1. * Package: sci-biology/gatk-1.5
  2. * Repository: gentoo
  3. * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
  4. * USE: amd64 elibc_glibc kernel_linux multilib test userland_GNU
  5. * FEATURES: sandbox test userpriv usersandbox
  6. * Using: icedtea-bin-7
  7. >>> Unpacking source...
  8. >>> Unpacking gatk-1.5.tar.gz to /tmp/portage/sci-biology/gatk-1.5/work
  9. >>> Source unpacked in /tmp/portage/sci-biology/gatk-1.5/work
  10. >>> Preparing source in /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
  11. Searching for bundled jars:
  12. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/org.broad/tribble-53.jar
  13. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf/sam-1.59.1066.jar
  14. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf/picard-1.59.1066.jar
  15. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf.snpeff/snpeff-2.0.5.jar
  16. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar
  17. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar
  18. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/gov.nist/Jama-1.0.2.jar
  19. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/edu.mit.broad/picard-private-parts-2181.jar
  20. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
  21. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.jar
  22. Searching for bundled classes (no output if none found):
  23. Search done.
  24. >>> Source prepared.
  25. >>> Configuring source in /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
  26. Rewriting attributes
  27. Rewriting ./build.xml
  28. >>> Source configured.
  29. >>> Compiling source in /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24 ...
  30. * Disabling all optional ANT_TASKS
  31. Buildfile: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build.xml
  32. git.describe:
  33. [exec] Result: 128
  34. tagged.build.version:
  35. git.rev-parse:
  36. [exec] Result: 128
  37. untagged.build.version:
  38. generate.build.version:
  39. init:
  40. [echo] GATK build : core
  41. [echo] Scala build : none
  42. [echo] source revision : exported
  43. [echo] build time : 2012/08/16 08:55:09
  44. [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build
  45. [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/lib
  46. [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build/java/classes
  47. [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build/java/contracts
  48. init.resolve:
  49. [mkdir] Created dir: /tmp/portage/sci-biology/gatk-1.5/work/.ant/lib
  50. [get] Getting: http://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar
  51. [get] To: /tmp/portage/sci-biology/gatk-1.5/work/.ant/lib/ivy-2.2.0.jar
  52. [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
  53. BUILD FAILED
  54. /tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build.xml:147: java.net.SocketException: Network is unreachable
  55. at java.net.PlainSocketImpl.socketConnect(Native Method)
  56. at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
  57. at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
  58. at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
  59. at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:391)
  60. at java.net.Socket.connect(Socket.java:579)
  61. at java.net.Socket.connect(Socket.java:528)
  62. at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
  63. at sun.net.www.http.HttpClient.openServer(HttpClient.java:378)
  64. at sun.net.www.http.HttpClient.openServer(HttpClient.java:473)
  65. at sun.net.www.http.HttpClient.<init>(HttpClient.java:203)
  66. at sun.net.www.http.HttpClient.New(HttpClient.java:290)
  67. at sun.net.www.http.HttpClient.New(HttpClient.java:306)
  68. at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:995)
  69. at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:931)
  70. at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:849)
  71. at org.apache.tools.ant.taskdefs.Get$GetThread.openConnection(Get.java:660)
  72. at org.apache.tools.ant.taskdefs.Get$GetThread.get(Get.java:579)
  73. at org.apache.tools.ant.taskdefs.Get$GetThread.run(Get.java:569)
  74. Total time: 3 seconds
  75. * ERROR: sci-biology/gatk-1.5 failed (compile phase):
  76. * eant failed
  77. *
  78. * Call stack:
  79. * ebuild.sh, line 85: Called src_compile
  80. * environment, line 4189: Called java-pkg-2_src_compile
  81. * environment, line 2159: Called eant 'dist' '-f' 'build.xml'
  82. * environment, line 739: Called die
  83. * The specific snippet of code:
  84. * ant ${antflags} "${@}" || die "eant failed"
  85. *
  86. * If you need support, post the output of `emerge --info '=sci-biology/gatk-1.5'`,
  87. * the complete build log and the output of `emerge -pqv '=sci-biology/gatk-1.5'`.
  88. !!! When you file a bug report, please include the following information:
  89. GENTOO_VM=icedtea-bin-7 CLASSPATH="" JAVA_HOME="/opt/icedtea-bin-7.2.2.1"
  90. JAVACFLAGS="-source 1.6 -target 1.6" COMPILER="javac"
  91. and of course, the output of emerge --info
  92. sed: couldn't open temporary file /etc/portage/package.mask/sedmGb7dA: Permission denied