Reading package lists... Building dependency tree... Reading state information... NOTICE: 'picard-tools' packaging is maintained in the 'Git' version control system at: git://anonscm.debian.org/debian-med/picard-tools.git Need to get 5,710 kB of source archives. Get:1 http://urika:3142/ftp.debian.org/debian/ sid/main picard-tools 1.113-1 (dsc) [2,203 B] Get:2 http://urika:3142/ftp.debian.org/debian/ sid/main picard-tools 1.113-1 (tar) [5,698 kB] Get:3 http://urika:3142/ftp.debian.org/debian/ sid/main picard-tools 1.113-1 (diff) [9,620 B] gpgv: keyblock resource `/tmp/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri 06 Jun 2014 09:44:46 PM UTC using RSA key ID 326D8438 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./picard-tools_1.113-1.dsc dpkg-source: info: extracting picard-tools in picard-tools-1.113 dpkg-source: info: unpacking picard-tools_1.113.orig.tar.xz dpkg-source: info: unpacking picard-tools_1.113-1.debian.tar.xz dpkg-source: info: applying use_libjbzip2-java dpkg-source: info: applying 01-build.xml Fetched 5,710 kB in 1s (5,648 kB/s) Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: libcofoja-java libcommons-jexl2-java libjbzip2-java libjcommander-java libsnappy1 libsnappy1.0.3-java testng 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 1,855 kB of archives. After this operation, 2,282 kB of additional disk space will be used. Get:1 http://urika:3142/ftp.debian.org/debian/ sid/main libcofoja-java all 1.1-r150-2 [608 kB] Get:2 http://urika:3142/ftp.debian.org/debian/ sid/main libcommons-jexl2-java all 2.1.1-2 [245 kB] Get:3 http://urika:3142/ftp.debian.org/debian/ sid/main libjcommander-java all 1.35-1 [58.1 kB] Get:4 http://urika:3142/ftp.debian.org/debian/ sid/main libsnappy1 amd64 1.1.3-1 [50.5 kB] Get:5 http://urika:3142/ftp.debian.org/debian/ sid/main libsnappy1.0.3-java all 1.0.3-rc3~dfsg-5 [28.0 kB] Get:6 http://urika:3142/ftp.debian.org/debian/ sid/main testng all 6.9.5-1 [825 kB] Get:7 http://urika:3142/ftp.debian.org/debian/ sid/main libjbzip2-java all 0.9.1-3 [39.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1,855 kB in 0s (8,738 kB/s) Selecting previously unselected package libcofoja-java. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 82591 files and directories currently installed.) Preparing to unpack .../libcofoja-java_1.1-r150-2_all.deb ... Unpacking libcofoja-java (1.1-r150-2) ... Selecting previously unselected package libcommons-jexl2-java. Preparing to unpack .../libcommons-jexl2-java_2.1.1-2_all.deb ... Unpacking libcommons-jexl2-java (2.1.1-2) ... Selecting previously unselected package libjcommander-java. Preparing to unpack .../libjcommander-java_1.35-1_all.deb ... Unpacking libjcommander-java (1.35-1) ... Selecting previously unselected package libsnappy1:amd64. Preparing to unpack .../libsnappy1_1.1.3-1_amd64.deb ... Unpacking libsnappy1:amd64 (1.1.3-1) ... Selecting previously unselected package libsnappy1.0.3-java. Preparing to unpack .../libsnappy1.0.3-java_1.0.3-rc3~dfsg-5_all.deb ... Unpacking libsnappy1.0.3-java (1.0.3-rc3~dfsg-5) ... Selecting previously unselected package testng. Preparing to unpack .../testng_6.9.5-1_all.deb ... Unpacking testng (6.9.5-1) ... Selecting previously unselected package libjbzip2-java. Preparing to unpack .../libjbzip2-java_0.9.1-3_all.deb ... Unpacking libjbzip2-java (0.9.1-3) ... Setting up libcofoja-java (1.1-r150-2) ... Setting up libcommons-jexl2-java (2.1.1-2) ... Setting up libjcommander-java (1.35-1) ... Setting up libsnappy1:amd64 (1.1.3-1) ... Setting up libsnappy1.0.3-java (1.0.3-rc3~dfsg-5) ... Setting up testng (6.9.5-1) ... Setting up libjbzip2-java (0.9.1-3) ... Processing triggers for libc-bin (2.19-19) ... Killed old client process Internet Systems Consortium DHCP Client 4.3.2 Copyright 2004-2015 Internet Systems Consortium. All rights reserved. For info, please visit https://www.isc.org/software/dhcp/ Listening on LPF/eth0/36:17:2d:0b:95:31 Sending on LPF/eth0/36:17:2d:0b:95:31 Sending on Socket/fallback DHCPRELEASE on eth0 to 10.0.3.1 port 67 dpkg-buildpackage: source package picard-tools dpkg-buildpackage: source version 1.113-1 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Olivier Sallou dpkg-source --before-build picard-tools-1.113 dpkg-buildpackage: host architecture amd64 debian/rules clean dh clean --with javahelper,python2 dh_testdir dh_auto_clean ant clean Buildfile: /picard-tools-1.113/build.xml [exec] Execute failed: java.io.IOException: Cannot run program "svnversion": error=2, No such file or directory clean: BUILD SUCCESSFUL Total time: 0 seconds jh_clean dh_clean dpkg-source -b picard-tools-1.113 dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building