- * Package: sci-biology/gatk-1.5
- * Repository: gentoo
- * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
- * USE: amd64 elibc_glibc kernel_linux multilib test userland_GNU
- * FEATURES: sandbox test userpriv usersandbox
- * Using: icedtea-bin-7
- >>> Unpacking source...
- >>> Unpacking gatk-1.5.tar.gz to /tmp/portage/sci-biology/gatk-1.5/work
- >>> Source unpacked in /tmp/portage/sci-biology/gatk-1.5/work
- >>> Preparing source in /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
- Searching for bundled jars:
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/org.broad/tribble-53.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf/sam-1.59.1066.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf/picard-1.59.1066.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf.snpeff/snpeff-2.0.5.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/gov.nist/Jama-1.0.2.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/edu.mit.broad/picard-private-parts-2181.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.jar
- Searching for bundled classes (no output if none found):
- Search done.
- >>> Source prepared.
- >>> Configuring source in /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
- Rewriting attributes
- Rewriting ./build.xml
- >>> Source configured.
- >>> Compiling source in /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
- * Disabling all optional ANT_TASKS
- Buildfile: /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 : 2012/08/16 08:55:09
- [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build
- [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/lib
- [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build/java/classes
- [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build/java/contracts
- init.resolve:
- [mkdir] Created dir: /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: /tmp/portage/sci-biology/gatk-1.5/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 /tmp/portage/sci-biology/gatk-1.5/work/.ant/lib/ivy-2.2.0.jar
- BUILD FAILED
- /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build.xml:147: java.net.SocketException: Network is unreachable
- at java.net.PlainSocketImpl.socketConnect(Native Method)
- at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
- at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
- at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
- at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:391)
- at java.net.Socket.connect(Socket.java:579)
- at java.net.Socket.connect(Socket.java:528)
- at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
- at sun.net.www.http.HttpClient.openServer(HttpClient.java:378)
- at sun.net.www.http.HttpClient.openServer(HttpClient.java:473)
- at sun.net.www.http.HttpClient.<init>(HttpClient.java:203)
- at sun.net.www.http.HttpClient.New(HttpClient.java:290)
- at sun.net.www.http.HttpClient.New(HttpClient.java:306)
- at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:995)
- at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:931)
- at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:849)
- 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: 3 seconds
- * ERROR: sci-biology/gatk-1.5 failed (compile phase):
- * eant failed
- *
- * Call stack:
- * ebuild.sh, line 85: Called src_compile
- * environment, line 4189: Called java-pkg-2_src_compile
- * environment, line 2159: Called eant 'dist' '-f' 'build.xml'
- * environment, line 739: 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-7.2.2.1"
- JAVACFLAGS="-source 1.6 -target 1.6" COMPILER="javac"
- and of course, the output of emerge --info
- sed: couldn't open temporary file /etc/portage/package.mask/sedmGb7dA: Permission denied