttpClient.java:211)
	at sun.net.www.http.HttpClient.New(HttpClient.java:308)
	at sun.net.www.http.HttpClient.New(HttpClient.java:326)
	at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1169)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999)
	at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:933)
	at org.apache.tools.ant.taskdefs.Get$GetThread.openConnection(Get.java:660)
	at org.apache.tools.ant.taskdefs.Get$GetThread.get(Get.java:579)
	at org.apache.tools.ant.taskdefs.Get$GetThread.run(Get.java:569)

Total time: 2 seconds
 * ERROR: sci-biology/gatk-2.4::gentoo failed (compile phase):
 *   eant failed
 * 
 * Call stack:
 *     ebuild.sh, line  133:  Called src_compile
 *   environment, line 3997:  Called java-pkg-2_src_compile
 *   environment, line 1901:  Called eant 'dist' '-f' 'build.xml'
 *   environment, line  671:  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-2.4::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/gatk-2.4::gentoo'`.
!!! When you file a bug report, please include the following information:
GENTOO_VM=oracle-jdk-bin-1.8  CLASSPATH="" JAVA_HOME="/opt/oracle-jdk-bin-1.8.0.74"
JAVACFLAGS="-source 1.6 -target 1.6" COMPILER="javac"
and of course, the output of emerge --info =gatk-2.4
 * The complete build log is located at '/var/log/portage/sci-biology:gatk-2.4:20160213-121713.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/gatk-2.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/gatk-2.4/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4'
 * S: '/var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4'