picard-tools using existing ./picard-tools_1.113.orig.tar.xz dpkg-source: info: building picard-tools in picard-tools_1.113-1.debian.tar.xz dpkg-source: info: building picard-tools in picard-tools_1.113-1.dsc debian/rules build dh build --with javahelper,python2 dh_testdir debian/rules override_dh_auto_configure make[1]: Entering directory '/picard-tools-1.113' [ -d lib ] || mkdir lib # This empty directory is lost in the packages's Git clone. dh_auto_configure make[1]: Leaving directory '/picard-tools-1.113' jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory '/picard-tools-1.113' dh_auto_build -- -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 ant -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 Buildfile: /picard-tools-1.113/build.xml [exec] Execute failed: java.io.IOException: Cannot run program "svnversion": error=2, No such file or directory init: compile-sam-jdk: [mkdir] Created dir: /picard-tools-1.113/classes [javac] /picard-tools-1.113/build.xml:490: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 139 source files to /picard-tools-1.113/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. sam-jar: [mkdir] Created dir: /picard-tools-1.113/dist [jar] Building jar: /picard-tools-1.113/dist/sam-1.113.jar compile-tribble: [javac] /picard-tools-1.113/build.xml:490: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 72 source files to /picard-tools-1.113/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. compile-variant: [javac] /picard-tools-1.113/build.xml:490: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 60 source files to /picard-tools-1.113/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. compile-picard: [javac] /picard-tools-1.113/build.xml:490: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 267 source files to /picard-tools-1.113/classes [javac] /picard-tools-1.113/src/java/net/sf/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java:31: warning: '_' used as an identifier [javac] public AtomicInteger make(final Byte _) { [javac] ^ [javac] (use of '_' as an identifier might not be supported in releases after Java SE 8) [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 warning compile-src: compile-sam-jdk-tests: [mkdir] Created dir: /picard-tools-1.113/testclasses [javac] /picard-tools-1.113/build.xml:513: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 37 source files to /picard-tools-1.113/testclasses [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. compile-picard-tests: [javac] /picard-tools-1.113/build.xml:513: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 85 source files to /picard-tools-1.113/testclasses [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. [copy] Copying 2 files to /picard-tools-1.113/testclasses compile-tribble-tests: [javac] /picard-tools-1.113/build.xml:513: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 22 source files to /picard-tools-1.113/testclasses [javac] warning: Implicitly compiled files were not subject to annotation processing. [javac] Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning compile-variant-tests: [javac] /picard-tools-1.113/build.xml:513: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 18 source files to /picard-tools-1.113/testclasses [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. compile-tests: compile: picard-jar: [jar] Building jar: /picard-tools-1.113/dist/picard-1.113.jar jar: BUILD SUCCESSFUL Total time: 23 seconds make[1]: Leaving directory '/picard-tools-1.113' jh_build dh_auto_test debian/rules binary dh binary --with javahelper,python2 dh_testroot dh_prep dh_auto_install dh_install jh_installjavadoc dh_installdocs dh_installchangelogs dh_installman dh_python2 W: dh_python2:479: Please add dh-python package to Build-Depends dh_perl debian/rules override_dh_link make[1]: Entering directory '/picard-tools-1.113' dh_link -p libsam-java usr/share/java/sam-1.113.jar usr/share/java/sam.jar dh_link -p picard-tools usr/share/java/picard-1.113.jar usr/share/java/picard.jar make[1]: Leaving directory '/picard-tools-1.113' jh_installlibs jh_classpath jh_manifest jh_exec jh_depends dh_compress dh_fixperms dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package picard-tools: unused substitution variable ${java:Depends} dh_md5sums dh_builddeb dpkg-deb: building package 'libsam-java' in '../libsam-java_1.113-1_all.deb'. dpkg-deb: building package 'picard-tools' in '../picard-tools_1.113-1_all.deb'. dpkg-genchanges >../picard-tools_1.113-1_amd64.changes dpkg-genchanges: including full source code in upload dpkg-source --after-build picard-tools-1.113 dpkg-buildpackage: full upload (original source is included)